Galapagos Manual

Galapagos
Version 1.1.2.0
Contents
Contents ............................................................................................................. 2
EZ Read Microplate Reader Health and Safety Information.............................. 5
Software Licence Agreement..............................................................................17
How to get Help ................................................................................................19
Display 'About' Information................................................................................22
Contact Biochrom Limited ..................................................................................24
User Interface Overview .................................................................................. 25
Starting the Application .....................................................................................27
Application Ribbons ...........................................................................................27
Data Window Overview......................................................................................30
Exiting the Application .......................................................................................35
Data Management ............................................................................................ 37
New .................................................................................................................38
Open................................................................................................................39
Save As............................................................................................................42
Database Connection and Management ..............................................................45
Import .............................................................................................................56
Export ..............................................................................................................57
Export Options..................................................................................................61
Print and Print Preview ......................................................................................65
Copy ................................................................................................................67
Recent .............................................................................................................68
Data Validity..................................................................................................... 69
Instrument Management ................................................................................. 70
Connecting to an Instrument .............................................................................70
EZ Read Models ................................................................................................75
Instrument Window .......................................................................................76
Instrument Properties: General ...................................................................78
Instrument Properties: Methods and Plate Data ............................................82
Instrument Properties: Plate Definitions .......................................................89
Instrument Properties: Transport.................................................................91
Instrument Properties: Wavelength Calibration .............................................92
Anthos Models ..................................................................................................96
Instrument Window .......................................................................................96
Instrument Properties: General ...................................................................98
ASYS Models................................................................................................... 100
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Instrument Window ..................................................................................... 100
Instrument Properties: General ................................................................. 103
Instrument Properties: Methods and Plate Data .......................................... 108
Instrument Properties: Plate Definitions ..................................................... 115
Instrument Properties: Transport............................................................... 117
Instrument Properties: Wavelength Calibration ........................................... 118
Methods .......................................................................................................... 122
Quick Measurement ........................................................................................ 123
Acquiring Using Quick Measurement ................................................................. 124
Changing the Plate Layout ............................................................................... 155
Saving a Method Template .............................................................................. 176
Opening a Method Template ............................................................................ 178
Plate Tools...................................................................................................... 180
Plate Definition Editor ...................................................................................... 180
Saving and Opening Plate Definitions ............................................................... 182
Creating Plate Definitions ................................................................................ 189
Removing Plate Definitions from the Database .................................................. 194
Plate Layout Editor .......................................................................................... 196
Saving and Opening Plate Layouts.................................................................... 204
Creating and Modifying Plate Layouts ............................................................... 210
Removing Plate Layouts from the Database ...................................................... 225
Graphical Data Display and Manipulation...................................................... 226
Detailed Well View .......................................................................................... 226
Applying Data Manipulations to Execute During the Measurement Process........... 228
Applying Data Manipulations to Previously Saved Measurement Data .................. 229
Setting Equations ............................................................................................ 229
Introduction to Quantitative Analysis ................................................................ 270
Creating a Quick Measurement Method Incorporating a Quantitative Analysis ...... 271
Importing QA Objects ...................................................................................... 283
Running a Quick Measurement Method Incorporating Quantitative Analysis ......... 291
Reporting ....................................................................................................... 296
Report Writer.................................................................................................. 296
Standard Reporting-Using Existing Report Templates......................................... 306
Installed Report Templates .............................................................................. 312
Standard Reporting-Using Data Options and Style Options ................................. 333
Data Options and Style Options........................................................................ 343
Advanced Reporting-Using Page Report Objects ................................................ 351
Producing Reports ........................................................................................... 374
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EZ Read Microplate Reader Health and Safety
Information
1.1 Safety Instroduction
The EZ Read Microplate Reader Health and Safety Manual cover the following range of microplate
readers:
1. EZ Read 400
2. EZ Read 800
3. EZ Read 800 Plus
4. EZ Read LED
5. EZ Read 2000
The Biochrom EZ Read Microplate Readers are used for microplate-based applications in optically clear
96-well microplates, in addition to -12, -24, -48 and 384-well plates for the EZ Read 2000.
Only trained laboratory personnel should operate the Biochrom EZ Read Microplate Readers. The
Biochrom EZ Read Microplate Readers are intended for general laboratory and research use only.
Model Wavelength Selection Variant
EZ Read 400 Filters ELISA: 405, 450, 492 & 620nm Research: 405,
450, 492, 562, 595 & 620nm
EZ Read 800 Filters ELISA: 405, 450, 492 & 620nm Research: 405,
450, 492, 562, 595 & 620nm
EZ Read 800 Plus Filters ELISA: 405, 450, 492 & 620nm Research: 405,
450, 492, 562, 595 & 620nm
EZ Read LED Filters ELISA: 405, 450, 492 & 620nm UV: 340, 405,
450, 492, 562 & 595
EZ Read 2000 Monochromator (340-800nm) N/A
1.2 General Safety

The EZ Read Microplate Readers have been designed to conform to the following directives:
2006/95/EC Low Voltage Equipment Safety Directive
2004/108/EC EMC Directive
2012/19/EU Waste Electrical and Electronic Equipment directive recast (WEEE recast)
2011/95/EC Restrictions of the use of certain Hazardous Substances in electrical and electronic
equipment (ROHS)
2006/42/EC Machinery directive
98/79/EC In Vitro Diagnostic Medical Devices Directive (Annex I & III)
Standards to which conformity is declared include:

EN61010-1:2010 Safety requirements for electrical equipment for measurement, control and
laboratory use.
EN61010-2-101:2002 Particular requirements for IVD equipment
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EN61326-1:2006 Electromagnetic compatibility*
EN ISO 12100:2010 Safety of machinery –General principles for design, risk assessment and
risk reduction
*These instruments have been tested and found to comply with the limits defined for a CLASS A,
digital device, pursuant to part 15 of the FCC Rules
1.3 Warnings and Hazards

There a number of warning labels and symbols on your instrument. These are there to inform you
where a potential danger exists or particular caution is required. Before commencing installation,
please take time to familiarise yourself with these symbols and their meaning.
Safety Symbols:
Warning
High Voltage
Biohazard
High Voltage
High voltages exist inside these instruments. Do not remove covers whilst connected to the
mains supply.
Repair, maintenance and service should only be carried out by individuals trained specifically to
work on these instruments and that have been made aware of the potential hazards.
Trained Users
These instruments are intended to be used by individuals trained in and familiar with the use of
plate readers and washers and their associated hazards. In the event of a malfunction or hazard
occurring, disconnect the unit from power and isolate for decontamination and /or repair.
Lamp Source
Lamp sources used within the reader units produce a light beam that passes through the well
positions and is normally confined within the instrument. The unit should not be operated with
the covers removed as prolonged exposure to the beam intensity and potential UV content of
the beam could cause eye damage.
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Personal Protective Equipment
There are no bio-hazardous materials within the instrument; however, this microplate reader
may well be used with bio-hazardous samples. Before using the instrument the user should have
in place decontamination procedures designed to protect laboratory workers from occupationally
acquired infections. A set of suggested decontamination procedures microplate readers are
provided in this manual.
Always read cautions and warnings supplied with assay kits reagents and samples
Decontamination. Equipment should be maintained in a clean state. Equipment returned
for repair should include an appropriate decontamination certificate (refer to website:
http://www.biochrom.co.uk/content/1/65/returns.html)
It is the responsibility of the laboratory manager to ensure that the user of the instrument
is provided with a safe working environment.
Any chemicals used with the microplate reader should be used, stored and disposed of in
accordance with manufacturer’s guidelines and local safety regulations.
Toxic Fumes. Efficient laboratory ventilation must be provided when working with volatile
solvents or toxic substances.
Waste disposal. Disposal of some solvents and chemicals may be classed as hazardous
waste and must be dealt with in accordance with local regulatory practice.
Personal protective equipment including but not limited to gloves, laboratory coats and
safety glasses is recommended when using this instrument. A local risk assessment
should be performed to determine the extent of required PPE.
Use of PCs for Controlling Software

These instruments may be connected and controlled from a PC. To preserve the integrity of
the measuring equipment it is essential that thye attached PC itself conforms to basic sefty
and EMC standards and is set up in accordance with the manufacterer’s instructions. If in
doubt consult the information that came with the PC. In common with all computer
operation, the following safety precautions are advised:
To reduce the chance of eye strain, set up the PC displaywitht he correct viewing
position, free from glare and with approprioate brightness and contrast settings.
To reduce the chance of cross contamination from biological samples, use
approprioate personnel protection measures and disinfectant wipes on keyboards and
attached mouse.
Lifting and Carrying

Instrument weights ranges from 6 to 15kg and when boxed will weigh more. No special
equipment is required but you should consult your local regulations for safe handling and
lifting of the equipment and observe the packing weights on the shipping labels
Changes or modifications
Any changes or modifications made to the instrument could void the user’s authority to operate the
instrument.
If the instrument is operated in a manner not specified, then the protection provided by the
equipment may be impaired and the instrument warranty withdrawn.
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1.4 Instrument Validation
An optional check plate (refer to Biochrom website for further information regarding microplate reader
accessories: http://www.biochrom.co.uk/subsubcategory/41/accessories.html) can be used for
instrument validation. Specific check plates are applicable for different EZ Read models (refer to the
appropriate microplate reader user guides). Additional tips include incorporating controls of known
concentrations to validate absorbance measurements.
1.5 Equipment Ratings
EZ Read 400 EZ Read 800 EZ Read 800 Plus EZ Read LED EZ Read 2000
Ambient temperature 15°C - +40°C 10°C - +35°C 10°C - +350°C 18°C - +48°C 10°C - +35°C
(operation) (operation) (operation) (operation) (operation)
25°C - +50°C 25°C - +50°C 25°C - +50°C 40°C - +70°C 25°C - +50°C
(storage) (storage) (storage) (storage) (storage)
Consumption 250VA 80VA 80VA 20VA 65VA

Dimensions (WxHxL) 31.5 x 18.2 x 43.5 41 x 17cm x 25cm 43 x 24 x 27cm 23 x 11.5 x 36cm 27 x 24 x 43cm
cm (12.4 x 7.2 x (16.4 x 6.8 x 10 (17.2 x 9.6 x 10.8 (9.2 x 4.6 x 14.4 (10.8 x 9.6 x 17.2
17.1 inches) inches) inches) inches) inches)
Frequency range 47 - 63 Hz (auto- 47 - 63 Hz (auto- 47 - 63 Hz (auto- 50-60Hz 47 - 63 Hz (auto-
sensing) sensing) sensing) sensing)
Height over sea level up to 2000m up to 2000m up to 2000m up to 2000m up to 2000m
(operation):
Power Requirements 12 VDC Max 4A 100 to 240 VAC 100 to 240 VAC 24 VDC Max 100 to 240 VAC
2.5A
Use only the 50/60Hz 50/60Hz 80VA 50/60Hz 65VA
supplied power Use only the
supply unit supplied power
supply unit
100 to 240 VAC~
100 to 240 VAC~
50/60Hz
50/60Hz
1.4A
1.4A
Fuse 3 A (UK power 3.15A TH 250VAC 3.15A TH 250VAC 3 A (UK power 3.15A TH 250VAC
plug only) plug only)
Outer lighting Precaution, avoid Precaution, avoid Precaution, avoid Precaution, avoid Precaution, avoid
influences direct sunlight direct sunlight direct sunlight direct sunlight direct sunlight
PC connection Standard cable, USB A to USB B USB A to USB B USB A to USB B USB A to USB B
USB A to B cable mini cable mini cable mini cable mini cable
Relative humidity 15 - 85% non 0 to 80 % (Non 0 to 80 % (Non 0 to 90 % (Non 5 to 95%, non
condensing condensing) condensing) condensing) condensing
(operation) (storage only)
Humidity 5 to 95%, Humidity <95%, Humidity 5 to
< 95% non- non-condensing non-condensing 95%, non-
condensing (storage only) (storage only) condensing
(storage) (storage only)
Warming-up time None required None required None required None required None required
Weight 6.6 kg (No special 12 kg (No special 12 kg (No special 7.2 kg (No 10 kg (No special
instructions are instructions are instructions are special instructions are
required for lifting required for lifting required for lifting instructions are required for lifting
or moving the or moving the or moving the required for lifting or moving the
instrument) instrument) instrument) or moving the instrument)
instrument)
Note: There are no user replacebale parts (except for replacement of fuses).
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1.6 Technical Specifications
EZ Read 400 EZ Read 800 EZ Read 800 Plus EZ Read LED EZ Read 2000
Lamp Source Tungsten halogen Tungsten halogen Tungsten halogen LED Tungsten halogen
Measurement 0-3.3 OD 0-3.4 OD 0-3.4 OD 0-3.4 OD 0-3.2 OD
range
Reproducibility / 0.25% at 1.0 OD 0.5% 0.1-2.5 OD 0.5% 0.1-2.5 OD 0.5% and 0.005OD 0.8% and 0.005 OD
Precision) at 450 nm to 3.5OD from 0.10-2.0 OD at
450 nm
Accuracy 0.5% at 1.0 OD at 1% from 0.100-2.5 1% from 0.100-2.5 <=1% and 0.005 to 0.5% and 0.005 OD
450 nm OD OD 3.5OD from 0.1-1.0 OD at
450 nm;
1.0% and 0.010 OD
from 1.0-2.0 OD at
450 nm
Standard Filters: 405, 450, 492 and 405, 450, 492 and 405, 450, 492 and 405, 450, 492, None
620nm for ELISA 620nm for ELISA 620nm for ELISA 620nm LED
reader 405, 450, reader 405, 450, reader 405, 450,
492, 562, 570, 595 492, 562, 570, 595 492, 562, 570, 595
and 620 for and 620 for and 620 for
Research reader Research reader Research reader
Wavelngth Range 400-750nm 400-750nm 400-750nm 340- 900nm 340-800nm
Plate Types Flat, round and v- Flat, round and v- Flat, round and v- Flat, round and v- 12, 24, 48 and 96-
bottomed 96-well bottomed 96-well bottomed 96-well bottomed 96-well well plates with
plates plates plates plates standard ANSI/SBS
footprint
Data Output Export to PC Export to PC Export to PC Export to PC Export to PC
Detection System Single channel 8 silicon 8 silicon 8 silicon 2 silicon diodes: one
silicon photodiode photodiodes photodiodes photodiodes for measurement,
one for reference
Reading Speed 25 seconds <5 seconds <5 seconds 5 seconds 35 seconds
Shaking None 4 speed standard 4 speed standard 4 speed standard Linear shaking
Tempertaure None None None None None
Control
Linearity 0.25% and 0.0025 0.25% and 0.0025 0.25% and 0.0025 0.5% and 0.005OD 0.5% and 0.005 OD
OD from 0.1 -2.5 OD from 0.1 -2.5 OD from 0.1 -2.5 to 3.5OD from 0.10-1.0 OD at
OD at 492 nm OD at 492 nm OD at 492 nm 492 nm 1.0% and
0.010 OD from 1.0-
2.0 OD at 492 nm
Computer interface USB 2.0 USB 2.0 USB 2.0 USB 2.0 USB 2.0
Optical system Filters Filters Filters Filters Monochromator
Validation Optional 2010 Optional Asys Optional Asys Optional 2010/2020 Optional Asys
check plate Check plate Check plate plate Check plate
Mode of operation PC control PC control Local or PC control PC control PC control
Analysis software Galapagos Galapagos Galapagos Galapagos Galapagos Software
Software Software Software Software
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1.7 Unpacking the EZ Read Microplate Reader
Note: The original packing has been especially designed to protect the instrument during
transportation. It is therefore recommended to keep the original carton with its foam parts and the
accessories box for re-use in case of future shipments. Warranty claims are void if improper packing
results in damage during transport.
1. Check the box for any visible damage during transportation. In case of damage inform your
supplier immediately and keep the damaged packing.
2. Place the device on a suitable working surface.
3. Remove the transportation lock (foam part) from the plate holder. The readers are also supplied
with a metal clip which also requires removal.
1.8 Powering up the EZ Read Microplate Reader

1. Connect the instrument power supply to amians source. The mains equipment must be earthed.
2. Connect the USB A to B cable from the PC to the instrument (unless using the EZ Read 800
ELISA Plus or EZ Read 800 Research Plus as this unit can be operated via the user interface).
3. Connect unit using only the supplied power cords.
4. Please Note: Keep the area around the instrument free from clutter to allow for easy access to
the standard mains plug. This is also important to allow an adequate flow of air around the
instrument.
5. Switch on main switch (back of the instrument).
6. The power indicator light is located on the front of the unit.
1.9 Performing a Quick Measurement

EZ Read Microplate Readers are controlled via PC using Galapagos software. Galapagos software can
be used on PCs using Microsoft Windows 7 and 8. Below is a short guide to performing a quick
measurement using on an EZ Read microplate reader using Galapagos software.
1. The application can be started by double clicking on the Galapagos icon on the Desktop or any
specific location where the software was saved or installed (e.g. network)
2. Connect the instrument to a computer or laptop and connect by clicking the ‘Find Instruments’
icon which detects the respective instrument. For subsequent use users can click the ‘Connect’
icon for recognition
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3. Click ‘Quick Measurement’
4. For sample measurements, select the appropriate measurement mode (Single, Dual or Multi-
wavelength). Dual wavelength refers to the measurement of a sample at one wavelength and
that absorbance from another wavelength will be subtracted. Multi-wavelength refers to
absorbance measurements at different wavelengths
5. Click ‘Start’ to begin acquisition
6. Raw absorbances are displayed in the wells:
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7. When users click onto a well, it is highlighted (dashed lines). In regards to dual wavelength
measurements, three absorbance values are displayed
The bold value refers to the absorbance measurement after wavelength subtraction
The second value refers to the absorbance value measured at a desired wavelength
The third value refers to the absorbance value measured at a reference wavelength
8. Results can be saved to ‘Database’. A database is useful for saving, sharing and extracting data
via communication with an external database system (LIMS). Users can save files and
templates onto the database, ‘File’ (save to own personal file), or ‘Save Method Template’
(saves the method protocol for future use)
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9. Results can also be exported as Excel, Extended Metafile, results exported as a HTML file, PDF,
Rich Text File, Text File, Word File and XPS File
2.0 Troubleshooting
The website is frequently updated with technical and supplications support information.
PROBLEM POSSIBLE CAUSE

Reader fails to start up Check plugged in and switched on.
Check power on light is ON.
Check Fuse.
This can be replaced, but only by the same type and rating.Note: Before replacing the
fuse, disconnect the power cord.
Check for jammed plate transport or failure.
Check lamp comes on.
Readings are higher or lower Check to see if samples are cloudy or mixed properly. If the sample is not mixed
than expected properly, sediments can settle at the bottom of the well which can lead to
measurement discrepancies.
Check for bubbles in solution.
Check plate orientation.
Check for poor, scratched plates.
Check if the correct plate format is used (96 well plate, flat, round and v-bottomed well
formats with standard ANSI SBS footprint).
Check for condensation on plate base.
If filters have been changed check that the filter positions have been entered and
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PROBLEM POSSIBLE CAUSE
calibrated correctly
Check assay preparation steps have been followed correctly.
Check correct sample volume has been dispensed. This is important as pathlength
(which is used to calculate sample concentration using Beer’s Law) is not standardised
and is dependent on sample volume. Therefore the volume must be equal throughout
the plate.
Readings have poor repeatability Check plate types used are suitable.
and are random or noisy
Check that plate transport passes start up checks. This refers to when the instrument
finds the home position of the plate immediately after being switched on. If the plate
reader has a display the status of the check is shown.
Check for any bubbles or wells where there is foam (likely to arise from pipetting or
shaking).
Use a background wavelength correction. For example measure the sample
absorbance at 405nm and wavelength reference at 620nm.
Check sample dilutions are such as to produce a response within the range 0.1 to 2.5
A. This is the recommended linear range of the plate readers.
Check assay preparation steps have been followed correctly.
Check correct sample volume has been dispensed, as mentioned above.
Recommended good laboratory Use a polystyrene plate with no scratches or evaporation which may affect absorbance
practice readings.
Check that pipettes (single and/or multi-channel) dispense the correct set volume.
Check that the correct tips are used for the appropriate pipettes.
Check plate for any bubbles or foam as mentioned previously.
Check readings with a QC plate (refer to user manual for specified plate) – refer to
section 1.4.
2.1 Cleaning and Disinfecting the Instrument

For disinfection, authorized trained personnel must operate in a well-ventilated room while wearing
disposable gloves, protective glasses and clothing. Details of cleaning procedures are listed below.
To disinfect the instrument:
1. Switch off the reader and disconnect it from the mains power supply and the PC.
2. Carefully wipe off the entire reader with lint-free tissues that have been moistened in a protein
degrading mild detergent or a saline solution.
3. Carefully wipe off the entire reader with non-lint tissues that have been moistened in a 70%
ethanol or a 0.5% bleach solution.
4. Soak non-lint tissues in a 70% ethanol or a 0.5% bleach solution onto the plate transport
mechanism and let it soak for 30 minutes.
5. If a bleach solution has been used, carefully wipe off the entire reader with non-lint tissues that
have been soaked in water.
6. Dry the reader by wiping it off with non-lint tissues.
Please Note: Before the reader can be returned to base for service, it must be disinfected and a
Declaration of Decontamination Certificate must be completed. This document can be downloaded
from the Biochrom website: http://www.biochrom.co.uk/content/1/65/returns.html
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The instrumentation will not be accepted for servicing or return until the above form is completed
fully. Instrumentation that has not been cleaned sufficiently or decontaminated may be subject to
additional charge.
2.2 Emergency Instructions

In the event of an emergency the instrument should be disconnect from the power supply, power
source and PC.
2.3 Safe Disposal of the Instrument
This symbol can be found on the outside of the instrument. It means that the Biochrom EZ Read
Microplate Reader cannot be disposed of in municipal waste. The instrument must be decontaminated
as detailed in part 2.0 of this section
2.4 Regular Maintenance

The EZ Read microplate readers do not require maintenance unless used under conditions outside of
the recommendations laid out in this manual.
We recommend that the instrument is kept clean and that the instrument is periodically checked (as
mentioned in section 1.4) Please contact Biochrom Support if you have any questions or concerns
regarding the performance of the instrument:
E-mail: support@biochrom.co.uk
Telephone: +44 (0)1223 427890
Fax: +44 (0)1223 427857
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Galapagos Expert
Online Help Topics
Version 1.1.2.0
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Software Licence Agreement
1. DEFINITION: This is BIOCHROM LTD’s (BIOCHROM) Software Licence Agreement (the
“Agreement”) which will govern your use of the Biochrom software product(s) contained in this
package (the “Software”).
2. LICENCE: BIOCHROM hereby grants you, and you accept a limited software licence subject to
the terms and conditions contained herein to use the Software. You may only use the Software
on a maximum of one computer at any one time where a computer means a single computer,
or its temporary replacement, or on a subsequent computer. If you wish to use the Software on
more than the designated number of computers at any one time, you must licence additional
copies of the Software from BIOCHROM.
3. TERM: This agreement commences when you begin to use the Software, and continues in
effect until you return the Software to BIOCHROM. At that time, you must also certify in writing
that you have destroyed any archival copies which you may have recorded on any memory
system or magnetic medium. Any such termination shall be without prejudice to the accrued
rights of the parties.
4. BIOCHROM LTD’S RIGHTS: You acknowledge that the rights to the Software and associated
documentation and other related materials are the sole and exclusive property of BIOCHROM.
By accepting this Agreement, you do not become the owner of the Software, but you do have
the right to use the Software in accordance with this Agreement. You agree to use your best
efforts and take all reasonable steps to protect the Software from unauthorised use, illegal
reproduction or illicit distribution.
5. COPYRIGHT: The Software and its associated documentation are copyrighted. You may make
one copy of the Software and the associated documentation for your own purposes
notwithstanding the requirements of the licence. Other than these you agree that no other
copies of the Software or associated documentation will be made.
6. OTHER RESTRICTIONS: You may not rent or lease the Software, but you may transfer the
rights under this Agreement on a permanent basis providing you transfer all copies of the
Software, and all associated documentation, and that the recipient agrees to the terms of this
Agreement.
7. LIMITED WARRANTY: BIOCHROM warrants for a period of one year from the date of receipt
by you, that the Software will perform substantially in accordance with the accompanying
documentation. BIOCHROM does not warrant that the functions contained in the Software will
meet your requirements or that the operation of the Software will be uninterrupted or error-free
or that defects in the Software will be corrected. To the maximum extent permitted by law,
BIOCHROM declaims all other warranties, express or implied, including but not limited to,
implied warranties of merchantability and fitness for a particular purpose with respect to the
Software, and its associated documentation.
8. SUPPORT AND UPGRADES: BIOCHROM will provide telephone support and advise on
questions of design or implementation for a period of 3 months after delivery. In addition but
notwithstanding the limited warranty BIOCHROM will provide any version upgrades issued for
maintenance purposes free of charge during the warranty period. Any further support will be
the subject of a separate maintenance quotation and contract. To obtain support and upgrades
users must register the purchase with BIOCHROM directly.
9. CUSTOMER REMEDIES: BIOCHROM entire liability and your exclusive remedy shall be at
BIOCHROM option, either (a) return of the price paid or (b) repair or replacement of the
Software that does not meet BIOCHROM limited warranty and is returned to BIOCHROM with a
copy of your receipt. This limited warranty is void if failure of the Software has resulted from
damage, accident, abuse or misapplication.
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10. LIABILITY: To the maximum extent permitted by applicable law, BIOCHROM and its agents
shall not be liable for any other damages whatsoever (including, but not limited to, damages for
loss of business profits, business interruption, loss of business information, or other pecuniary
loss) arising out of the use or inability to use the BIOCHROM product, even if BIOCHROM or its
agents have been advised of the possibility of such damages. In any case, BIOCHROM entire
liability under any provision of this Agreement shall be limited to the amount actually paid by
you for the Software.
11. TERMINATION OF AGREEMENT: If any of the terms and conditions of this Agreement is
broken, BIOCHROM has the right immediately to terminate in writing the Agreement and
demand that you return the Software to BIOCHROM. At that time, you must also certify in
writing that you have not retained any copies of the Software.
12. GOVERNING LAW: This Agreement is to be governed by, and interpreted in accordance with
the laws of England. Any terms and conditions of this Agreement found to be unenforceable will
be deleted, but will not alter the remaining terms and conditions of this Agreement. The
exclusive jurisdiction of an English court of law shall apply in the event of any dispute
13. ENTIRE AGREEMENT: This Agreement constitutes the entire Agreement between you and
BIOCHROM relating to the licensing of the Software, and applies to you if purchased for your
own use, or to you, your company and the company’s employees if purchased for company use.
No variation or amendment of or addition to the terms and conditions of the Agreement shall be
effective unless prior agreement is obtained in writing from BIOCHROM.
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How to get Help
To display tooltips:
o Hover the mouse cursor over the ribbon buttons
Concise explanations of the button are given
While working with Galapagos you may wish to consult the application online help topics or the
application manual for clarification or information on a certain function or option.
To show online help:

o Display the Help tab and click on Help
Keyboard shortcut: Press ALT, H, H

or
1. Click on the File tab and click Help
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2. Click on the Help icon
or
o Click on Help -
or
o Press F1 at any time
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To display the manual:
o Display the Help tab and click on Manual
Keyboard shortcut: Press ALT, H, M

or
2. Click on the Manual icon
or
o Select Manual from the help drop-down
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Display 'About' Information
To show the application 'About' dialog:

1. Show the Help tab
2. Click About
Keyboard shortcut: Alt, H, A
The 'About' dialog is displayed
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or
Selecting About from the Help drop-down
or
2. Click on the About icon
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Contact Biochrom Limited
Biochrom Limited
22 Cambridge Science Park
Cambridge
CB4 0FJ
UK
Tel: +44 (0)1223 423723
www.biochrom.co.uk
Technical Support:
Tel: +44(0)1223 427890
support@biochrom.co.uk
Sales:
Tel: +44 (0)1223 423723
enquiries@biochrom.co.uk
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User Interface Overview
The Galapagos user interface is composed of a main application window with a ribbon interface and a
data window where acquired data can be displayed.
The currently logged in user, the current instrument connection status and database connection status
are shown in the status bar at the bottom right of the application:
Logged in user is 'Rob'
Instrument connected
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Instrument not connected
Instrument details shown when the mouse is hovered over connection status
Database is connected
Database is not connected, working offline
Database details shown when the mouse is hovered over database status
See also:
o Ribbons
o Data Window
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Starting the Application
To start Galapagos:
1. Select Start > All Programs > Biochrom Limited > Galapagos > Galapagos
You can also start the application by double clicking on the Galapagos icon on the Desktop
It is possible to have open multiple instances of the application
Application Ribbons
Galapagos has four ribbons which are always shown and through which all application options can be
accessed. These are:
o File
o Setup
o Methods
o Help
The File tab is shown by selecting File or pressing Alt, F
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The File tab contains the following:
o Open
o Save As
o Recent
o New
o Print
o Export
o Help
o Copy
o Options
o Exit
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The setup tab is shown by selecting Setup or pressing Alt, S
The Setup tab contains the following:

o Connect
o Disconnect
o Find Instrument
o Connect to Database
o Work Offline
o Select Server
o Select Database
o Add Database
o Plate Layout
The Methods tab is shown by selecting Methods or by pressing Alt, M
The Methods tab contains the following:

o Quick Measurement
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The Help tab is shown by selecting Help or pressing Alt, H
The Help tab contains the following:

o Help
o Manual
o About
Data Window Overview
It is possible to have multiple data files open at any time in Galapagos. In addition, it is possible to
open more than one instance of a single file.
To Select which File is Displayed:

1. Click on the tab of the file to be displayed
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With multiple files open you can also select which file to display by clicking the window selection
button and selecting the graph to show:
To Close a File:
1. Click on the tab of the file to be closed
2. Click on the close button
To View the Method Properties of the Current Results File:

1. Select the file whose properties you wish to display
2. Click the Method Properties tab
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The properties for the current file are displayed:
3. Click on the pin to keep the pane in view.

To remove the pane from view, click on the symbol
Note: It is not possible to edit or delete information in the Method Properties view
To View the Plate Layout Groups of the Current Results File:

1. Select the file whose data you wish to display
2. Click the Groups tab
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The groups for the current layout are displayed:

Note: It is not possible to edit or delete information in the Groups view
To View a Well's Chart data for the Current Results File:

2. Select the well of interest
3. Click the Chart tab
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The plotted data is displayed:

Note: Not all well data can be plotted as a chart. In this case, 'Insufficient Data to Chart' is
displayed in the chart view.
To View a Well's Data in Tabular Format for the Current Results File:
2. Select the well of interest
3. Click the Data tab
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The data is displayed:

Exiting the Application
To exit Galapagos:
1. Click the close in the upper-right corner of the application window.

The application is closed
or,
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1. Select the File tab
2. Select Exit
The application is closed.
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Data Management
Galapagos can store results data in a database or save to disk files. The following topics are detailed in
this section:
o New
o Open
o Save As
o Database connection and management
o Import
o Export
o Print
o Copy
o Recent
o Options
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New
To initiate a new method:

1. Click on New
2. Click on the required method from those available
3. The corresponding acquire tab for the chosen method is displayed
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Open
Galapagos data can be opened from either a database or disk file.
To open a data source from file:

2. Click on Open
3. Click on Open Results from File
4. From the dialog that is displayed, select the required file and click Open
The data is displayed in a new tab in the data window
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To open a data source from a database:
2. Click on Open
3. Click on Open Results from Database
or
Launch the Open from Database dialogue from the quick access toolbar by clicking on the
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4. Select the result to be opened from the list displayed
Together with the results name, the dialog specifies the method that was used to acquire that
data and the date the data was created
Single and multiple results can be selected by using the Shift and Ctrl keyboard buttons
Each result is displayed in a new tab in the data window
Note: It is not possible to open data from an empty database. If attempted, a warning dialog is
displayed.
See also:
o Applying data manipulations to previously saved data
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Save As
Galapagos data can be stored in a database or saved to disk file.
Storing data in a database:

2. Click on Save As
3. Click on Save to Database
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4. Enter the results name and Click OK
Galapagos offers a default name in the format: Measurement [YYYYMMDDHHMMSS] [Computer

Name].
The first bracketed section is the time when the acquisition completed and is specified as year
(YYYY), month of the year (MM), day of the month (DD), hour of the day (HH), minute of the
hour (MM) and second of the minute (SS). The second bracketed section is the name of the
computer
Note: The results name must be unique. If an attempt is made to store a result with the same
name as an existing result an error message is displayed.
Note:In order to save data to a database, Galapagos must be connected to a database. For
help on connecting to a database, refer to the help section on database connection and
management.
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Saving data to a file:
2. Click on Save As
3. Click on Save to File
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4. Enter the file name and select the file location and click on Save
Galapagos offers a default name in the format: Quick Measurement [YYYYMMDDHHMMSS]

[Computer Name].
computer
Database Connection and Management
This topic contains the following sub-topics:

o Database requirements
o Connecting to a database for the first time
o Disconnecting from a database
o Connecting to the last used database
o Connecting to a different database
o Creating a new database and connecting to it
o Upgrading the database
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Database requirements:
Galapagos is designed to work with a database. The database can be located locally or across a
network. If you do not already have a suitable accessible database connection then it is recommended
that you allow the application to create a local Microsoft SQL Server Express 2008 database for you.
The software is designed to work with databases supporting the Structured Query Language (SQL) but
you will only be able connect to an existing database if you are a user on the system and have the
appropriate connection knowledge. Please contact your database manager for support.
Connecting to a database for the first time:

1. When Galapagos is launched and there are no database connections setup, the database
connection dialog is displayed
Select Automatic Database Connection to connect to SQL Server Express and create a
database called Galapagos for data storage
2. If the database connection is unsuccessful, a connection error dialog is displayed
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3. Select whether to attempt manual database configuration or proceed to work offline
The Methods tab is displayed
Note: The automatic database connection will only connect to servers which have names in
the following format: [Computer Name]\SQLEXPRESS. Additionally, when configured
automatically, Windows Authentication is used. To use a server with a different name or to
use SQL Server Authentication, select Manual Database Configuration.
Note: When working offline, all results are saved to disk file.
Select Manual Database Configuration to manually select the database server and database
name to use
1. Galapagos will search for available database servers
2. If the required server has not been found, type in the name of the server in the Server edit
box
3. Choose which type of authentication to use and click OK
Windows authentication: Windows users can logon to the database
SQL Server authentication: Enter a valid SQL server user name and password combination
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4. Enter the name of the database to connect to and click OK
Galapagos connects to the database and displays the Methods tab
Note: If it is not possible to connect to the database, a warning dialog is displayed
Select Work Offline to save data as disk files

1. To always work offline in the future select Yes. On exit, Galapagos stores this preference
and will not prompt or attempt to connect to a database the next time it is launched
Click No and Galapagos will prompt or attempt to connect to a database the next time it is
launched
The Methods tab is displayed
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Disconnecting from a database:
1. Click on the Setup tab
2. Click on Work Offline
Galapagos disconnects from the database and works offline
Note: When a database is not connected, results data is saved to disk file.
Connecting to the last used database
Galapagos will attempt to connect to the last used database on start-up, unless always work offline
has been selected.
To reconnect to the last used database:
1. Select the Setup tab
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2. Click on Connect to Database
A connection is made to the database

If the database is not available, a connection error is displayed
Connecting to a different database

2. Disconnect from an existing database connection by clicking on Work Offline
3. Click on Select Server
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box
Windows authentication: Windows users can log on to the database

Choose which type of authentication to use and click OK
5. Select Connect to existing database
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6. Select the database from the list of available databases and click OK
A connection is made to the database
Creating a new database and connecting to it:

2. Disconnect from an existing database connection by clicking on Work Offline
3. Click on Select Server
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box
Windows authentication: Windows users can log on to the database

Choose which type of authentication to use and click OK
5. Select Create a new database
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3. Enter the name of the database to be created and click OK
The database is created and a connection made
Note: The standard rules for the format of database names apply. These are summarised
below.
The first character must be one of the following:
o A letter as defined by the Unicode Standard 3.2. The Unicode definition of letters includes
Latin characters from a through z, from A through Z and also letter characters from other
languages
o The underscore (_), at sign (@) or number sign (#)
Subsequent characters can include the following:
o Letters are defined in the Unicode Standard 3.2
o Decimal numbers from either basic Latin or other national scripts
o The at sign (@), dollar sign ($), number sign or underscore (_)
o Embedded spaces, special characters or supplementary characters are not allowed
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Upgrading the database:
1. When a Galapagos software upgrade has been installed and a database upgrade is required, the
following message is displayed when Galapagos is started.
Note: It is good practice to backup all data before performing a database upgrade.
2. Click on Upgrade Database
3. The upgrade is performed
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Import
Several data formats can be imported into Galapagos, including:
o Text files
o KPL files (Kontrol Plus software file containing measurement data)
To import a data file:

2. Click on Import
3. From the list of options available, select the format of the data to be imported by clicking on the
corresponding icon
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4. Select the file to import and click Open
The data is displayed
Note: If the data file imported comprises multiple data sets, each data set will be opened into a
separate data window.
Export
Measurement, instrument and manipulated data can be exported to several data formats, including:
o Microsoft Excel
o Extended metafile
o HTML
o PDF
o Rich text format (RTF)
o Text
o Microsoft Word
o XPS
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The following information is exported. Only sections appropriate to the data are included:
o Method
o Method type
o Originator
o Date created
o Settings
o Wavelengths
o Measurement mode
o Shaking mode settings
o Timing settings
o Equations
o Data manipulation algorithms applied to the measurement data
o Qualitative Analysis
o Details of the QA object
o Standard details and statistics
o Coefficient and goodness of fit parameters
o Results
o Date & time
o Result Validity
o Data Validity
o Operator
o Instrument type
o Instrument serial number
o Firmware version
o Layout
o Plate Definition
o Plate Layout
o Group assignments
o Data
o Measurement data and results of data manipulations
For the export functions to be enabled, there must be measurement data open in the software.
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To Exporting Data to a File:
2. Click on Export
3. From the list of options available, select the format of the data to be exported by clicking on the
corresponding icon
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4. Enter the file name and location and click Save
Galapagos offers a default name in the format: Quick Measurement [YYYYMMDDHHMMSS]

[Computer Name].
computer.
The files are stored in Public Documents/Biochrom/Galapagos/[User]
Note: When exporting to Excel, the measurement data and manipulated data is written to a
separate worksheet.
See Also
o File tab Options for export options
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Export Options
Options are available to set the page format (orientation) and the list separator type when exporting
data.
To change the page format:

2. Click on Options
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3. Select one of the options from the Page Format drop down list
Note: This option does not apply to the export to Microsoft Excel or text file formats
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To change the list separator:
2. Click on Options
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3. Select one of the options from the List Separator drop down list
The options are:

o Default: The separator used is read from the Windows settings
o Tab: A tab is used to separate data entries in the file
o Semicolon: A semicolon is used to separate data entries in the file
o Comma: A comma is used to separate data entries in the file
o Space: A space is used to separate data entries in the file
Note: The List Separator option only applies to the text file formats and Copy command
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Print and Print Preview
To Print Preview the Current Method Results and Settings:

1. Open or show the file containing the results and settings to preview
2. Select the File tab and click on Print
A preview of the method results and settings are displayed

3. Use the Print Preview tool bar to zoom in and out of the preview
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To print the current method results and settings:
1. Open or show the file containing the results and settings to print
2. Select the File tab and click on Print
3. Click Print
The method results and settings are printed
See Also
o File tab Options for page format options
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Copy
To copy the contents of the current window:

1. Open or select the file containing the data that you wish to copy
3. Click on Copy
The current data are copied as text.
Note: The list separator is defined in the Export Options option
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Recent
Recently opened results data can be quickly accessed through the Recent option. This applies to
results data stored in a database or saved to disk files if working offline.
To open data from the Recent results list:

1. Select the File tab and click on Recent
2. Select the result to open from those listed

Database records are displayed on the left hand side and disk files on the right hand side
The data is displayed in the data display window
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Data Validity
When Galapagos measurement data is opened, Galapagos uses a data integrity routine to check that
the results file has not been altered since it was last viewed in Galapagos. The outcome of this data
validity routine is displayed in the Results section of the Method Properties pane.
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Instrument Management
Galapagos can be used to connect to a variety of different instruments. For more information relating
to the configuration of Galapagos for use with your instrument please see the following topics:
o EZ Read Models
o Anthos Models
o ASYS Models
Connecting to an Instrument

o Connecting to an instrument for the first time
o Connecting to the last used instrument
o To disconnect from an instrument
o To connect to a different instrument
Connecting to an instrument for the first time:

1. Select the Setup Tab
2. Select Find Instruments
Keyboard Shortcut: Alt, S, F
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3. Select the instrument to connect to from the instruments available
Note: Where only one instrument is found, Galapagos will automatically connect to it.
Galapagos cannot automatically identify some types of instrument. When selected, such
instruments require the user to identify the instrument type from the options available.
Galapagos will store this information for future use.
Galapagos connects to the instrument and the Methods tab is displayed
Note: On connection, some instruments perform an initialisation sequence.
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Connecting to the last used instrument:
When launched, Galapagos will automatically connect to the last used instrument if available. If the
instrument is not available, the connection error dialog is displayed.
If Galapagos has disconnected from the instrument, to reconnect:

2. Click on Connect
Keyboard Shortcut: Alt, S, C
Note: On connection, some instruments perform an initialisation sequence
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To disconnect from an instrument:
2. Click on Disconnect
Keyboard Shortcut: Alt, S, D
To connect to a different instrument:

1. Disconnect from the instrument currently connected
3. Click on Find Instruments
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4. Select the instrument to connect to from the instruments available
Note: Where only one instrument is found, Galapagos will automatically connect to it.
Galapagos cannot automatically identify some types of instrument. When selected, such
instruments require the user to identify the instrument type from the options available.
Galapagos will store this information for future use.
Galapagos connects to the instrument and the Methods tab is displayed
Note: On connection, some instruments perform an initialisation sequence
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EZ Read Models
The topics available in this section are:
Instrument Connection
Instrument Window
Instrument Properties: General tab (status, filters, acquire raw energy, data and load & eject
plates)
Instrument Properties: Methods and Plate Data tab
Instrument Properties: Plate Definitions tab
Instrument properties: Transport
Instrument Properties: Wavelength Calibration tab
Note: The instrument type connected will determine which instrument property tabs are
accessible.
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Instrument Window
To display the Instrument Window:

1. Click on the Instrument tab below the data window
2. The Instrument general properties are displayed
To show the instrument properties:

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2. Click the Instrument group dialog box launcher -
Keyboard shortcut: To show the Instrument properties, press ALT, S, I
See also:
o Instrument Properties: General
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Instrument Properties: General
The General tab of the Instrument Property page displays details about the connected instrument and
allows certain instrument functions to be executed.
The following topics are covered in this section:
Displaying the general tab
Modifying the instrument's filter settings
Performing an absorbance linearity calibration of all the instrument's filter set
Acquiring raw energy data
Loading and ejecting a plate
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To show the instrument general properties page:
1. Open the instrument property sheet
2. Click the General tab
The status information displayed is for information only and cannot be modified
To modify the instrument's filter settings:

The instrument general property page shows at which filter positions the instrument has filters
installed and their corresponding wavelengths. The listing can be updated to reflect a change in the
instrument's filter setup
1. Click in the filter position's check box to indicate a filter is installed in that filter position
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2. Enter the corresponding filter wavelength
Note: All available filter positions are shown. It is not necessary to have filters installed in all
available filter positions. The occupied filter positions do not need to be contiguous.
3. Click Apply
If any filter details have been modified, the filter absorbance linearity calibration routine is
performed for those filter positions. This can take several minutes to complete.
Note: The instrument general property page shows at which filter positions the instrument has
filters installed and their corresponding wavelengths. The instrument cannot detect any filter
position changes made by the user so if any filter positions are changed or added then the filter
list must be updated.
To perform an absorbance linearity calibration of all the instrument's filter set:

1. Click on Recalibrate All
The Filter Calibration dialog is displayed whilst the calibration is performed. This can take
several minutes to complete
To acquire raw energy data:

To measure the amount of energy (or light) received at the detector:
1. Choose the Wavelength at which to measure the raw energy by selecting the wavelength from
the drop down list.
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2. Click on Acquire Raw Energy
The raw energy measurement dialogue is displayed whilst the data is acquired.
3. The data is shown in counts for each well
Note: The data can be saved, printed and exported.

Note: A new data window is used to display the data if the measurement is repeated at the
same or a different wavelength.
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To load a plate:
1. Click on Load Plate
To eject a plate:
1. Click on Eject Plate
Instrument Properties: Methods and Plate Data
The Methods and Plate Data tabs of the Instrument Property page allows instrument stored methods
and plate results to be downloaded to Galapagos and instrument compatible methods to be uploaded
to the instrument from Galapagos. Note that these features are only available when connected to
instrument types that support the transfer of methods and plate data.
Downloading methods from the instrument to Galapagos
Uploading methods to the instrument
Downloading results data from the instrument to Galapagos
All topics require connection to an instrument that supports the transfer of method and plate data to
Galapagos, such as the EZ Read 800 Plus.
To download methods from the instrument:


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3. Click on the Methods tab
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4. Click on Download and enter a file name to save the data
Note: The method files are saved in the KMT file format.
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5. The methods that have been downloaded are displayed in the methods tab
Note: All methods present on the instrument are downloaded.
To upload methods to the instrument:


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2. Click on Upload and select the methods file to upload
Note: The methods file is uploaded in the KMT file format.
The Upload Methods dialogue is displayed during the file upload process:
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To download results data from the instrument:

3. Click on the Plate Data tab
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4. Click on Download
The downloaded data sets are displayed and saved as text files:
Note: All available result data sets are downloaded

Note: The downloaded results are named using the format 'PlateData_[Instrument Serial
Number]_[YYYYMMDDHHMMSS]_[Index]'. The first bracketed section is the instrument's serial
number. The second bracketed section is the time when the download executed, stated as year
hour (MM) and second of the minute (SS). The third bracketed section increments in whole
numbers starting from 1 for each results data set downloaded.
5. The results data can be viewed by importing the text files using the software's Import feature
Instrument Properties: Plate Definitions
The Plate Definitions tab of the Instrument Property page allows instrument stored plate definitions to
be downloaded to Galapagos, modified and uploaded to the instrument. Note that these features are
only available when connected to instrument types that support the transfer of plate definition
information.
Downloading plate definition data from the instrument
Editing plate definitions and uploading to the instrument
All topics require connection to an instrument that supports the transfer of plate definition of data to
Galapagos, such as the EZ Read 2000.
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To download plate definition data from the instrument:

3. Click on the Plate Definitions tab
Plate definition data are downloaded from the instrument and displayed
The size, column & row offsets and columns & row spacing are displayed for each plate
definition.
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To edit a plate definition and upload to the instrument:
1. Download the plate definitions from the instrument
2. Click on the variable to edit and enter the value required.
Note: The size variable cannot be edited.

Note: As many variables can be edited as required.
3. Click on Upload
The edited plate definition data is uploaded to the instrument
Instrument Properties: Transport
The Transport tab of the Instrument Property page reports status information for the X and Y plate
transport drives and the wavelength drive. Note that these features are only available when connected
to instrument types that support the reading of this information.
A connection is required to an instrument that allows Galapagosto read drive information from the
instrument, such as the EZ Read 2000.
To view drive status information:


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3. Click on the Transport tab
Status information is displayed separately for each of the drives
Instrument Properties: Wavelength Calibration
The Wavelength Calibration tab of the Instrument Property page enables a wavelength calibration of
the instrument to be performed. Note that these features are only available when connected to
instrument types that support wavelength calibration.
Wavelength recalibration using the inbuilt reference LED only
Wavelength recalibration using the inbuilt reference LED and Holmium filter
Moving to a specific wavelength
All topics require connection to an instrument that supports wavelength recalibration, such as the EZ
Read 2000.
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To perform a wavelength recalibration using the inbuilt reference LED only:

3. Click on the Wavelength Calibration tab
4. Click on Recalibrate
The instrument performs the calibration routine and recalibrates the wavelength. The
instrument's status information is updated.
5. Click OK
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To perform a Wavelength recalibration using the inbuilt reference LED and Holmium filter:

4. Click on the Use Holmium Filter check box and click on Recalibrate
5. Click OK
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To move to a specific wavelength:

4. Enter the required wavelength in the Wavelength edit field and click on Go To Wavelength
The instrument is set to the required wavelength. The instrument's status information is
updated.
5. Click OK
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Anthos Models
Instrument Window
Instrument Properties: General (status and filters)
Instrument Window

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See also:
o Instrument properties: General
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3. Click Apply
To perform an absorbance linearity calibration of all the instrument's filters:

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ASYS Models
Instrument Window
Instrument Properties: General tab (status, filters, acquire raw energy, data and load & eject
plates)
Instrument Properties: Methods and Plate Data tab
Instrument Properties: Plate Definitions tab
Instrument properties: Transport
Instrument Properties: Wavelength Calibration tab
Note: The instrument type connected will determine which instrument property tabs are
accessible.
Instrument Window
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See also:
o Instrument properties: General
o Instrument properties: Method and Plate Data
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Acquiring raw energy data
Loading and ejecting a plate
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3. Click Apply
To perform an absorbance linearity calibration of all the instrument's filter set:

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To acquire raw energy data:
To measure the amount of energy (or light) received at the detector:
1. Choose the Wavelength at which to measure the raw energy by selecting the wavelength from
the drop down list.
2. Click on Acquire Raw Energy
The raw energy measurement dialogue is displayed whilst the data is acquired.
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3. The data is shown in counts for each well
Note: The data can be saved, printed and exported.

Note: A new data window is used to display the data if the measurement is repeated at the
same or a different wavelength.
To load a plate:
1. Click on Load Plate
To eject a plate:
1. Click on Eject Plate
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Instrument Properties: Methods and Plate Data
The Methods and Plate Data tabs of the Instrument Property page allows instrument stored methods
and plate results to be downloaded to Galapagos and instrument compatible methods to be uploaded
to the instrument from Galapagos. Note that these features are only available when connected to
instrument types that support the transfer of methods and plate data.
Downloading methods from the instrument to Galapagos
Uploading methods to the instrument
Downloading results data from the instrument to Galapagos
All topics require connection to an instrument that supports the transfer of method and plate data to
Galapagos, such as the ASYS Expert Plus.
To download methods from the instrument:


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4. Click on Download and enter a file name to save the data
Note: The method files are saved in the KMT file format.
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5. The methods that have been downloaded are displayed in the methods tab
Note: All methods present on the instrument are downloaded.
To upload methods to the instrument:


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2. Click on Upload and select the methods file to upload
Note: The methods file is uploaded in the KMT file format.
The Upload Methods dialogue is displayed during the file upload process:
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To download results data from the instrument:

3. Click on the Plate Data tab
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4. Click on Download
The downloaded data sets are displayed and saved as text files:
Note: All available result data sets are downloaded

Note: The downloaded results are named using the format 'PlateData_[Instrument Serial
Number]_[YYYYMMDDHHMMSS]_[Index]'. The first bracketed section is the instrument's serial
number. The second bracketed section is the time when the download executed, stated as year
hour (MM) and second of the minute (SS). The third bracketed section increments in whole
numbers starting from 1 for each results data set downloaded.
5. The results data can be viewed by importing the text files using the software's Import feature
Instrument Properties: Plate Definitions
The Plate Definitions tab of the Instrument Property page allows instrument stored plate definitions to
be downloaded to Galapagos, modified and uploaded to the instrument. Note that these features are
only available when connected to instrument types that support the transfer of plate definition
information.
Downloading plate definition data from the instrument
Editing plate definitions and uploading to the instrument
All topics require connection to an instrument that supports the transfer of plate definition of data to
Galapagos, such as the UVM340.
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To download plate definition data from the instrument:

3. Click on the Plate Definitions tab
Plate definition data are downloaded from the instrument and displayed
The size, column & row offsets and columns & row spacing are displayed for each plate
definition.
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To edit a plate definition and upload to the instrument:
1. Download the plate definitions from the instrument
2. Click on the variable to edit and enter the value required.
Note: The size variable cannot be edited.

Note: As many variables can be edited as required.
3. Click on Upload
The edited plate definition data is uploaded to the instrument
Instrument Properties: Transport
The Transport tab of the Instrument Property page reports status information for the X and Y plate
transport drives and the wavelength drive. Note that these features are only available when connected
to instrument types that support the reading of this information.
A connection is required to an instrument that allows Galapagosto read drive information from the
instrument, such as the UVM340.
To view drive status information:


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3. Click on the Transport tab
Status information is displayed separately for each of the drives
Instrument Properties: Wavelength Calibration
The Wavelength Calibration tab of the Instrument Property page enables a wavelength calibration of
the instrument to be performed. Note that these features are only available when connected to
instrument types that support wavelength calibration.
Wavelength recalibration using the inbuilt reference LED only
Wavelength recalibration using the inbuilt reference LED and Holmium filter
Moving to a specific wavelength
All topics require connection to an instrument that supports wavelength recalibration, such as the
UVM340.
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To perform a wavelength recalibration using the inbuilt reference LED only:

4. Click on Recalibrate
5. Click OK
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To perform a Wavelength recalibration using the inbuilt reference LED and Holmium filter:

4. Click on the Use Holmium Filter check box and click on Recalibrate
5. Click OK
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To move to a specific wavelength:

4. Enter the required wavelength in the Wavelength edit field and click on Go To Wavelength
The instrument is set to the required wavelength. The instrument's status information is
updated.
5. Click OK
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Methods
The following measurement methods are available in Galapagos:
Quick Method:
o Quick Measurement - Basic sample measurement
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Quick Measurement
The Quick Measurement application enables you to perform a quick sample check at a specified
wavelegth.
To open the Quick Measurement window:

1. Select the Methods tab
2. Click Quick Measurement
Keyboard shortcut: Alt, M, Q

or
1. Launch from the quick access toolbar by clicking on the Quick Measurement icon -
Note: Certain instrument types eject the plate when a method type is selected.
See also:
o Acquiring using Quick Measurement
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Acquiring Using Quick Measurement

o Running a Quick Measurement - single wavelength acquisition
o Running a Quick Measurement - dual wavelength acquisition
o Running a Quick Measurement - multiple wavelength acquisition
o Running a Quick Measurement - wavelength scan
o Running a Quick Measurement incorporating sample shaking control
o Running an Quick Measurement incorporating temperature control
o Using timed measurement cycling for Quick Measurements
To run a Quick Measurement - single wavelength acquisition:

Either follow all the steps below or Open a Method Template and continue from Step 8 below.
1. Display the Quick Measurement window
2. Select the Acquire tab from the Method Tools context group
3. Select the Single Wavelength measurement mode

4. Enter the Wavelength at which to perform the measurement by either selecting the required
wavelength from the those available or by typing in the required value in nanometers
Note: The wavelengths available for selection vary according to the instrument type connected.
Some instrument types have a limited set of discrete wavelengths available for selection and
other instrument types have available for selection a continuous range of wavelengths.
Note: If the wavelength entered is not a permitted value, it is automatically changed to the
nearest permitted value when the measurement is started.
5. Select the Manipulate tab from the Method Tools context group
6. Click on Change Plate Layout
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7. Create, open or modify a plate layout using the tools available
To confirm the use of the layout for the measurement and return to the Acquire tab, click on
Accept Layout
To return to the Acquire tab without selecting a plate layout, click on Discard Layout
Note: The acquisition of data cannot be started if the Layout tab remains open. Return to the
Acquire tab by clicking Accept Layout or Discard Layout.
Note: On accepting a plate layout, any data previously acquired and displayed will be cleared
from the display.
8. Select the Acquire tab from the Method Tools context group and click Start
Note: For measurements involving more than one physical plate, prompts will request the
correct plate is loaded before the measurement is started
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9. Acquisition is initiated and a progress monitor displayed
If Stop is clicked during data acquisition, the measurement processes will complete but no
measurement data will either be saved or displayed
10. Once acquisition is complete, the measurements for each well are displayed in the data window
Note: It is not possible to edit any of the measurement values in the data window.
Note: If a well cannot be measured because too much or too little light is passing through it, no
well value is shown.
Note: Data from only the current quick measurement can be displayed. To display multiple
quick measurement data sets, first save the data and then open the required data sets.
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11. Select a well to display the well's measurement data in tabular form in the data window
The arrow keys can be used to navigate between wells.
12. The acquired data is automatically stored to either the connected database or, if working offline,
to file using the default naming scheme. Additional copies of the data can be saved using the
Save As command in the File tab
Note: It is not possible to change any measurement settings while data acquisition is in
progress.
Note: Certain instrument types eject the plate once the measurement sequence is complete.
To run a Quick Measurement - dual wavelength acquisition:

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3. Select the Dual Wavelength measurement mode
4. Enter the Wavelength at which to perform the measurement and the reference by either
selecting the required wavelength from the those available or by typing in the required value
Note: The measurement and reference wavelengths must be different. If they are set to be the
same, a warning dialog is displayed.
Some instrument types have a limited set of discrete wavelengths available for selection and

Accept Layout
Acquire tab by clicking Accept Layout or Discard Layout
from the display.
8. Click Start
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9. Acquisition is started and a progress monitor is displayed
measurement data will either be saved or displayed.
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Three values are shown for each well:
The upper number, shown in bold, is the difference between the measurement and
reference values
The middle number is the measurement value
The lower number is the reference value
The Equations section of the Method Properties dialogue displays the equation used to calculate
the difference between the measured and reference value. This equation cannot be edited or
removed. For information on managing equations, see the section on graphical data display and
manipulation.
quick measurement data sets, first save the data and then open the data.
progress.
Note: Certain instrument types eject the plate once the measurement sequence is complete
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To run a Quick Measurement - multiple wavelength acquisition:
3. Select the Multiple Wavelength measurement mode
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4. Click Wavelengths and enter the number of different wavelengths to be measured by either
entering the required value into the edit field or using the arrows to increment the existing
value. Select the wavelengths to be measured by either selecting the required wavelengths
from the those available or by typing in the required values into the corresponding wavelength
edit fields.
Note: Each measurement wavelength must be different. If two or more are set to be the same
a warning dialog is displayed when Start is clicked.
Some instrument types have available for selection a limited set of discrete wavelengths and
Note: The minimum number of wavelengths selectable is two. The maximum number of
wavelengths that can be selected depends on the instrument type connected. For instrument
types supporting a limited number of discrete wavelengths, the maximum number of
wavelengths selected cannot be greater than the number of discrete wavelengths supported by
the instrument. For instrument types supporting a continuous range of wavelengths, the
maximum number of wavelengths selected cannot be greater than 10.
Note: The measurements are acquired in the order in which the wavelengths are specified.
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Accept Layout
from the display.
8. Click Start
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Absorbance values for each different wavelength are displayed in each well in the order
specified in step 4. Where more than three wavelengths are selected, the plots of absorbance
against wavelength are displayed in each well. The axes of all plots cover the same range to
allow comparison of data between wells.
Note: The absorbance values are plotted from lowest to highest wavelength, irrespective of the
order the wavelengths are specified in Step 4.
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11. Select a well to display the well's measurement data in graphical and tabular form in the chart
and data windows respectively
progress.
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To run a Quick Measurement - wavelength scan:
Note: Wavelength scanning is supported by certain instrument types. If the instrument

connected does not support wavelength scanning, the wavelength scan measurement mode will
not be available to select.

3. Select the Wavelength Scan measurement mode

4. Enter the wavelength scan range by entering the Low and High wavelengths and the
wavelength Step Size by either selecting the required values from the those available or by
typing in the required value.
Note: The low and high wavelengths must be different. If they are set to be the same, a
warning dialog is displayed.
Note: The step size cannot be larger than the spectral range. A warning dialog is displayed is
the spectral range is less than the step size.
Note: The combination of spectral range and step size selected must allow for there to be at
least two data points in the spectrum. If the settings do not allow this, a warning dialog is
displayed.
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Accept Layout
from the display.
8. Select the Acquire tab and click Start
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The display updates after each well measurement has completed.

10. Once acquisition is complete, the measurements for all wells are displayed in the data window
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Note: The spectrum displayed in each well are each thumbnails of the full spectrum obtained
during data acquisition. When a well is selected, the spectrum displayed in the chart window
shows the entire data set.
progress.
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Running a Quick Measurement incorporating sample shaking control:
Note: Sample shaking can be incorporated into a quick measurement if the instrument
connected supports shaking.

Accept Layout
from the display.
6. Select the measurement mode and the wavelength(s)
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7. Select the shaking Mode:
The options are:

o Off: No shaking
o Single: Shaking is performed before the measurement irrespective of the number of
wavelengths measured or timed cycles
o Cycle: Shaking is performed before each timed measurement cycle
8. Select the shaking Amplitude:

Select the amplitude settings required from those available for the instrument type
9. Select the shaking Speed:
The options are:

o Slow
o Medium
o Fast
o Very fast
Note: Not all instrument types that support shaking require the shaking speed to be specified.
10. Select the shaking Duration:
The current duration is displayed in the format: hours : minutes : seconds

To modify the duration click on the displayed duration.
Change the duration by selecting the units from the drop down list and either entering the
required value in the edit field or using the arrows to increment the existing value. The
updated duration is displayed. Click anywhere outside the Shaking Duration dialog to set the
duration.
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11. Click Start
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progress.
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Running an Quick Measurement incorporating temperature control:
Note: Temperature control can be incorporated into a quick measurement if the instrument connected
supports temperature control.

Accept Layout
from the display.
6. Select the measurement mode, the wavelength(s) and shaking conditions (if supported by the
instrument connected and if required)
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7. Click in the Use Temperature Control check box
Enter the required setpoint temperature into the edit field or use the arrows to increment
the existing value.
Note: Instruments that support temperature control have factory set temperature ranges at
which they can operate. This determines the value the setpoint can be set to.
8. Click Start
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progress.
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Using timed measurement cycling for Quick Measurements:
All Quick Measurement modes can be cycled by defining the timing parameters.

Accept Layout
from the display.
6. Select the measurement mode, the wavelength(s) and shaking conditions (if supported by the
instrument connected and if required)
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7. Click on Timing Off to enable timed measurements
8. Set the length of the Delay before acquisition begins by clicking on the Delay time arrow
Use of a time delay can be disabled by unchecking the Use Delay option.
The delay time can be entered into the first edit box in the format hours : minutes : seconds or
by using the arrows to increment the existing value in seconds. Alternatively, the delay time
can be entered into the second edit box in the format hours : minutes : seconds or by using the
arrows to increment the existing value in the units selected from the drop down list.
Note: The delay is the time before the first measurement cycle is started. If shaking is enabled,
the delay time is in addition and before an initial shaking time.
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9. Set the length of the Interval between measurement cycles by clicking on the Interval time
arrow
Use of an interval time can be disabled by unchecking the Use Interval option.
The interval time can be entered into the first edit box in the format hours : minutes : seconds
or by using the arrows to increment the existing value in seconds. Alternatively, the interval
time can be entered into the second edit box in the format hours : minutes : seconds or by
using the arrows to increment the existing value in the units selected from the drop down
list.
Note: The interval is the time between the start of successive cycles. The minimum value is set
by the cycle time.
Note: The cycle time is determined by the time taken by the instrument to acquire the data for
each cycle and, if selected, the shaking duration if the shaking mode is set to Cycle.
10. Set the duration by clicking on the duration time arrow
The duration is a multiple of the cycle time and is determined by the number of cycles which is
entered in the Total Cycles text field or using the arrows to increment the existing value.
Alternatively, the duration time can be entered into the second edit box in the format hours :
minutes : seconds or by using the arrows to increment the existing value in multiples of the
cycle time. Any value entered that is not a multiple of the cycle time is rounded off to the
nearest multiple of the cycle time.
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Alternatively, the duration time can be entered into the third edit box in the format hours :
minutes : seconds or by using the arrows to increment the existing value in multiples of the
cycle time in the units selected from the drop down list. Any value entered that is not a multiple
of the cycle time is rounded off to the nearest multiple of the cycle time.
Note: The cycle time is determined by the time taken by the instrument to acquire the data for
each cycle and, if selected, the shaking duration if the shaking mode is set to Cycle.
11. Click Start
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For each wavelength measured, the absorbance is plotted against time. The axes of all plots
cover the same range to allow comparison of data between wells.
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progress.
See also:
o Detailed well view
o Applying data manipulations during the measurement process
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Changing the Plate Layout
The Layout tab of the Method Tools context group provides tools to create, open, modify and save
plate layouts for use when making Quick Measurements.

Managing Plate Layouts:
Returning to Quick Measurement
Saving a plate layout to the database
Saving a plate layout to file
Open a plate layout from the database
Open a plate layout from file
Removing a plate layout from the database
Creating Plate layouts:

Selecting the plate definition
Modifying the number of plates in a layout
Viewing the plates in a layout
Selecting wells
Deleting a group from a layout
Clearing all groups from a layout
Adding a group to a layout
Adding a group to the layout that overlaps an existing group
Adding wells to an existing group
Removing wells from an existing group
Adding a constant to a well or group
Editing a constant assigned to a well or group
Deleting a constant assigned to a well or group
Adding sample replicates to a group
Editing sample replicates
Returning to the default plate layout
Returning to Quick Measurement:

After using the tools described below to create or edit a plate layout, either:
Click on Accept Layout to return to the Quick Measurement Acquire tab and use the new plate
layout when taking a measurement
Click on Discard Layout to return to the Quick Measurement Acquire tab and use the previously
defined plate layout when taking a measurement.
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Saving a Plate Layout to the Database:
1. Connect to a database
Refer to Database Connection and Management for help
2. Create or open a plate layout
3. Click on Save To Database
4. Enter the filename and Click OK
Note:The layout name and file name must be the same. If the plate layout is saved and the file
name is not the same as the plate layout name, Galapagoswill automatically adjust the name to
be the same as the file name.
Note: The layout name must be unique. If an attempt is made to save the layout with the same
name as an existing layout an error message is displayed.
Note: When saving a plate layout to the database, the corresponding plate definition must have
previously been saved to the database or an identical plate definition must exist in the
database. If this is not the case, a prompt will allow the following options:
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Select an existing plate definition from the database - clicking on this option will
prompt the selection of a plate definition from those existing in the database. The
options will be limited to those with the corresponding number of rows and columns.
Create a new plate definition from the details already assigned to the layout and save
to the database - clicking on this option will prompt for a plate definition name before
saving to the database.
Saving a Plate Layout to File:

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Note: Plate layout files are saved with the file extension .layout
Note: The layout name must be unique. If an attempt is made to save the layout with the
same file name as an existing layout an error message is displayed.
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Open a Plate Layout from the Database:
2. Click on Open From Database
3. Select the layout to be opened from the list displayed and click Open
The plate layout is displayed in the active tab in the plate layout display
displayed.
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Open a Plate Layout from File:
1. Click on Open From File
Note: Plate layout files have the file extension .layout
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Removing a Plate Layout from the Database:
1. Open the plate layout from the database
2. Click on Remove from Database
3. Click on Yes
The plate layout entry is removed from the database
Note: If a plate layout is not stored in the database, a warning dialogue is displayed:
Selecting the Plate Definition

The information contained in the plate definition determines the physical plate characteristics of
the plates in the plate layout. Click here for help on creating a plate definition.
1. Click on Plate Definition
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2. Select whether to choose a plate definition stored in the database or on file
3. Select the plate definition file from the database or file list
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The selection list is filtered to show only plate definitions compatible with the connected
instrument.
All plates in the plate layout will be of the type defined by the plate definition file.
4. The Properties tab will show the plate definition details in the Plate Definition entry in the
Layout section.
The entry can be expanded to show all plate parameters using the symbol and reduced to
hide the parameters using the symbol. The fields are read only and cannot be edited.
Note: Instruments are compatible with a limited number of plate definitions. If an incompatible
plate definition is selected a warning message is displayed and the selection rejected.
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Modifying the Number of Plates in a Layout:
By default, a plate layout is created comprising a single plate using a standard 96-well definition plate
with all wells assigned to a single group of sample wells called Group 1.
1. To increase the number of plates in a layout, click on No. of Plates
2. Enter the number of plates required in the edit field
The group tab updates to show an entry for each plate with the groups assigned to each plate
detailed.
The watermark displayed on the plate indicate its plate number in the plate series
Note: If additional plates are added to the default layout, then the new plates will be created
comprising the same layout. If additional plates are added to a non-default layout, then the
new plates will be created with all wells assigned to a new group of samples wells.
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3. To reduce the number of plates in a layout, click on No. of Plates
5. Click Yes to proceed
Note: When reducing the number of plates in a layout, the most recently added plate is
removed.
Note: Groups that only appear on a plate which has been removed are deleted from the layout
all together.
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Viewing the Plates in a Layout:
1. Select the plate to view by clicking on the plate name in the Groups tab
Select the group of interest by clicking on the corresponding group name from those listed in
the Group tab
Selecting Wells:
1. To select a single well, click on the well of interest
The well is highlighted with a grey dashed border.
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2. To select multiple wells, use one of the following methods:
Multiple individual well selection: Click on each well whilst pressing and holding the
keyboard Control key
Area selection: Click on a well and drag to create a rectangular selection of wells
Row selection: Click on a row letter to select the entire row
Column selection: Click on a column number to select the entire column
Select all wells: Click on the box to the left of Column 1 and above Row A
The keyboard Control key enables well selection methods to be combined. With a well or
set of wells selected, press and hold the keyboard Control key before selecting the next
set of wells. Any combination of the above selection methods is permitted.
The selected wells are highlighted with a grey dashed border.
Note: Multiple well selection is confined to wells from the same plate. To configure a group to
comprise wells from more than one plate, see Adding Wells to Existing Groups.
Note: Wells on plates that have been assigned as masked wells during the plate's definition
cannot be selected. These masked wells are labelled N/A.
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Deleting a Group from a Layout:
1. Select the group by selecting a well within the group of interest
2. Click Delete Groups
3. Click on Yes
Note: If default group naming is used, when a group is removed from the layout, the groups
using default naming are renumbered so the first of the remaining groups to be added to the
layout is called 'Group '1, the next 'Group 2' and so on.
Clearing All Groups from a Layout:

1. Click on Clear Groups
2. Click on Yes
Note: The Clear Groups command removes all groups from all plates of the layout.
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Adding a Group to a Layout:
1. Select a well or set of wells
Note: To add a group which has wells on more than one plate, first add a group on one plate
and then add wells from other plates to the group. See topic below entitled 'Adding Wells to
Existing Groups'.
2. Click Add Group
3. Edit the fields in theAdd Group dialog and click OK
Name: By default, groups are named 'Group n' where n is a number and for the first group
created is 1 and which is incremented by 1 for each subsequent group created. Group names
can be edited by clicking in the name edit field but have to be unique
Description: By default, no description is provided. Click in the description edit field to enter a
description
Well Type: Each group must be assigned one of the four well types from the drop down list. By
default this is set to the Sample option
The border used to highlight the group is coloured according to the well type selected. The
colours are:
Sample: red
Reference: green
Control: blue
Standard: orange
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Wells: A list of the well positions comprising the group. Positions are reported as well
coordinate in the main plate layout display. The coordinates have the format row letter then
column number. The field can be edited to add or remove wells to the group. Contiguous
rectangular groups of wells are defined using a colon written in between the coordinate
positions of the top left and bottom right corners of the rectangle. Contiguous groups are
separated using a comma.
To update the group's well assignment, click on button. This will update the plate layout
display to reflect the revised assignment.
Note: Name, description and well type can be modified using the plate layout property pane.
Note: A well can be part of only one group.
Note: Set group replicates through the Plate Properties pane.
Note: For a group comprising standards, set the concentration of the standards by clicking on
Edit Constant.
Adding a Group to a Layout that Overlaps an Existing Group:

1. Select a well or set of wells that has complete or partial overlap with an existing group
2. Click Add Group
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4. Select the appropriate option from Overlapping Group dialog
Note: Name, description and well type can be modified using the plate layout property pane
Note: A well can be part of only one group
Adding Wells to Existing Groups:

1. Select an existing group
2. If necessary, display the appropriate plate by clicking on the plate name in the Groups tab,
press and hold the keyboard Control key and select a well or set of wells
3. Click Add To Group
4. Select the group from the displayed list
Note: This operation can be performed on plate layouts which comprise multiple plates.
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Adding a Constant to a Well or Group:
1. Select the well or group to which a constant is to be added
Note: A constant can only be added a an individual well if the well is part of a group.
2. Click on Add Constant
3. Select whether to add to the group or well using the selection list displayed
4. Enter the name of the constant and, optionally a description, in the Name and Description edit
fields of the Add Constant dialogue
5. Select the type of constant to assign by selecting either Static or Prompted from the Type
drop down list
Note: A static constant always has the same value. The value of a prompted constant is
requested before it is used in a data manipulation.
If a Static constant has been selected, enter the value to be used in the Value edit field
Click OK
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Editing a Constant Assigned to a Well or Group:
1. Click on Edit Constant
2. Select the constant to edit from the list displayed and click OK
3. Edit the fields as required and click OK
Note: The Name, description and value of standard concentrations are added through the Edit
Constants option and standard concentration constants do not appear in Delete Constants list.
Standard concentration constants are automatically added and removed according to the
replicate statistics for each of the groups comprising standards. For additional information, see
Creating a Quick Measurement incorporating Quantitative Analysis.
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Deleting a Constant Assigned to a Well or Group:
1. Click on Delete Constant
2. Select the constant to delete from the list displayed and click OK
Removing Wells From Existing Groups:

1. Select a well or set of wells from within an existing group
2. Click Remove From Group
Note: To remove wells from a group that comprises wells from more than one plate, remove
the necessary wells from each plate separately.
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Adding Sample Replicates:
Sample replicates can be added to any group.
1. Launch the plate layout editor configuration tools
2. Select the group of interest
3. Click on the Plate Properties tab to display the Plate Properties window
4. Input the required value into the Replicates edit field (part of the Selected Group section) or
use the arrows to adjust the current value.
Note: By default, the number of replicates for a group is set to a value of one. The range of
valid values is one to ten.
Note: The replicates run in sequence through the wells.
Editing Sample Replicates:

Returning to the Default Plate Layout:

1. If a plate layout is displayed, click on New Layout
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2. If the existing plate layout has not been saved, a prompt will be displayed warning of possible
data loss. Click Yes to continue.
The default plate layout is displayed.
Saving a Method Template

Method templates can be saved for later use.
To Save a Method Template to the Database:

2. Click on the Acquire tab within the Method Tools context group and select the measurement
mode and set the method parameters as required
3. Click on the Manipulate tab within the Method Tools context group and then click on Change
Plate Layout to select, create or edit a plate layout as required
4. Click on the Manipulate tab within the Method Tools context group and use the equation tools
to define manipulations to be applied to the measurement data as required
6. Click on Save As and Save Method Template to Database
7. Enter a method template name
Click on OK
Note: Method templates can be overwritten
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To Save a Method Template to File:
2. Select the measurement mode and set the method parameters as required
3. Click on the Manipulate tab within the Method Tools context group and then click on Change
Plate Layout to select, create or edit a plate layout as required
4. Click on the Manipulate tab within the Method Tools context group and use the equation tools
to define manipulations to be applied to the measurement data as required
6. Click on Save As and Save Method Template to File
7. Enter a method template name
Click on Save
Note: Method templates can be overwritten

Note: Method template files are saved as .method files.
See also:
o Opening method template files
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Opening a Method Template
Previously saved method templates can be open for use.
To Open a Method Template from the Database:

2. Click on Open and Open Method Template from Database
Note: All active quick measurement tabs must be closed before attempting to open a method
template
3. Select a method template to open
Click on OK
The method is displayed
To Open a Method Template from File:

2. Click on Open and Open Method Template from File
Note: All active quick measurement tabs must be closed before attempting to open a method
template
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3. Select a method template to open
Click on OK
The method is displayed
Note: Method template files are saved as .method files.
See also:
o Saving method template files
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Plate Tools
Galapagos has tools to define plate settings. Click below for additional information on how to use
these tools:
o Plate definition editor
o Plate layout editor
Plate Definition Editor
Galapagos provides tools to define plate characteristics and save them for use when taking
measurements.
To launch the plate definition configuration tools:

2. Click on Plate Layout in the Configuration group
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3. The user interface shows the Layout Tools Display ribbon and on each plate definition tab the
parameters of a plate split into plate details, plate geometry and well geometry categories.
Each plate definition tab can display a single plate definition, whether newly created or opened
from a previously saved layout. Additional plate definition tabs can be created by repeating
Steps 1 & 2 above.
Close a plate definition tab using the tab's button
Click on the user interface items below for additional details:

o Layout Tools Display ribbon
o Plate definition display
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Layout Tools Display Ribbon
The Create group enables a new plate definition to be created from the default standard plate
definition. The Database and File groups enable plate definitions to be saved, previously saved
layouts opened and unused plate definitions to be removed from the database.
Plate Definitions Display

The information on the plate definitions tab is split into three sections that identify a plate type
and define both the plate and its corresponding well geometry. Previously saved plate
definitions are used for creating plate layouts.
See also:
o Saving and opening plate definitions
o Creating plate definitions
o Removing plate definitions from the database
Saving and Opening Plate Definitions

Galapagos can save plate definitions to the database or to file. Previously saved plate definitions can
be opened for use.
o Saving a plate definition to the database
o Saving a plate definition to file
o Opening a plate definition from the database
o Opening a plate definition from file
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Saving a Plate Definition to the Database:
2. Click on the Setup tab and then on Plate Definition
3. Create or open a plate definition

Note:The plate definition name and file name must be the same. If the plate definition is saved
and the file name is not the same as the plate definition name, Galapagoswill automatically
adjust the name to be the same as the file name.
Note: The layout name must be unique. If an attempt is made to save the plate definition with
the same name as an existing plate definition an error message is displayed.
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Saving a Plate Definition to File
2. Create or open a plate definition

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Note: Plate definition files are saved with the file extension .plate
Note: The plate definition name must be unique. If an attempt is made to save the plate
definition with the same file name as an existing plate definition an error message is displayed.
Opening a Plate Definition from the Database

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4. Select the plate definition to be opened from the list displayed and click Open
The plate definition is displayed in the active tab in the plate definition display
Note: With the Open from Database dialogue displayed, access the content filter for each field
by moving the mouse over the field name and clicking on the that appears. In the filter
dialogue box that is displayed, select whether to limit the displayed output for the field to those
item(s) selected or not to filter by checking Select All.
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Conditions allow filters to operate on ranges of values and logic. Conditions can be applied to
the filters by clicking on Conditions in the filter dialogue box. Select an operators from the
drop down list, input the required values, select linking logic and click Apply.
displayed.
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Opening a Plate Definition from File
3. Select the plate definition to be opened from the list displayed and click Open
The plate definition is displayed in the active tab in the plate definition display
Note: Plate definition files have the file extension .plate
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Creating Plate Definitions
Plate definitions can be created by inputting data into the three sections of the plate definition setup.
o Creating a new plate definition from the default standard plate definition
o Creating a new plate definition from an existing plate definition
To Create a New Plate Definition from the Standard Default Definition

1. Either, select the Setup tab
and click on Plate Definitions
or, if a plate definition is already displayed, click on New Definition
If the existing plate definition has not been saved, a prompt will be displayed warning of
possible data loss. Click Yes to continue.
Note:For details of how to save a plate definitions, see Saving and Opening Plate Definitions.
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3. Enter the required information into the plate details fields. The fields in bold most be completed
before the definition can be saved and used.
Name: The name of the plate definition. This name given has to be unique and the same
as the filename used to save the plate definition.
Description: The description of the plate, including, for example, plate characteristics
and compatibility
Manufacturer: The manufacturer's details. By default, the entry is 'Not Defined'.
Material: Details of the material from which the plate is manufactured. By default, the
entry is 'Not Defined'.
Surface Treatment: Details of any surface treatment applied to the plate. By default,
the entry is 'Not Defined'.
Sterile: Indicates whether the plate is sterile or not sterile. The check box should be
checked if the plate has been sterilised.
Strip Well Type: Details of the type of strip well in use. By default, the entry is 'No'.
Masked Wells: Allows wells to be defined that are not to be used for measurement
purposes. Click on the symbol and graphically select the masked wells using the
well selection options and click OK. The selected wells are shown with a dashed border
around them. The coordinates of the selected masked wells are reported in the Selection
field. This field cannot be edited. To clear a selection click on .
Columns: The number of wells in each column of the plate.

Rows: The number of wells in each row of the plate.
Wells: The total number of wells on the plate. This is calculated from the columns and
row fields and is not an editable field.
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By clicking on the in the manufacturer, material, surface treatment and strip well type fields, a
list of commonly and previously used entries is displayed for selection. When typing into these
fields, the software will automatically complete entries that have been entered previously.
Note: When entering details into the fields, the mandatory fields will be displayed in red until
all have been completed.
Note: The well selection methods for defining masked wells are the same as used for selecting
wells in the plate layout. View the Well Selection section on the Creating and Modifying Plate
Layouts page for details.
4. Enter the required information into the plate geometry fields by either entering numbers into
the fields or using the field's arrows to increment the existing values. All fields must be
completed before the plate definition can be saved and used.
Plate Length: The total length of the plate
Plate Width: The total width of the plate
Plate Height: The total height of the plate
A1 Column Offset: The distance in the x direction from the edge of the plate to the
centre of well A1 (column one, row one)
A1 Row Offset: The distance in the y direction from the edge of the plate to the centre
of well A1 (column one, row one)
Column Spacing: The distance in the x direction between the centre of adjacent wells
Row Spacing: The distance in the y direction between the centre of adjacent wells
Well Diameter: The well diameter
The plate geometry schematic updates to reflect the values entered into the fields.
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Invalid entries results in the offending field being highlighted in red together with an
explanation of the problem. Adjust the parameters until all entries are valid.
Note:All values are in millimetres and are displayed to two decimal places unless the plate
comprises 384 wells or more in which case the values are displayed to three decimal places .
Note: Each field has minimum and maximum limits.
Note: The Well Diameter parameter in the plate geometry section and Diameter at Top
parameter in the well geometry section correspond to the same physical parameter. The Plate
Height parameter in the plate geometry section imposes a maximum limit on the Depth
parameter in the well geometry section. This coupling can result in invalid entries in one section
effecting entries in the other section.
5. Enter the required information into the well geometry fields by either entering numbers into the
fields, using the field's arrows to increment the existing values or the drop down list. All
fields must be completed before the plate definition can be saved and used.
Well Bottom Profile: Select the profile from the options available in the drop down list
Diameter at Top: The diameter at the top of the well
Depth:The distance from the bottom to the top of the well
Diameter at Bottom: The diameter at the bottom of the well
Recommended Minimum Volume: The recommended minimum fill volume for each
well when taking measurements
Recommended Maximum Volume: The recommended maximum fill volume for each
well when taking measurements
Actual Maximum Volume: The maximum fill volume for each well
The well geometry schematic updates to reflect the values entered into the fields.
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Invalid entries results in the offending field highlighted in red together with an explanation of
problem. Adjust the parameters until all entries are valid.
Note:All values are in millimetres and are displayed to two decimal places unless the plate
comprises 384 wells or more in which case the values are displayed to three decimal places .
Note: The well diameter field in the plate geometry section and diameter at top field in the well
geometry section correspond to the same physical parameter. This can result in invalid entries
in one section effecting entries in the other section.
6. Save the plate definition
To Create a New Plate Definition from an Existing Plate Definition

1. Open a plate definition from the database or file
2. Modify the fields as required
3. Save the plate definition
Note: The modified plate definition cannot have the same name, or be saved with the same
name, as an existing plate definition.
See also:
o Saving and opening plate definitions
o Removing plate definitions from the database
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Removing Plate Definitions from the Database
Unused plate definitions can be removed from the database.
To Remove a Plate Definition from the Database:

3. View a plate definition that has been saved to the database. If necessary, open a plate
definition from the database
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Note: If the plate definition cannot be removed from the database because a copy has not been
saved to the database, a warning dialog is displayed.
Note: If the plate definition cannot be removed from the database because it is used by a plate
layout that has been saved into the database, a warning dialog is displayed.
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Plate Layout Editor
Galapagos provides tools to create plate layouts comprising single or multiple physical plates. Wells
can be grouped together by well type and multiple groups can be assigned across a plate layout.
To launch the plate layout configuration tools:

2. Click on Plate Layout in the Configuration group
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3. The user interface shows the Layout Tools Display ribbon and on each plate layout tab the plate
layout Groups and Properties tabs together with the plate layout display
Each plate layout tab can display a single plate layout, whether newly created or opened from a
previously saved layout. Additional plate layout tabs can be created by repeating Steps 1 & 2
above.
Close a plate layout tab using the tab's button
Click on the user interface item below for additional details:

o Display Tab of the Layout context group
o Plate Layout Groups tab
o Plate Layout Properties tab
o Plate layout display
o Zoom Tool
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Display Tab of the Layout Context Group
The layout Tools Display ribbon provides access to the tools to create, open and save a plate
layout.
The Database and File groups enable plate layouts to be saved and previously saved layouts
opened
The Plates group enables the plate definition (the type of plate) to be selected and plates to be
added and removed to a plate layout
The Groups and Wells groups provides tools to organise wells into groups
Groups Tab
Click on the Groups tab to display the corresponding Groups pane. The Groups pane lists the
groups assigned to each plate on the plate layout and displays the name and description of
each.
To always show the pane, click on the pin symbol.
By default, groups are named 'Group n' where n is a number and for the first group created is 1
and which is incremented by 1 for each subsequent group created. Group names can be edited
but have to be unique. Each group can be given an optional description.
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Each group must be assigned one of the four well types. These are Sample (displayed in red),
Reference (displayed in green), Control (displayed in blue) and Standard (displayed in orange).
Clicking on a group in the Groups pane highlights the wells within the group in the plate layout
display.
Plate Properties Tab

Click on the Plate Properties tab to display the corresponding Plate Properties pane. The Plate
Layout Properties pane displays details of the plate layout, the selected group and selected well.
To always show the pane, click on the pin symbol. A horizontal splitter bar in between the
Layout and Selected Group sections and Selected Groups and Selected Well sections enables
the layout of the pane to be customised.
To expand the plate definition category, click on the symbol. The reduce the plate definition
category, click on the symbol.
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Note: The fields shown when the plate definition category is expanded do not include Diameter
at Top and Depth as these are equivalent to the fields Well Diameter and Height, respectively,
that are shown.
The Layout section displays properties of the plate layout.

o The name & description of the plate . By default the name is 'Plate Layout' and there
is no description. These fields can be edited by clicking in the Name and Description
edit fields. The name has to be unique and the same as the file name used to save
the plate layout.
o The plate definition field displays the physical parameters of the plate can be
expanded to show all plate parameters using the symbol and reduced to hide the
parameters using the symbol. The fields are read only and cannot be edited.
Note: If the plate layout is saved and the file name is not the same as the plate layout name,
Galapagos will automatically adjust the name to be the same as the file name.
The Selected Group section displays the properties of the group of currently selected wells.
o The name and description can be edited by clicking in the Name and Description edit
fields. The group name has to be unique.
o For each group, the well type has to be defined by selecting an option from the drop-
down list. The options are Sample, Reference, Control and Standard.
o The Seed is the prefix used to identify each well within the group. By default, the
seed takes the name of the Well Type. The seed can be edited by clicking in the Seed
edit field. The suffix is a number starting at 1 and incremented by 1 for each
additional well in the group.
o The number of wells in the group is reported. This field cannot be edited and is
therefore displayed in grey.
o The well locations of the group are reported using their coordinates in the main plate
layout display. The coordinates are reported row letter then column number. This field
cannot be edited and is therefore displayed in grey.
o The number of replicates is shown. By default, the number of replicates is set to a
value of 1. The value can be increased and decreased to an integer value between 1
and 10000, inclusive, by clicking on the arrows to adjust the current value or
typing directly into the edit field.
o The number of replicates can be set to equal the number of wells in a given group by
setting the field to be True. The default setting for all group types is True.
o The details of any constants applied to the group are shown. This field cannot be
edited and is therefore displayed in grey.
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The Selected Well section displays the properties of any selected well.
o By default, the name of the well is derived from the seed prefix defined in the
selected group section and it's relative location in the group. The name can be edited
by clicking in the Name edit field. The well name has to be unique.
o The well's identity is by default the same as its location. The identity can be edited by
clicking in the Identity edit field. The Identity has to be unique.
o The location is reported as its coordinate in the main plate layout display. The
coordinates are reported row letter then column number. This field cannot be edited
and is therefore displayed in grey.
o The details of any constants applied to the well are shown. This field cannot be edited
and is therefore displayed in grey.
Note: The Seed and Selected Well Name can be returned to default values by deleting the
custom entry.
Note: When replicates are set, replicates are organised first by row and then by column. For
example, a group comprising 8 wells in locations A1, A2, A3, B1, B2, B3, C1 and C2 with
replicates set to 4 has wells A1, A2, A3 and B1 as one replicate set and B2, B3, C1 and C2 as a
replicate set.
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Plate Layout Display
The plate layout display shows a representation of the plate, with each cell of the grid
representing a well.
Groups of wells are highlighted using a coloured border around the wells and each well of the
group has the group number at its centre. A contiguous set of wells belonging to a group have a
border around the perimeter of the set of wells only, i.e., not round each of the individual wells.
The group's well type determines the group's border colour. Samples are displayed in red,
references are displayed in green, controls are displayed in blue and standards are displayed in
orange. The selected group has a dashed border to distinguish it from any other groups.
Likewise, any wells that are selected are highlighted using a dashed grey border.
To select a well, click on a well. To select a group, click on one of the wells within the group. To
select a well that is part of a group, first select the group then click on the well of interest.
The plate layout display has a watermark to indicate which plate is being displayed. This uses
the nomenclature 'P n', where n is 1 for the first plate and is incremented by 1 for each
additional plate in the plate layout.
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Zoom Tool
To zoom in and out of the plate display, click on the symbol and symbol respectively.
Alternatively, click and drag the slider bar toward the symbol to zoom in
and toward the symbol to zoom out.
See Also:
o Saving and opening plate layouts
o Creating and modifying plate layouts
o Removing plate layouts from the database
Saving and Opening Plate Layouts

Galapagoscan save plate layouts to the database or to file. Previously saved plate layouts can be
opened for use or modification.
Saving a plate layout to the database
Saving a plate layout to file
Open a plate layout from the database
Open a plate layout from file
Removing a plate layout from the database
Saving a Plate Layout to the Database:

2. Click on the Setup tab and then on Plate Layout

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Note:The layout name and file name must be the same. If the plate layout is saved and the file
name is not the same as the plate layout name, Galapagoswill automatically adjust the name to
be the same as the file name.
Note: The layout name must be unique. If an attempt is made to save the layout with the same
name as an existing layout an error message is displayed.
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Note: When saving a plate layout to the database, the corresponding plate definition must have
previously been saved to the database or an identical plate definition must exist in the
database. If this is not the case, a prompt will allow the following options:
Select an existing plate definition from the database - clicking on this option will
prompt the selection of a plate definition from those existing in the database. The
options will be limited to those with the corresponding number of rows and columns.
Create a new plate definition from the details already assigned to the layout and save
to the database - clicking on this option will prompt for a plate definition name before
saving to the database.
Saving a Plate Layout to File:


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Note: Plate layout files are saved with the file extension .layout
Note: The layout name must be unique. If an attempt is made to save the layout with the
same file name as an existing layout an error message is displayed.
Open a Plate Layout from the Database:

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displayed.
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Open a Plate Layout from File:
Note: Plate layout files have the file extension .layout
Removing a Plate Layout from the Database:

1. Open the plate layout from the database
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3. Click on Yes
The plate layout entry is removed from the database
Note: If a plate layout is not stored in the database, a warning dialogue is displayed:
Creating and Modifying Plate Layouts

Plate layouts can be created and modified using the tools available.
o Selecting the plate definition
o Modifying the number of plates in a layout
o Viewing the plates in a layout
o Selecting wells
o Deleting a group from a layout
o Clearing all groups from a layout
o Adding a group to a layout
o Adding a group to the layout that overlaps an existing group
o Adding wells to an existing group
o Removing wells from an existing group
o Returning to the default plate layout
o Adding a constant to a well or group
o Editing a constant assigned to a well or group
o Deleting a constant assigned to a well or group
o Adding sample replicates to a group
o Editing sample replicates
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Selecting the Plate Definition:
The information contained in the plate definition determines the physical plate characteristics of
the plates in the plate layout. Click here for help on creating a plate definition.

2. Click on Plate Definition
2. Select whether to choose a plate definition stored in the database or on file
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3. Select the plate definition file from the database or file list
All plates in the plate layout will be of the type defined by the plate definition file.
4. The Properties tab will show the plate definition details in the Plate Definition entry in the
Layout section.
The entry can be expanded to show all plate parameters using the symbol and reduced to
hide the parameters using the symbol. The fields are read only and cannot be edited.
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Modifying the Number of Plates in a Layout:
1. Launch the plate editor configuration tools
By default, a plate layout is created comprising a single plate using a standard 96-well
definition plate with all wells assigned to a single group of sample wells called Group 1.
2. To increase the number of plates in a layout, click on No. of Plates
The group tab updates to show an entry for each plate with the groups assigned to each plate
detailed.
Note: If additional plates are added to the default layout, then the new plates will be created
comprising the same layout. If additional plates are added to a non-default layout, then the
new plates will be created with all wells assigned to a new group of samples wells.
Note: Wells from different plates can be assigned to belong to the same group.
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4. To reduce the number of plates in a layout, click on No. of Plates
6. Click Yes to proceed
Note: When reducing the number of plates in a layout, the most recently added plate is
removed.
Note: Groups that only appear on a plate which has been removed are deleted from the layout
all together.
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Viewing the Plates in a Layout:
1. Select the plate to view by clicking on the plate name in the Groups tab
Select the group of interest by clicking on the corresponding group name from those listed in
the Group tab
Selecting Wells:
1. To select a single well, click on the well of interest
The well is highlighted with a grey dashed border.
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2. To select multiple wells, use one of the following methods:
Multiple individual well selection: Click on each well whilst pressing and holding the
keyboard Control key
Area selection: Click on a well and drag to create a rectangular selection of wells
Row selection: Click on a row letter to select the entire row
Column selection: Click on a column number to select the entire column
Select all wells: Click on the box to the left of Column 1 and above Row A
The keyboard Control key enables well selection methods to be combined. With a well or
set of wells selected, press and hold the keyboard Control key before selecting the next
set of wells. Any combination of the above selection methods is permitted.
The selected wells are highlighted with a grey dashed border.
Note: Multiple well selection is confined to wells from the same plate. To configure a group to
comprise wells from more than one plate, see Adding Wells to Existing Groups.
Note: Wells on plates that have been assigned as masked wells during the plate's definition
cannot be selected. These masked wells are labelled N/A.
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Deleting a Group from a Layout:
1. Select the group by selecting a well within the group of interest
2. Click Delete Groups
3. Click on Yes
Note: If default group naming is used, when a group is removed from the layout, the groups
using default naming are renumbered so the first of the remaining groups to be added to the
layout is called 'Group '1, the next 'Group 2' and so on.
Clearing All Groups from a Layout:

1. Click on Clear Groups
2. Click on Yes
Note: The Clear Groups command removes all groups from all plates of the layout.
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Adding a Group to a Layout:
1. Select a well or set of wells
Note: To add a group which has wells on more than one plate, first add a group on
one plate and then add wells from other plates to the group. See topic below entitled
'Adding Wells to Existing Groups'.
2. Click Add Group
Name: By default, groups are named 'Group n' where n is a number and for the first group
created is 1 and which is incremented by 1 for each subsequent group created. Group names
can be edited by clicking in the name edit field but have to be unique
Description: By default, no description is provided. Click in the description edit field to enter a
description
Well Type: Each group must be assigned one of the four well types from the drop down list. By
default this is set to the Sample option
The border used to highlight the group is coloured according to the well type selected. The
colours are:
Sample: red
Reference: green
Control: blue
Standard: orange
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Wells: A list of the well positions comprising the group. Positions are reported as well
coordinate in the main plate layout display. The coordinates have the format row letter then
column number. The field can be edited to add or remove wells to the group. Contiguous
rectangular groups of wells are defined using a colon written in between the coordinate
positions of the top left and bottom right corners of the rectangle. Contiguous groups are
separated using a comma.
To update the group's well assignment, click on button. This will update the plate layout
display to reflect the revised assignment.
Adding a Group to a Layout that Overlaps an Existing Group:

1. Select a well or set of wells that has complete or partial overlap with an existing group
2. Click Add Group
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4. Select the appropriate option from Overlapping Group dialog
Adding Wells to Existing Groups:

1. Select an existing group
2. If necessary, display the appropriate plate by clicking on the plate name in the Groups tab,
press and hold the keyboard Control key and select a well or set of wells
3. Click Add To Group
4. Select the group from the displayed list
Note: This operation can be performed on plate layouts which comprise multiple plates.
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Removing Wells From Existing Groups:
1. Select a well or set of wells from within an existing group
2. Click Remove From Group
Note: To remove wells from a group that comprises wells from more than one plate, remove
the necessary wells from each plate separately.
Returning to the Default Plate Layout:

1. If a plate layout is displayed, click on New Layout
2. If the existing plate layout has not been saved, a prompt will be displayed warning of possible
data loss. Click Yes to continue.
The default plate layout is displayed.
Adding a Constant to a Well or Group:

1. Select the well or group to which a constant is to be added
Note: A constant can only be added a an individual well if the well is part of a group.
2. Click on Add Constant
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3. Choose whether to add to the group or well using the selection list
4. Enter the name of the constant and, optionally a description, in the Name and Description edit
fields of the Add Constant dialogue
5. Select the type of constant to assign by selecting either Static or Prompted from the Type drop
down list
Note: A static constant always has the same value. The value of a prompted constant is
requested before it is used in a data manipulation.
If a Static constant has been selected, enter the value to be used in the Value edit field
Click OK
Editing a Constant Assigned to a Well or Group:

1. Click on Edit Constant
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2. Select the constant to edit from the list displayed and click on OK
3. Edit the required fields as required and click OK
Deleting a Constant Assigned to a Well or Group:

1. Click on Delete Constant
2. Select the constant to delete from the list displayed and click on OK
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Adding Sample Replicates:
Sample replicates can be added to any group.
Editing Sample Replicates:

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Removing Plate Layouts from the Database
Unused plate layouts can be removed from the database.
To Remove a Plate Layout from the Database:

3. View a plate layout that has been saved to the database. If necessary, open a plate layout from
the database
Note: If the plate layout cannot be removed from the database because a copy has not been
saved to the database, a warning dialog is displayed.
Note: If the plate layout cannot be removed from the database because it is has been used
when taking a measurement, a warning dialog is displayed.
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Graphical Data Display and Manipulation
Galapagos provides a range of tools to display and manipulate measurement data.
Results data can be manipulated during the data acquisition process or manipulations can be applied
retrospectively to previously saved data sets. For more information on how to setup manipulations,
select the an item from the list below:
o Applying manipulations to execute during the measurement process
o Applying manipulations to previously saved results data
o Performing a Quantitative Analysis
Select an item from the list below for further information on the presentation of measurement and
manipulation results:
o Detailed Well View
Detailed Well View

Detailed information pertaining to the measurement data collected for each well can be displayed for
further evaluation.
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To Show the Detailed Well View:
1. Either Acquire data or Open previously saved results data
2. Either double-click on the well of interest or select the well of interest and press the Enter key
on the keyboard
Note: Wells can be selected using the mouse and a single-click or by using the keyboard arrow
keys.
Well selection, results data (both measured and manipulated) and graphical data are shown
where relevant.
The layout of the view can be modified by dragging the vertical splitter located between the
results data and chart display sections. The cursor is located above the splitter when it is
displayed as an arrow.
Note: When displaying data comprising two or more cycles, the time stamp of the data in the
Results Data section is quoted as the time the data was acquired and is stated as HH:MM:SS
(hour of the day : minute of the hour : second of the minute).
3. To exit the detailed well view and return to the main results display, either press the keyboard
Escape button, keyboard Enter button or click on the .
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Applying Data Manipulations to Execute During the
Measurement Process
Galapagos provides tools to include data manipulation routines in the measurement process.
Equations that are specified are executed after the data has been acquired and the corresponding
results are displayed.
To Apply Manipulations:
1. Configure a Quick Measurement but do not start the measurement_Ref-1999240534
2. Click on the Manipulate tab
3. Define, save, edit and remove equation(s) to apply to the raw measurement data or the results
of previously manipulated data
4. Click on the Acquire tab from the Method Tools context group and click Start
The data window updates to show the measurement results. Each well can display a maximum
of three values and can be a combination of raw and manipulated data. Well data displayed in
bold corresponds to manipulated data, i.e. calculated values.
Where there is more than three data values (measured and manipulated data) for a well, only
the results of the data manipulations are displayed with the outcome of any screening equations
taking president over the results of other manipulation types. If there are more than three
manipulation results, only the last three of the sequence are displayed. Both raw and processed
data values can be displayed in the data view pane by selecting a well of interest. Double-
clicking on a well of interest displays the Detailed Well View which shows both raw and
manipulated results data.
Note: There is no limit to the number of manipulations that can be applied to the results
data.
Note: The Method Properties pane displays the details of any specified equations.
Note: The manipulations and the results of manipulations are stored together with the raw
measurement data and other properties when the file is saved.
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Applying Data Manipulations to Previously Saved
Measurement Data
Galapagos provides tools to perform data manipulation routines to previously saved results data.
Equations that are specified are executed and the corresponding results are displayed.
To Apply Manipulations:
1. Open a previously saved results file
2. Define, save, edit and remove equation(s) to apply to the raw measurement data or the results
of previously manipulated data
3. Click on Perform Manipulation
The data window updates to show the measurement results. Each well can display a maximum
of three values and can be a combination of raw and manipulated data. Well data displayed in
bold corresponds to manipulated data, i.e. calculated values.
Where there is more than three data values (measured and manipulated data) for a well, only
the results of the data manipulations are displayed with the outcome of any screening equations
taking president over the results of other manipulation types. If there are more than three
manipulation results, only the last three of the sequence are displayed. Both raw and processed
data values can be displayed in the data view pane by selecting a well of interest. Double-
clicking on a well of interest displays the Detailed Well View which shows both raw and
manipulated results data.
Note: There is no limit to the number of manipulations that can be applied to the results
dataa.
Note: The Method Properties pane displays the details of any specified equations.
Note: The manipulations and the results of manipulations are stored together with the raw
measurement data and other properties when the file is saved.
Setting Equations
Manipulations are configured in Galapagos by defining equations that are applied to the measured
results data or to previously manipulated data sets. Manipulations can be applied to individual wells or
groups of wells.
o Available mathematical operations
o Applying a new equation
o Discarding an equation
o Editing an existing equation
o Removing an existing equation
o Removing all existing equations
o Changing the order of equations
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Available Mathematical Operators:
Galapagos supports the following operators:
Arithmetic:
o Addition
o Subtraction
o Multiplication
o Division
Note: These operators require two inputs to be specified.
Functions:
o Power
o Natural log
o Log base 10
o ex
o 10x
Note: The power operator requires two inputs to be specified. The others within this category
only require a single operator to be specified.
Concentration:
o Concentration (note: Concentration = [Absorbance] x [Concentration Factor] x [Dilution Ratio]
x [Weight Correction])
Note: Concentration requires four inputs to be specified. Dilution Factor and Weight Correction
are defined as follows:
Dilution Factor = Aliquot Volume / (Aliquot Volume + Diluent Volume)
Weight Correction = Sample Weight / Nominal Weight
o Quantitative Analysis (note: Concentration = [QA (Absorbance)] x [Dilution Ratio] x [Weight

Correction])
Note: For information on how to setup a quantitative analysis see Introduction to Quantitative
Analysis.
Note: The Quantitative Analysis operator is only available when the method includes a plate
layout with at least 2 standards present.
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Statistics:
o Population size (equal to the number of wells in each replicate set)
o Mean (the sum of well values divided by the number of wells in the replicate set)
o Standard deviation (the square root of the sample variance)
o Variance (the sum of the squares of the difference from the mean divided by the number of
wells in the replicate set)
o Sample variance (the sum of the squares of the difference from the mean divided by the
number of wells in the replicate set minus one)
o Coefficient of variation (the standard deviation divided by the mean)
o Coefficient of variation % (100 times the coefficient of variation)
o Standard error of mean (the standard deviation divided by the square root of the number of
wells in the replicate set)
o Range (the difference between the maximum and minimum values within the set of replicates)
o Minimum (the smallest value in the replicate set)
o Maximum (the largest value in the replicate set)
o Deviation (the deviation of the value in the well from the mean value for the set of replicates)
o Deviation % (the difference between the value and the mean is divided by the mean and then
multiplied by 100)
o Lower quartile (the value 25% of the way through the list when all values are ordered from
lowest to highest)
o Median (the middle value when all values are ordered from lowest to highest)
o Upper quartile (the value 75% of the way through the list when all values are ordered from
lowest to highest)
Note: The statistical group of operators are applicable to replicates only. They require a single
input to be specified.
Comparison:
o Greater than: >
o Greater or equal to: >=
o Less than: <
o Less than or equal to: <=
These manipulations can be used to determine the Results Validity.
Note: These operators require two operators to be specified.
Screening:
o Screen
This operator is used to partition wells into different categories according to their value.
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Loops:
o Remove Outliers
This operator is used to remove erroneous well results - outliers - from manipulations that affect the
Results Validity. Following removal of an outlier, the manipulations are recalculated using the
remaining wells. Outliers continue to be removed until either the Results Validity changes from Invalid
to Valid or the maximum number of specified outliers has been removed.
The criteria for selecting which well value to remove is the well value which is furthest from the mean
value. The maximum number of outliers that can be removed is configurable. Note that the Remove
Outlier operator must refer to a group for which the number of replicates and wells are equal.
Note: the Comparison manipulation types can be used to determine Results Validity.
To Apply a New Equation:

Galapagos supports a range of different data manipulations. For information on how to setup
equations, select the operator type of interest from the list below:
o Arithmetic
o Functions
o Concentration
o Statistics
o Comparison
o Screening
o Loops
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Arithmetic:
1. From the Manipulate tab of the Method Tools context group, click on New Equation
2. From the list displayed, select an Arithmetic manipulation type
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3. Using the equation editor that appears in the Equation group, select the inputs for the
equation by clicking on the arrows in the operand edit fields and selecting the
appropriate item from the prompted lists
4. For the first input to the equation, select either All, Group or Well from the displayed
list
If All was selected, click on the arrow displayed after the previous selection and
select the appropriate measurement wavelength and proceed to Step 5.
If Group or Well was selected, click on the arrow displayed after the previous
selection and either select the appropriate group or well from the displayed list of
options. The groups are referred to by their given group name. Only wells that are
part of a group can be selected
or
Click on the arrow displayed after the previous selection and either select the
appropriate measurement wavelength or result from an existing manipulation (if a
manipulation has been previously configured)
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5. For the second input to the equation, select either All, Group, Well or Fixed from
the displayed list
If fixed has been selected, enter the required value into the edit field or use the
arrows to increment the existing value by a unit of 1 and proceed to Step 6
If group or well has been selected, click on the arrow displayed after the previous
or
appropriate measurement wavelength. or if acting on a group a result from an
existing manipulation (if a manipulation has been previously configured) or a constant
that has been assigned to a well or group
Note: The number of different measurement wavelengths available for selection is

determined by the selected measurement mode.
Note: Constants are assigned to wells or groups through the plate layout tools.
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6. Enter a name for the equation in the edit field next to the equals symbol
This is not a mandatory entry. The default name will be applied if a custom name is
not specified. The equation name is used to reference the equation in the Method
Properties window and when selecting to remove or edit an equation
7. Click on Save Equation
A validation error dialogue is displayed if the defined equation contains errors that
prevent it from executing on the data. The equation is not saved and requires
correction before saving can be attempted again
8. Additional equations can be defined and set
Note: There is no limit to the number of manipulations that can be applied to the
results data.
Note: Equations run sequentially in the order they are specified.
Functions:
2. From the list displayed, select a Functions manipulation type
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appropriate item from the prompted lists. The Power operator requires two inputs to
be defined. The other operators in this category only require a single input specified.
list
or
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appropriate measurement wavelength or result from an existing manipulation (if a
5. To define the second input for the power operator, select either All, Group, Wellor
Fixed from the displayed list
If Fixed has been selected, enter the required value into the edit field or use the
or
appropriate measurement wavelength or if acting on a group a result from an existing
manipulation (if a manipulation has been previously configured) or a constant that
has been assigned to a well or group
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Properties window and when selecting to remove or edit an equation.
correction before saving can be attempted again.
results data.
Concentration:
Concentration:
2. From the list displayed, select the Concentration manipulation type
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appropriate item from the prompted lists.
4. For the first (absorbance) input to the equation, select either All, Group or Well from
the displayed list
or
manipulation (if a manipulation has been previously configured)
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5. For each of the second (concentration factor), third (dilution ratio) and fourth (weight
correction) inputs to the equation, select either Group, Well or Fixed from the
displayed list
If group or well was selected, click on the arrow displayed after the previous
or
Click on the arrow displayed after the previous selection and select the appropriate
constant that has been assigned to a well or group.

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results data.
Quantitative Analysis:
2. From the list displayed, select the Quantitative Analysis manipulation type
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Note: The Quantitative Analysis option is only available if a QA object has been added to
the Quick Measurement method. For setup information see Introduction to Quantitative
Analysis
4. For the first (absorbance) input to the equation, select either All, Group or Well from
the displayed list
or
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manipulation (if a manipulation has been previously configured). The selection has to
match the input used for the QA object specified in the next step.
Note: Only manipulations that are applicable to all wells (use the 'All' option in the
equation editor) can be referenced in the equation.
5. For the second (Quantitative Analysis) input select the QA object to use. Select QA
and then the choose the QA object from the list displayed
6. For both the third (dilution ratio) and fourth (weight correction) inputs to the
equation, select either Group or Fixed from the displayed list
If group has been selected, click on the arrow displayed after the previous selection
and select the appropriate group from the displayed list of options. The groups are
referred to by their given group name.
Click on the arrow displayed after the previous selection and select the appropriate
standard concentration that has been assigned to the group.
Note: Standard concentrations are assigned to Standard groups through the plate
layout tools or the QA object tools.
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results data.
Statistics:
Replicates are set through the Plate Properties tab.
2. From the list displayed, select a Statistics manipulation type
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3. Using the equation editor that appears in the Equation group, select the input for the
4. For the input to the equation, select All or Group from the displayed list
Note: When using the All option, the number of replicates is taken to be one and
the calculations are based on all the wells that are part of a group.
If Group was selected, click on the arrow displayed after the previous selection and
select the appropriate group. The groups are referred to by their given group name.
Click on the arrow displayed after the group name and either select the appropriate
measurement wavelength, a result from an existing manipulation (if a manipulation
has been previously configured) or constant that has been assigned to a group

Note: Constants are assigned to groups through the plate layout tools.
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results data.
Note: The result of all statistical equations with the exception of deviation can be
used in other manipulations and applied to wells and groups of any type and size.
For this to be allowed, the number of replicates must be equal to the number of
wells in the group from which the statistics are calculated.
Note: The result of a manipulation involving the outcome of any statistical
equation (with the exception of deviation) and a fixed value can be used in other
manipulations and applied to wells and groups of any type and size. For this to be
allowed, the number of replicates must be equal to the number of wells in the
group from which the statistics are calculated. An example would be to obtain the
mean value from a group of wells, add a fixed value to this mean and the divide
the value of the wells in another group by this value.
Note: When the number of replicates is set to one, all wells in the group are
included in the calculation.
Note: The number of replicates can be set to be equal the number of wells in a
group through the Plate Properties tab.
Comparison:
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2. From the list displayed, select a Comparison manipulation type
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list
or
appropriate measurement wavelength or if acting on a group, a result from an
existing manipulation (if a manipulation has been previously configured)
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5. For the second input, select either All, Group, Well or Fixed from the displayed list
select the appropriate measurement wavelength and proceed to Step 6
If fixed was selected, enter the required value into the edit field or use the arrows
to increment the existing value by a unit of 1 and proceed to Step 6
If group or well was selected, click on the arrow displayed after the previous
or
appropriate measurement wavelength, constant assigned to a group or well, or, if
acting on a group, a result from an existing manipulation (if a manipulation has been
previously configured)

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6. Optionally, enter an alternative label name for both the True and False fields. The
label name will be displayed in the appropriate wells when the results are displayed
for the true and false outcomes of the comparison. By default True and False are
displayed for the true and false fields respectively.
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7. Select whether the outcome of the comparison is to effect the result validity by
clicking on the result validly drop down menu
For the outcome of the comparison not to effect the results validity, select 'No effect
on result validity'
For the outcome of the comparison to effect the results validity and the results to be
invalid if the outcome of the comparison is True, select 'Results invalid if true'
For the outcome of the comparison to effect the results validity and the results to be
invalid if the outcome of the comparison is False, select 'Results invalid if false'
Note: The result validity is displayed in the Results section of the Method
Properties pane
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results data.
Screen:
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2. From the list displayed, select the Screen manipulation type
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4. For the input to the equation, select either All, Group or Well from the displayed list
or
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appropriate measurement wavelength or if acting on a group, a result from an
existing manipulation (if a manipulation has been previously configured)

5. Click on Set Categories
Input the required number of categories into the Categories edit field by either typing
the required number into the edit field or using the arrows to increment the
existing value.
Note: The number of categories has to be between 2 and 10, inclusive.

Note: The data span for each category is from the lower threshold level to below
the upper threshold level.
Define the data range limits for each of the categories by clicking on the arrow and
selecting either All, Group, Well or Fixed from the displayed list for each of the
required threshold levels.
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select the appropriate measurement wavelength
arrows to increment the existing value by a unit of 1
If Group or Well has been selected, click on the arrow displayed after the previous
or
appropriate measurement wavelength, a constant that has been assigned to a well or
a group or if acting on a group, a result from an existing manipulation (if a
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Enter a name for each category. The category below the first level also requires a
name. Alternatively, use the default category name of 'Cat. N', where N is a number
starting at 1 and incrementing by 1 for each required category.
Click OK
Note: Values entered for the level threshold values must not be equal and be in
ascending order. A warning dialogue is displayed if the level thresholds are not in
ascending order.
Note: For a group to be used to define a category's limits, it must represent a

single value. An instance where this arises is where a group comprises a single
well.
results data.
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Remove Outliers
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2. From the list displayed, select the Remove Outliers type
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equation by clicking on the arrows in the operand edit field and selecting the
4. For the input to the equation, select either Allor Group from the displayed list
If Group was selected, click on the arrow displayed after the previous selection and
either select the appropriate group from the displayed list of options. The groups are
referred to by their given group name.
appropriate measurement wavelength or a result from an existing manipulation (if a

5. Enter the number of proceeding equations that need recalculating after the outlier has
been removed
Note: Where more than one remove outlier equation is included in a sequence of
equations, the equation count for a given remove outlier equation cannot be set to
include another remove outlier equation.
6. Enter the maximum number of outliers that can be removed
Note: The minimum number of outliers will be removed to produce a valid results
validity. If this has not been achieved the maximum number of outliers has been
removed the routine will complete the results validity will remain invalid.
Note: After the remove outliers equation has completed, the wells that have been
removed are indicated with the label 'Excluded'.
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9. Additional Remove Outlier equations and other equations can be defined and set
results data.
To Discard an Equation:
1. To cancel either the process of defining a new equation or editing an existing equation, click on
Discard Equation from the Manipulate tab of the Method Tools context group
Note: The equation being edited is not removed from the saved list of equations.
Edit an Existing Equation:

1. Click on Edit Equation from the Manipulate tab of the Method Tools context group
2. Select the equation to edit from the list displayed
3. Edit the equation as required using the equation editor in the Equations group of the ribbon
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The equation is updated
Note: The equation used to calculate the difference between the measurement and reference
values in dual wavelength mode cannot be edited.
To Remove an Existing Equation:

1. Click on Remove Equation from the Manipulate tab of the Method Tools context group
2. Select the equation to be removed from the list displayed
3. Click Yes
The equation is removed and is no longer part of the method
values in dual wavelength mode cannot be removed.
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To Remove all Existing Equations:
1. Click on Remove All Equations from the Manipulate tab of the Method Tools context group
2. Click Yes
All equations are removed and are no longer part of the method
values in dual wavelength mode cannot be removed.
To Change the Order of Equations:

Equations are run sequentially in the order they are displayed.
1. Click on the Equations group dialogue launcher
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2. Select an equation and either click on Move Up or Move Down to change the position of the
equation is the sequence
3. To remove an equation, select the equation and click on Remove Equation
4. Click OK
Introduction to Quantitative Analysis

Quantitative analysis makes it possible to determine the concentration of samples using concentration
standard curves that have been created by measuring the absorbance of standards of known
concentration.
The Quantitative Analysis tools group is part of the Manipulate tab of the Method Tools ribbon.
These tools enable quantitative analysis objects to be created, edited and the standard curve viewed.
Previously configured quantitative analysis objects can also be imported and validated. Quantitative
analysis objects comprise the details of which standards to analyse and how to analyse the standards
to create the standard curve. These are plots of concentration against measured absorbance.
Once a quantitative analysis object has been setup it can be used to calculate the concentration of
samples. This is performed by adding a manipulation that uses the Quantitative Analysis equation.
There are two parts to performing a quantitative analysis. These are:
1. Creating a Quick Measurement method that incorporates Quantitative Analysis
2. Performing a Quantitative Analysis to measure the concentration of samples
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Creating a Quick Measurement Method Incorporating
a Quantitative Analysis
Before a Quantitative Analysis can be performed on samples to determine their concentration, a Quick
Measurement method incorporating a Quantitative Analysis (QA) needs to be created.
To create a Quick Measurement method incorporating a QA, complete the following:
1. Open a new Quick Measurement and define a plate layout that includes standards
2. Add and configure QA objects
3. Add a manipulation using the Quantitative Analysis equation
4. Save the method template
To Open a New Quick Measurement and Define a Plate Layout Incorporating Standards:
1. Click on the Methods tab and on Quick Measurement
2. Click on the Manipulate tab and click on Change Plate Layout
3. Either Open from database or from file a previously saved plate layout that includes standard
groups
Or,
Create a plate layout that includes standard groups
Note: A plate layout does not require standard groups if the quantitative analysis uses an
imported QA object See Importing QA Objects for more information.
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4. For each standard group, select the group and set the number of replicates using the Plate
Properties pane
Note: The number of standards defined by a standards group is given by the number of wells
divided by the number of replicates. By default, groups comprising standards are set to have
the number of replicates equal to the number of wells. Setup in this way, a standard group
comprises one standard for the purposes of the QA. Alternatively, by setting the number of
replicates to less than the number of wells within a group, the number of standards in the
group can be greater than one and up to a value equal to the number of wells in the group.
The minimum number of standards required to perform a quantitative analysis is determined by
the interpolation or fitting function specified when configuring a QA object. Some functions
require a minimum of two standards, others a minimum of six standards.
Note: When replicates are set, replicates are organised first by row and then by column. For
example, a group comprising 8 wells in locations A1, A2, A3, B1, B2, B3, C1 and C2 with
replicates set to 4 has wells A1, A2, A3 and B1 as one replicate set and B2, B3, C1 and C2 as a
replicate set.
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5. For each standards group, select the group and click on Edit Constants
From the displayed list, double-click on each standard in turn and enter the corresponding
name, description and concentration value and click OK
The concentration values must be different for each standard
Note: Standard concentration constants do not appear in Delete Constants list.

Note: Standard concentration constants are automatically added and removed according to the
replicate statistics for each of the groups comprising standards.
6. Click on Accept Layout
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To Add and Configure QA Objects:
New QA objects can be added or previously configured QA objects can be imported. To add and
configure a new QA object to the method, follow the steps below. To import a previously configured
QA object see Importing a QA Object.
1. Click on the Acquire tab and select the measurement mode and wavelength
Note: The measurement mode and wavelength(s) must be compatible with the input to the QA
object(s) defined in Step 3 below.
2. Click on the Manipulate tab and click on Add Analysis
3. Configure the QA Object by editing each of the fields and click OK
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Name: Each QA object has to have a unique name. The name is used to reference the object
in Quantitative Analysis equations
Description: Enter a description. This field is not mandatory
Input: The input is used to build the standard curve. Select the required input from the drop
down list, the contents of which is determined by the measurement mode and wavelength set
in Step 1 and any manipulations added. Valid inputs can be an absorbance measurement or the
result of a manipulation.
Note: Only manipulations that are applicable to all wells (use the 'All' option in the equation
editor) can be used as an input.
Groups: Lists the standards groups that are used by the QA object. By default, all standard
groups are included. To modify which standard groups are used and the order of the groups:
Click Edit
Uncheck the standard groups that are not required

Select the standard group to move higher up the order or lower down the order and click
on Move Up or Move Down.
Click Finished
Note: The standard groups must be listed in ascending order of concentration. If

groups are not correctly ordered, the Invalid Settings dialogue is displayed
Standards: Lists the details of the standards that have been defined. The Concentration field
for each standard can be used to edit the concentration value.
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Units: Enter the units used for the concentration values of the standards. This is used to label
the x-axis of the standards curve.
Function: Sets the interpolation or fitting function to use to create the standard curve. Select
the required option from the drop down list. The options and number of minimum standards
required for their use are:
o Linear Interpolation: Minimum of 2 standards
o Cubic Spline Interpolation: Minimum of 4 standards
o Akima Spline Interpolation: Minimum of 4 standards
o Linear Fitting: Minimum of 2 standards
o Polynomial Fitting: Minimum of 3 standards
o 4 Parameter S Fitting: Minimum of 5 standards
o 5 Parameter S Fitting: Minimum of 6 standards
Other Function related options are:

Include Origin: Sets whether the origin (0, 0) is to be included when generating the
standards curve. This option is not available for either of the S fitting functions.
Check the checkbox to enable.
Extrapolated Range: Sets how far the standard curve is to be extended outside the range
of the standard concentrations. This option is only available for fitting functions. The
range is defined as a percentage of the concentration range and is applied to both the
low and high end of the standard curve.
Polynomial Order: Set the order of the polynomial. The value can be between 2 and 10
inclusive.
4. Click Add Analysis to add and define an additional QA object if required
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5. Click Edit Analysis or click on the Quantitative Analysis group dialogue launcher to edit the
QA object.
If more than one QA objects have been added, the QA Object selection dialogue is displayed.
Select the QA object of interest and click Edit to modify the QA object or Delete to delete the
QA object.
To delete all listed QA objects, click on Clear
Click Close
6. Click on the Acquire tab, confirm the acquisition parameters and click on Start
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7. Click on the Manipulate tab and click on View Analysis to view the standard curve and
related details
Note: The plate display reports the measurement results, but no sample concentrations since
the manipulation using the Quantitative Analysis equation has not yet been set.
The upper pane shows the concentration - absorbance plot, the data points for each of the
standards and the corresponding standard curve.
The two tabular panes display the standard measurements & statistics and coefficient &
goodness of fit parameters. If all standards have a single replicate, the statistics columns are
not shown. The coefficient and goodness of fit parameters are not shown if the function selected
in the QA object is an interpolation.
If more than one QA object has been added, click on the Quantitative Analysis drop-down list to
select which QA object to display.
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To resize the area used to display each of the panes, move the mouse over the horizontal
and vertical splitters and drag to the required position.
o To view the analysis of a different QA object (if more than one QA object has been
added):
o To change the x-axis type, click on the X-Axis Type drop down list and select either
Linear or Log:
o To change which statistics are displayed, click on Columns
Select the statistic type to display by checking the appropriate tick box. To select all
types, check the Column tick box.
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The statistics are:
o Mean: The sum of values divided by the number of values
o StdDev (Standard Deviation): The square root of the sample variance
o CV (Coefficient of Variation): The standard deviation divided by the mean
o SEM (Standard Error of Mean): The standard deviation divided by the square root
of the number of values
o Deviation: The deviation of the value from the mean value
o Range: The difference between the maximum and minimum values
o Minimum: The smallest value
o Maximum: The largest value
o Median: The middle value when all values are ordered from lowest to highest
o To change the standards and replicates that are included in the calculation of the
standard curve, select the required standards and replicates by checking the appropriate
tick boxes.
The standard curve updates to show only the standards that are included in the
calculation and the new line of best fit.
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Note: the Method Properties updates to show the details of the QA object
To Add a Manipulation using the QA Equation:

To add and configure a manipulation using the QA equation view the Quantitative Analysis section of
the Setting Equations page
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To Save the Method Template:
A quantitative analysis can be run without first saving the method template to file. To run a
quantitative analysis see Running a Quantitative Analysis.
1. Click on File and Save As
2. Click on either Save Method Template to Database or Save Method Template to File:
3. Enter a filename and click on OK or Save
See also:
o Running a Quick Measurement method incorporating Quantitative Analysis
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Importing QA Objects
Previously configured QA objects can be imported into Quick Measurement methods. The standard
curve can be validated by acquiring and applying new measurement data.
For details of how to setup a Quick Measurement method incorporating quantitative analysis see
Creating a Quick Measurement Method Incorporating Quantitative Analysis.
o Importing a QA object into a Quick Measurement method
o Validating the standards curve of an imported QA object
To Import a QA Object:
1. Click on the Method tab and click on Quick Measurement
2. Click on the Manipulate tab and click on Import Analysis
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3. Click on From Database or From File
If importing from the database, select the Quick Measurement results file or methods template
file and which quantitative analysis object to import and click on Import
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If importing from file, click on Browse, select a Quick Measurement or method template and
click Open.
Select the quantitative analysis object to import and click Import
4. Click on View Analysis to view the standard curve and related details
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added):
Linear or Log:
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tick boxes.
Note: Imported QA objects cannot be edited.

Note: Imported QA objects can be removed from a method by clicking on the Quantitative
Analysis ribbon dialogue launcher , selecting the QA object and clicking on Delete
5. To Validate the imported QA object see To Validate a QA Object

6. To setup a Quick Measurement method incorporating quantitative analysis, define a plate
layout, add a manipulation using the QA equation and save the method template.
Note: When using an imported QA object, the plate layout does not have to include any
standard groups.
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To Validate a QA Object:
Galapagos allows the standard curve of imported QA objects to be validated again new measurement
data.
1. Import a QA object
3. Either Open from database or from file a previously saved plate layout that includes standard
group(s)
Or,
Create a plate layout that includes standard group(s) and click on Accept Layout
Note: All standard groups must have the number of replicates equal to the number of wells.
4. Click on the Acquire tab and set the acquisition parameters to be compatible with the imported
QA object and click Start
Note: The measured data has to include the input to the QA object
5. Click on Validate Analysis
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6. Select the required standard from the Standard drop down list. If the concentration values have
not been entered for each standard when setting the plate layout in Step 3, enter the
concentration value of the selected standard.
The data for the standard is plotted on the standard curve and shown using a blue triangle.
The Measurement Offset is the y-axis offset from the new data point to the existing standard
curve
The Concentration Offset is the x-axis offset from the new data point to the existing
standard curve
The Calibration Offset is the same as the Measurement Offset
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7. Click Accept to use the validated standard curve or to continue without validating the standard
curve click Reject
Note: The Method Properties pane updates to show in the Quantitative Analysis section the
validated QA object's settings
8. To setup a Quick Measurement method incorporating quantitative analysis, define a plate

layout, add a manipulation using the QA equation and save the method template.
Note: When using an imported QA object, the plate layout does not have to include any
standard groups.
See Also:
o Creating a Quick Method Incorporating Quantitative Analysis
o Running a Quick Measurement method incorporating Quantitative Analysis
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Running a Quick Measurement Method Incorporating
Quantitative Analysis
To Run a Quick Measurement Method Incorporating a QA:

1. Either create Quick Measurement method incorporating a QA
or,
to open a previous saved method template:
Click on the File tab and click on Open
Click on Open Method Template from Database or Open Method Template from File
Select the required method template

3. Click on the Acquire tab, confirm the acquisition settings and click on Start
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4. The plate display updates to show the results
The concentration results for the QA manipulation are shown in bold for the sample group (the
two groups highlighted with a yellow border are standards groups).
The input values into the QA object for wells marked U/R and O/R are out of the range of the
standard curve. Concentration data cannot be calculated for these wells and they are labelled
under-range (U/R) and over-range (O/R) respectively.
6. Click in a well of interest to see well details in the Data pane
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7. Double-click in a well to see the Detailed Well View
Exit the detailed well view and return to the main results display by either pressing the
keyboard Escape button, keyboard Enter button or clicking on the .
8. Click on the Manipulate tab and click on View Analysis
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added):
Linear or Log:
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The statistics are:
o Mean: The sum of values divided by the number of values
o StdDev (Standard Deviation): The square root of the sample variance
o CV (Coefficient of Variation): The standard deviation divided by the mean
o SEM (Standard Error of Mean): The standard deviation divided by the square root
of the number of values
o Deviation: The deviation of the value from the mean value
o Range: The difference between the maximum and minimum values
o Minimum: The smallest value
o Maximum: The largest value
o Median: The middle value when all values are ordered from lowest to highest
tick boxes.
9. Click on View Results to return to the plate display
10. Save the results if required
Note: The method is also saved with the results data.
See also:
o Creating a Quick Measurement Method Incorporating Quantitative Analysis
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Reporting
Galapagos provides functionality to create custom report templates from which reports can be
produced. The reporting capability of Galapagos has two parts:
1. Designing reports - creating report templates
2. Producing reports - combining measurement, manipulated and instrument data with report
templates to create reports
Help on each of these is accessed by clicking on the links above.
Report Writer
The report writer provides an integrated collection of tools to create and configure report templates
from which reports can be produced when combined with measurement, manipulated and instrument
data.
o Launching the report writer
o The components of the Report Designer tab
o Creating and editing a report template
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To Launch the Report Writer:
2. Click on Report Writer
The Report Designer tab is opened.
Report Designer Tab:

The Report Designer tab comprises the following components:
o Report Designer ribbon
o Design surface
o Report Preview
o Page Reports object pane
o Report Explorer pane
o Object properties pane
o Object properties dialogue launcher
o Selected property information
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Report Designer Ribbon:
Provides options to create new report templates, open and save report templates to and from the
database and file, set the data source to report on, add data and style objects to the design surface
and access advanced report design tools.
Design surface:
The design surface is the area on to which report objects are placed, aligned and formatted and where
reports can be previewed.
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By default, the report template comprises three sections. A header at the top of the page, a footer at
the bottom of the page and the main body of the page in between the header and footer sections. The
size of the header and footer sections can be modified by dragging the horizontal line separating the
section from the body to the required position.
To remove the header or footer regions of the report template, right mouse click on PageHeader or
PageFooter in the Report Explorer pane and click on Delete.
To add a header or footer to a report template, right mouse click on Report in the Report Explorer
pane and click on either Page Header or Page Footer.
The design surface tool bar provides the following viewing and alignment options:
Click on the Designer tab to show the design surface and manipulate the report
objects
Click on the Preview tab to preview the report (requires a data source to have been
set). See section below for more details.
Click on the Dimension Lines icon to display dimension lines when dragging objects around the
design surface that run from the borders of the report to the object
Click on the Hide Grid icon to hide the grid lines and dots on the design surface
Click on the Show Dots icon to show dots in between the grid lines on the design surface
Click on the Show Lines icon to show lines in between the grid lines on the design surface
Click on the Snap Lines icon to display snap lines when the object being dragged is aligned with
other objects on the design surface
Click on the Snap to Grid icon to restrict the placement of an object to coincide with the grid
lines when dragging an object around the design surface
Click on the Select Mode icon to set the cursor mode to allow object selection and alignment
Click on the Pan Mode icon to set the cursor mode to pan navigation
Drag the slider bar anchor or click on the minus and positive buttons
to set the design surface zoom level
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Report Preview:
The report produced using the report template active on the design surface can be previewed by
clicking on the Preview tab on the design surface
A data source is required to have been set for any report objects to report on measurement,
manipulated or instrument data. The entire data set can be reported on or filters can be set to limit
the data reported on to a subset of the whole data set.
Select which data channels to include in the report preview by checking the appropriate check box. A
tick denotes the data channel is selected for inclusion.
Note: Data channels include measured and manipulated data.
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Select which wells to include in the report preview by clicking on the tree view nodes to show the
wells selected within each group. Select the groups and wells to include in the preview by checking on
the appropriate check boxes. A tick denotes the data channel is selected for inclusion.
To view the preview based on the loaded data set and any applied data filters, click Refresh on
the Preview toolbar.
The Preview window displays the report and the toolbar provides numerous tools to aid viewing,
copying and printing.
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Sidebar Toggle Click to reveal report page thumbnails. Click on a
page thumbnail to display the page
Print Click to launch the print dialogue to print the report
Galley mode Click to view the galley proof of the report. Page
breaks are removed in this viewing mode
Copy Places selected text on the clipboard (see Selection
Mode below)
Find Click to launch the textual search dialogue
Zoom Out Click to reduce the zoom level
Zoom In Click to increase the zoom level
Zoom Value Click on the arrow to select a zoom level or type the
required zoom level value in the edit field
Fit Width Click to adjust the display properties so the full width
of each page of the report is displayed
Fit Page Click to adjust the display properties so the each
page of the report is displayed in full
Single Page View Click to display a single page. To view other pages,
use the Page Controls (see below)
Continuous Page Click to view pages using the scroll bar to scroll
View through the pages or by using the Page Controls (see
below)
Page Controls Click on the arrows to view the first page, previous
page, next page and last page respectively
Backward Displays the last viewed page (once clicked, the
Forward button is enabled)
Forward Displays the last viewed page before the Backward
button was clicked
Pan Click to use pan navigation control
Selection Mode Click to allow content to be selected (see Copy

above)
Snapshot Click to enable selection of a region that can be
pasted into an external application as an image
Page Reports Pane:

The visible state of the Page Reports pane is toggled from visible to hidden by clicking on More
Options. The Page Reports pane is used for advanced reporting requirements and by default the pane
is not visible.
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The Page Reports pane lists the object types that can be used to create report templates. Selected
objects are dragged from the pane to the design surface and configured.
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Report Explorer Pane:
The Report Explorer gives a visual overview of the elements of a report in the form of a tree view and
allows fields such as measured data, date & time and page numbers to be linked to the report objects.
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Object Properties Pane:
Lists the properties of the selected object and allows these to be edited
Object Properties Dialogue Launcher:

For the selected object, any relevant property dialogues are listed. Click on these to launch the
dialogue.
Selected Property Information:

Provides a summary of the property selected in the Object Properties Pane
To Create and Edit a Report Template:

There are two standard approaches to create and edit report templates. These are:
o Standard Reporting-using existing report templates
o Standard Reporting-using Data Options and Style Options
There is also an advanced approach to create and edit report templates. This is:
o Advanced Reporting-Using objects from the Page Reports pane
Report templates can be created and edited using any combination of these methods.
Report templates are combined with measurement, manipulated and instrument data to produce
reports.
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Standard Reporting-Using Existing Report Templates
Installed with Galapagos are several report templates that provide reporting formats suitable for
commonly required reports. These templates can be combined with results, instrument and method
data to produce reports. The report templates that are installed include:
o Plate
o Table
o Well
o Quantitative Screening (Table)
o Quantitative Screening (Plate)
o Quantitative Analysis (Table)
o Quantitative Analysis (Plate)
o Default
Existing report templates can also be used into create new templates. The two approaches to
achieving this are:
o To open an existing report template, modify the content and layout and save as a new report
template
o To create a new (empty) report template and paste content into it by copying parts of existing
report templates
Together with using Data and Style Options, these methods fall into the category of standard
approaches to create report templates.
Templates saved to the database can be removed from the database.
To Modify an Existing Report Template:

3. Open a previously saved report template by clicking on either Open from Database or Open
from File, selecting the template of interest and clicking OK or Open
The report template is displayed on the design surface.
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4. Edit the report as required
To move existing content to a new location on the design surface, first select the object or
group of objects by dragging a selection box around an object or group of objects.
An alternatively method of selecting the object of interest is to click on the object in the
Report Explorer tree view. Then click on the group select symbol and drag to a new
location.
To delete an object or group of objects, first select the object or group of objects by
draging a selection box around an object or group of objects.
Then either press the keyboard Delete key or right mouse click on the group select
symbol and select Delete. A dialogue is displayed requesting confirmation to delete. Click
OK.
An alternative method of deleting an object is to click on the object in the Report Explorer
tree view, right mouse click and select Delete.
To modify the properties of an object, select the object of interest and then modify the
property of interest in the Object Properties pane.
To insert an image into the report template, right mouse click on Embedded Images in the
Report Explorer and click on Add Embedded Image
Select the required image from the Open File dialogue and click Open. The Report Explorer
pane updates to show the image file in the tree view below Embedded Images. Select the
image in the Report Explorer's tree view and drag on to the design surface as required.
To add content to the report template, use one of the following methods:
o Copying content from other report templates
o Adding Data and Style Options
o Adding report objects
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5. Save the report template by clicking on either Save to Database or Save to File, entering the
required filename and clicking OK or Save
6. Click on Set Data
From the list that appears, select the source as either From Database or From File
From the displayed dialogue, select the required results file and click OK or Open
The name of the loaded results file is displayed in the status bar
Note: Ensure that the selected data is compatible with the report template. Blank reports can
result from reporting on data sets that do not comprise the data types the report template is
set to report on.
7. Click on the design surface Preview tab
The report preview is displayed using the measurement, manipulated and instrument data
specified in Step 6.
Note: If a new data set has been specified since the report was last previewed, click on the
Refresh icon to update the report preview.
Note: Undo the previous operation by pressing the keyboard Ctrl and Z keys together.
Note: Content that is linked to measurement, manipulated or instrument data cannot be
located in either the header or footer sections of the report template.
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To Create a New Report and Use Content from an Existing Report:
3. Open a previously saved report template from which to copy content by clicking on either Open
from Database or Open from File, selecting the template of interest and clicking OK or Open

4. Click on the Setup tab and then click on Report Writer
A new report template window is displayed that has no content
5. Click on the report template window tab which includes content to be copied.
To select the content of interest, drag a selection box around the object or group of objects.
An alternatively method of selecting the object of interest is to click on the object in the Report
Explorer tree view. Then right mouse click on the group select symbol and select Copy
6. Click on the new report template window tab
Right mouse click in the section (header, body, footer) of the report the content is to be pasted
and select Paste
The content appears in the new report in the centre of the selected section. Move the content to
the required location on the design surface.
To open a different report template from which to copy content, repeat Steps 1-3.
Note: Content that is linked to measurement, manipulated or instrument data cannot be

located in either the header or footer sections of the report template.
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And from the list that appears, select either From Database or From File
9. Select which data channels to include in the report preview by checking the appropriate check
box. A tick denotes the data channel is selected for inclusion.
Select which wells to include in the report preview by clicking on the tree view nodes to show
the wells selected within each group. Select the groups and wells to include in the preview by
checking on the appropriate check boxes. A tick denotes the data channel is selected for
inclusion.
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Note: If a new data set has been specified since the report was last previewed, click on the
Refresh icon to update the report preview.
To Remove an Existing Report Template from the Database:

1. Click on the Setup tab and click on Report Writer
2. Click on Open from Database
3. From the dialogue that is displayed, select the report template to open from the list displayed
and click on OK
5. From the dialogue that is displayed, click on Yes

6. From the dialogue that is displayed, click on OK
See also:
o Standard Reporting-Using Data Options and Style Options
o Advanced Reporting -Using Page Reports Objects
o Producing reports
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Installed Report Templates
The following report templates are installed with Galapagos. For each, an example report is shown.
o Plate
o Table
o Well
o Quantitative Screening (Table)
o Quantitative Screening (Plate)
o Quantitative Analysis (Table)
o Quantitative Analysis (Plate)
o Default
Plate
A general purpose report layout suitable for single, dual and multiple wavelength data and time
cycling data with one or more wavelengths
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Table
A report aimed at providing a plate report format where a large amount of data is collated per well
and all the values are displayed.
Only the first page of the example report is been shown below. Pages two and three continue to show
the data for each well.
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Well
A layout that reports on individual wells. The well(s) reported on are selected using the Select Well
tool.
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Quantitative Screening (Table)
A template for displaying quantitative analytics results where the results are tabulated
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Quantitative Screening (Plate)
A template for displaying quantitative analytics results where the results are displayed in a plate view
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Quantitative Analysis (Table)
A template for displaying quantitative analysis results where the results are tabulated
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Quantitative Analysis (Plate)
A template for displaying quantitative analysis results where the results are displayed in a plate view
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Default
The main section of this template is blank. The header contains the date and time and the footer the
instrument name, instrument serial number and page number
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Standard Reporting-Using Data Options and Style
Options
Data and Style Options provide a quick and easy mechanism to incorporate both simple and composite
report objects into report templates that have been preconfigured for immediate use.
Data Options relate to report objects that report on measurement data such as data tables and charts.
Style Options relate to report objects that add style items to a report and measurement data
independent items such as signature boxes, page numbering and text boxes.
Galapagos provides a range of Data and Style Options to meet the requirements of many report
templates and additionally offers a straight forward means to create new Data and Style Options for
future use.
Data and Style Options can be inserted into new or existing report templates.
Although Data or Style Options cannot be used to insert images (such as Corporate logos) into report
templates, the steps to do so are detailed in the Image section of the advanced reporting page.
This section covers the following topics:
o Inserting a Data or Style Options into a report template
o Available Data and Style Options
o Creating a new Data or Style Option
Together with using existing report templates, this method fall into the category of standard
approaches to create report templates.
To Insert a Data Option or Style Option:

3. Either, open a previously saved report template by clicking on either Open from Database or
Open from File,selecting the template of interest and clicking OK or Open
or,
Start a new report by clicking on New Report
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4. Click on the section (header, body, footer) of the design surface the Data or Style Option is be
placed
5. Click on Data Option or Style Option
Select the required item from the list displayed.
Data Options:
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Style Options:
The item appears in the centre of the chosen report section.
See section 'Available Data and Style Options' for details of the Data and Style Options
available.
6. Configure the Data and Style Options as required

To move the Data or Style Option to a new location on the design surface, click on the
group select symbol and drag to a new location.
To reselect the Data or Style Option, either drag a selection box around the contents of the
Data or Style Option or click on the name of the Data or Style Option in the Report Explorer
tree view.
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Note: Immediately after a Data or Style Option has been placed on the design surface the
keyboard cursors can be used to move the Data or Style Option to a new location on the
design surface.
To modify the properties of a Data or Style Option, select the Data or Style Option by
either dragging a selection box around the contents of the Data or Style Option or clicking
on the name of the Data or Style Option in the Report Explorer tree view.
For Data or Style Options comprising several elements, individual elements can be selected
in the same way as Data or Style Options.
Modify the property of interest in the Option Properties pane.
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To delete a Data or Style Option, select the Data or Style Option by dragging a selection
box around the contents of the Data or Style Option .
Then either press the keyboard Delete key or right mouse click on the group select
symbol and select Delete. A dialogue is displayed requesting confirmation to delete. Click
OK.
Alternatively, select the object in the Report Explorer, right mouse click and select Delete.
7. To add additional Data or Style Option to the report template, repeat Steps 4 and 5.
Note: The default names given to Data or Style Options, and any elements they comprise,
when added to the design surface are unique. If names are modified (to be more descriptive)
they must be unique. The object's name is modified by editing the Name field in the Design
section of the Object Property pane.
8. To add additional content to the report template, use one of the following methods:
o Adding report objects
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set to report on.
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inclusion.
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The Available Data and Style Options:
The Data and Style Option installed by Galapagos include:
Data Options:
o Equations: Contains details of all manipulations defined for the method
o Group Details: Shows the details of the plate layout
o Group Equation Result: Tabulates group equation results (a group equation is a manipulation
that sources data from more than one well in the group but produces a single outcome. This
also applies to any result of this type which is further manipulated by a single term).
o Group Result: Tabulates all well results for a given group
o Instrument Identification: Contains instrument specific details
o Layout: Shows the grouping of wells in the plate layout
o Layout Identification: Shows the name and description of the plate layout
o Method Identification: Contains method specific information
o Multiple Well Chart: Displays chart data (absorbance vs time and absorbance vs wavelength)
from more than one well
o Operator Identification: Contains the compounded name comprising the computer and operator
name associated with the result
o Parameter Settings: Contains the method settings associated with the method
o Plate Definition: Displays information relating to the plate definition used
o Plate Result: Shows the results for each well organised by plate and group
o Plate View: Shows the plate view as displayed after a measurement
o Result Header: Contains basic results information and shows the results validity flag
o Standards: Contains details of the Quantitative Analysis Options
o Well Details: Displays details of individual wells defined in the plate layout
o Well Result: Displays individual well data
Style Options:
o Current Date & Time: Displays the current PC date and time
o Line: Displays a configurable line
o Page Number (N of M): Shows page numbers
o Signature Box: Displays a signature box
o Textbox: Inserts a text box for adding user specified text
To Create a New Data Option or New Style Option:

New Data or Style Options can be created and added to the list of Data Options or Style Options for
future use. Data or Style Option can be objects such data tables, charts, page numbers, textual areas
and can comprise single and multiple elements.
Either open or create a report template that includes the content from which to create the Data
or Style Option.
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3. Select the objects on which to base the new Data or Style Option
Either drag a selection box around the required content or click on the name of the object in the
Report Explorer tree view
4. Right mouse click on the group select symbol and click on Copy.
5. Click on Data Option or Style Option
Click on Create New Data Option from Contents of the Clipboard or Create New Style
Option from Contents of the Clipboard
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6. Enter a name for the Data or Style Option and click OK
The Data or Style Option list is updated to include the new Data or Style Option
Note: Data and Style Options are stored as .control files in the ProgramData/Biochrom
Limited/Galapagos folder.
Note: Remove Data or Style Options by deleting the corresponding .control file using Windows
Explorer.
See also:
o Standard Reporting-Using Existing Report Templates
o Advanced reporting-Using Page Reports Options
o Producing reports
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Data Options and Style Options
Examples of the Data and Style Objects combined with data are shown below:
Data Options:
Equations: Contains details of all manipulations defined for the method
Group Details: Shows the details of the plate layout
Group Equation Result: Tabulates group equation results (a group equation is a manipulation that
sources data from more than one well in the group but produces a single outcome. This also applies to
any result of this type which is further manipulated by a single term).
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Group Result: Tabulates all well results for a given group
Instrument Identification: Contains instrument specific details
Layout: Shows the grouping of wells in the plate layout
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Layout Identification: Shows the name and description of the plate layout
Method Identification: Contains method specific information
Multiple Well Chart: Displays chart data (absorbance vs time and absorbance vs wavelength) from
more than one well
Operator Identification: Contains the compounded name comprising the computer and operator
name associated with the result
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Parameter Settings: Contains the method settings associated with the method
Plate Definition: Displays information relating to the plate definition used
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Plate Result: Shows the results for each well organised by plate and group
Plate View: Shows the plate view as displayed after a measurement
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Result Header: Contains basic results information and shows the results validity flag
Standards: Contains details of the Quantitative Analysis Objects
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Well Details: Displays details of individual wells defined in the plate layout
Well Result: Displays individual well data
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Style Options:
Current Date & Time: Displays the current PC date and time
Line: Displays a configurable line
Page Number (N of M): Shows page numbers
Signature Box: Displays a signature box
Textbox: Inserts a text box for adding user specified text
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Advanced Reporting-Using Page Report Objects
Objects from the Page Reports pane are used to add content to new and existing report templates.
Report objects enable a wide range of report components to be added to report templates. Report
objects include components such as tables, charts, text boxes and graphical elements and are listed in
the Page Reports pane. Setup of report objects is required before use.
This method is an advanced approach to creating content on report templates.
Data and Style Options enable the insertion of several report object types that have been
preconfigured for immediate use.
This section covers the following topics:
o Page Report objects types
o Adding a Page Reports object to a report template
o Setup of Page Reports objects
Page Reports Object Types:

Page Reports objects are accessed from the Page Reports pane. The display state of the Page Reports
pane is toggled from visible to hidden by clicking on More Options from the Report Group of the
Report Designer context group.
The most relevant Page Reports objects are:

o BandedList: An object that reports measurement, manipulated & instrument data. Comprising
three sections, the central section can repeat data for every row in a data set
o Chart: An object that reports measurement and manipulated data using a variety of chart types
(bar, column, scatter, line and dot plot)
o Container: A graphical element used to keep the object(s) it contains together that may
otherwise grow apart by placing a border around them
o Image: An object that displays a specified image
o Line: A graphical element that displays a straight line
o Matrix: An object that reports measurement, manipulated & instrument data with dynamic
numbers of rows and columns determined by the data set
o Shape: A graphical element that displays a variety of shapes (rectangle, ellipse)
o Table: An object that reports measurement, manipulated & instrument data with a static
number of columns and a dynamic numbers of rows determined by the data set
o TextBox: An object used to display freehand text.
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To Add a Page Reports Object to a Report Template:
3. Either, open a previously saved report template by clicking on either Open from Database or
Open from File, selecting the template of interest and clicking OK or Open
or,
start a new report by clicking on New Report
The empty report template is displayed on the design surface.
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4. Click on More Options
From the Page Reports pane, select and drag the required object type in to place on the design
surface
5. Configure the object's properties and/or measurement, manipulated & instrument data binding
settings
For details of how to configure the different Page Reports objects, see topic Setup of Page
Reports Objects
6. To add other Page Reports objects, repeat Steps 4 & 5
7. To add additional content to the report template, use either of the standard methods:
o Using Data and Style Objects
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set to report on.
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inclusion.
Setup of Page Reports Object:

Once a Page Report object has been placed on the design surface, work through the setup of the
object as required:
o Delete the object from the design surface
o Locate the object in the required position on the design surface
o Results data types that can be reported
o Configure the data binding of BandedList, Table, Matrix and Chart objects (to report on
measurement, manipulated and instrument data)
o Configure the Container, Image, Line and Shape objects
o Set the object's properties
To Delete the Object from the Design Surface:
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1. Select the object by either dragging a selection box around the object or clicking on the name
of the object in the Report Explorer tree view.
2. Press the keyboard Delete key or right mouse click on the group select symbol and select
Delete. A dialogue is displayed requesting confirmation to delete. Click OK.
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To Locate the Object to the Required Position on the Design Surface:
1. Select the object by either dragging a selection box around the object or clicking on the name
of the object in the Report Explorer tree view.
2. Move the object to a new location on the design surface by clicking on the object's group select
symbol and either dragging the object to the required position or use the keyboard cursor
keys to move the object to the required position
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Results Data Types that be Reported:
The measurement, manipulate and instrument data that can be included in reports is listed in the
Report Explorer within the Results subfolder of the Data Sources folder:
Clicking on the tree view nodes expands each of these groups to show the data that can be reported
on:
Instrument: Details of the instrument used
Method: Details of the method used
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Settings: The instrument's data acquisition settings
Equation: The name and description of user-specified manipulations that directly manipulate
well results to create a manipulated well result
Equation (Group): The details of user-specified manipulations that produce a single result from
a group of wells
Layout: The number of physical plates in the plate layout
Groups: Details of the groups specified in the plate layout
Constants: Details of constants specified in the plate layout
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Plate: Details of the plate's manufacture, type and geometry
Results: Details of the results
Data: Measurement and manipulated data
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Plate Data: Plate information
Group Data: Group information
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Well Data: Well information
Chart Data: Chart information
QA Object Data: Configuration details of the QA Object
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QA Standard Curve Data: Data values for the standards used in the standards curve and the
line of best fit
QA Standards Details: Measurement and statistical information for the standards
QA Coefficients: The QA coefficients
QA Coefficient & Fit: Standard curve coefficient and fitting parameters
QA Fit Image: The QA standards curve image
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Plate Image: Image of the plate view
Layout Image: Image of the layout
The common values available for reports are listed in the Report Explorer in the Common Values
folder:
To Configure Objects that can Report on Measurement, Manipulated and Instrument Data:
Certain Page Reports objects can be combined with data sources to report on measurement,
manipulated and instrument data and with common values such as page numbers and time & date.
Of the Page Reports objects described above, the following can be configured to report on results
data:
o BandedList
o Table
o Matrix
o Chart
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Click on the object of interest for specific configuration guidance.
BandedList:
A BandedList is used for creating lists of results types such as the Instrument group (name,
serial number and firmware version) or the Method group. It is also used for handling data
sources that have multiple values.
A BandedList comprises three sections - header, footer and central sections.
To add a data source or common value to a section of the BandedList, select the data source of
interest from the Report Explorer and drag in to the required section. More than one data
source or common value can be added, but results sources have to be from the same results
type, such as from the Instrument group or from the Plate group.
To add additional freehand text, select TextBox from the Page reports pane, drag into the
required section and edit the text box with the required text.
Example 1:
An example use of a BandedList is to list the instrument details. To do this:
1. Drag a Bandedlist onto the design surface
2. From the Page Reports pane, drag three TextBoxes into the central section of the
BandedList and arrange them one above the other on the left hand side
3. From the Report Explorer, drag the Name, Serial Number and Firmware Version fields
of the Instrument group into the central section of the BandedList. Arrange them one
above the other on the right hand side and aligned with the Textboxes on the left
4. Type an appropriate label into each of the Textboxes (Name, SN, FW Version)
5. From the Page Reports pane, drag another TextBox into the header section of the
BandedList, align it with the other Textboxes on the left hand side and type a title
(Instrument Settings)
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The plate view, plate layout and the quantitative analysis standards curve can be displayed as
images. The examples below describe how to configure BandedLists to show these images.
Example 2:
An example use of a BandedList is to show the plate view. To do this:
1. From the Page Reports pane drag a BandedList on to the design surface
2. From the Page Reports pane drag an Image into the main section of the BandedList
3. Select the Image object and click on the results Selector icon, click on Plate
Image and then click on Image
4. Select the Image object and from the Data section of the Properties pane change the
Source field to 'Database' from the list of options
5. Select the BandedList and Image objects and resize as required
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Example 3:
An example use of a BandedList is to show the plate layout. To do this:
3. Select the Image object and click on the results Selector icon, click on Layout
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Example 4:
An example use of a BandedList is to show the quantitative analysis standards curve . To do
this:
3. Select the Image object and click on the results Selector icon, click on QA Fit
Note: Adjust the size of objects to meet the report requirements by selecting the object and
dragging the perimeter markers accordingly.
Note: All objects on the design surface must have a unique name. The object's name is
modified by editing the Name field in the Design section of the object's property pane.
Note: A data source must be set to preview the report.
Table:
A Table is used to show data in rows. The number of rows in a table varies with the data
source, but unlike a Matrix, the number of columns is fixed during the design process.
A table comprises three columns and three rows by default. The top row is the header section
used for column headings. The bottom row is the footer section. Text can be entered into these
cells as required or left blank if not required. Drag the required data sources into the middle
row. These can include items from the Data group.
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Example:
An example use of the a Table would be to list the absorption values of each well organised by
the group the wells are part of. To do this:
1. From the Page Reports pane, drag a Table on to the design surface
2. From the Report Explorer, drag the Group item from the Data group into the far
middle left cell, drag the Well field from the Data group into the centre middle cell and
drag the Value field from the Data group into the right middle cell
3. The header cells for each column will be populated automatically, but these can be
modified if required by typing the required text into each cell
More columns and rows can be added to a table. To add a row, click on the object, right mouse
click on the far left of the object and select either Insert Row Above or Insert Row Below. To
add a column, click on the object, right mouse click on the top of the object and select either
Insert Column to the Left or Insert Column to the Right.
Note: Only the first measured absorbance value can be reported in a table. Use a Matrix to
report on more than one absorbance value and any manipulated data.
Matrix:
A Matrix is used for creating a grid of data where the number of row and columns can vary
according to the data set. This object is well suited to displaying fields from the Data group
where the Value field varies with one or more of the other Data fields such as Well or Cycle.
A Matrix comprises two columns and rows by default. The top left cell can be left blank or text
can be input to act as a label. The bottom left cell is the row header and the top right cell is the
column header. Drag the required Data fields into these cells. The bottom right cell is used to
display the value of the intersection of columns and rows.
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Example:
An example use of a Matrix would be to display the measured absorption value against each
well. To do this:
1. From the Page Reports pane, drag a Matrix on to the design surface.
2. From the Reports Explorer, drag the Well field from the Data group into the bottom
left cell, drag the Name field from the Data group into the top right cell and drag the
Value field from the Data group into the bottom right cell.
3. Select the bottom right cell and in the Properties pane edit the Value field in the Data
section to remove 'Sum' after the equals sign.
More columns and rows can be added by clicking on the object and right mouse clicking on the
far left or top of the object, selecting Add Column Group or Add Row Group and clicking OK on
the dialogue that appears.
Example:
Another example use of a Matrix would be to display how the measured absorption value and
manipulated absorption value varied within each well and by cycle. To do this:
1. From the Page reports, drag a Matrix on to the design surface and create an
additional row group
2. Drag the Cycle field from the Data group into the bottom left cell, drag the Well field
from the Data group into the bottom centre cell, drag the Name field from the Data
group into the top right cell and drag the Value field from the Data group into the
bottom right cell
3. Select the bottom right cell and in the Properties pane edit the Value field in the Data
section to remove 'Sum' after the equals sign
If the data set selected to report on includes more than one measured wavelength or one or
more manipulations then these values will also be displayed.
Note: All measured and manipulated data channels can be reported in a Matrix.
Page 370 of 381

Chart:
A chart is used for plotting Data types against one another. Charts can display multiple series.
The five different chart types are bar, column, scatter, line and dot plot.
After dragging a Chart on to the design surface, a Chart type is selected. Click on the chart to
configure the chart. The data (y-axis ), category (x-axis) and, optionally, series fields need to
be defined. The chart's title and axis labels can also be defined.
Example:
An example use of a Chart would be to plot how the absorbance varies with wavelength for a
series of wells. To do this:
1. From the Page Reports pane drag a Chart on to the design surface and select Line
2. Click on the chart and from the Reports Explorer drag the Value field from the Data
group into the region above the plot (region entitled: Drop data fields here), drag the
Name field from the Data group into the region below the plot (region entitled: Drop
category fields here) and drag the Well field from the Data group into the region to
the side of the plot (region entitled: Optionally drop series fields here)
3. Click twice on the chart and right mouse click over Value in the top left corner and
select Edit. In the dialogue that is displayed, edit the Value field by removing 'Sum'
after the equals sign and click OK
4. To edit the axis labels and chart title, select the default label on the chart and edit the
name in the Properties pane
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To Configure the Container, Image, Line and Shape Objects:
With the exception of the Image object, these objects cannot report on reports data directly (although
objects that can report on results data can be inserted into the container object) but have options to
be configured.
Container:
The Container is graphical element used to keep the object(s) it contains together that may otherwise
grow apart by placing a border around them.
1. Drag a container on to the design surface
2. Drag other Page Report objects such as Matrix, Table, TextBox into the container
3. Select the container and configure the container's border styles through the Object Properties
pane.
Image:
The Image object enables images to be displayed.
1. Right mouse click on Embedded Images in the Report Explorer and click on Add Embedded
Image. Using the displayed dialogue, browse and select the require image file.
2. Drag an image object on to the design surface
3. Select the image object on the design surface and through the Object Properties pane change
the Source field within the Data section to Embedded and select the name of the image
previously embedded in the Value field within the Data section.
Line:
The Line object allows straight lines to be displayed.
1. Drag a line on to the design surface
2. Each end of the line can be move to a new location on the design surface by selecting the line
and dragging each end to the required location.
3. Line styles are configured through the Object properties pane.
Shape:
The Shape object allows rectangles, circles and ellipses to be displayed.
1. Drag a shape on to the design surface
2. Adjust the size of the shape to meet the report requirements by selecting the object and
3. Change the shape through the Object Properties pane by selecting the required shape from the
ShapeStyle field in the Appearance section.
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To Change an Object's Properties:
All objects have properties that can be changed by editing the appropriate field in Object Property
pane. Properties include Display properties (such as colour, font face, border styles), Layout (such as
location on the design surface) and Design (such as the name the object is referred to as on the
design surface).
To edit an object's properties, select the object and then edit the required fields displayed in the
Object Properties pane.
All objects on the design surface must have a unique name. The object's name is modified by editing
the Name field in the Design section of the object's property pane.
See also:
o Standard Reporting-Using existing report templates
o Standard Reporting-Using Data Options and Style Options
o Producing reports
Page 373 of 381

Producing Reports
Reports are produced by combining data with report templates that have been created and designed
using the report writer. The data types that can be linked to reports include measurement results,
manipulated data, method details and instrument details.
o Loading a data source
o Loading report templates
o Removing report templates
o Opening a report template from the list of loaded reports templates
o Setting the data channels and wells on which to report
o Viewing the report
o Adjusting the settings of the report viewer
o Printing the report
o Exporting the report to different formats
To Load a Data Source:

Before a report can be produced, data needs to be available to report on. Either,
1. Open previously saved data from either the database or from file
or,
2. Perform a quick measurement and leave the resulting data window open
Note: Where there is more than one data window open, the report takes data from the active
data window.
To Load Report Templates:

Once loaded, report templates can be opened for use.
1. Click on the File tab
2. Click on Reports
3. Click on Configure Reports
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4. Select whether to load a report template from the database or from file by clicking on Add
from Database or Add from File from the Configure Reports dialogue
Page 375 of 381

5. Select the required report template and click OK or Open
6. The Configure Reports dialogue updates to show the selected report template. Repeat steps 4
and 5 to add additional report templates to the Configure Reports dialogue.
Click OK to load the listed reported templates.
Note: Report templates only require loading into Galapagos once. On restarting the software,
previously loaded report templates are available to open.
Page 376 of 381

To Remove Report Templates:
Report templates that have been loaded can be removed.
2. Click on Reports
3. Click on Configure Reports
4. Select which report template to remove and click Remove
To remove additional report templates, repeat this step.

Click on OK
To Open a Report Template from the List of Loaded Report Templates:

2. Click on Reports
3. Click on the report arrow to display the list of available report templates
Page 377 of 381

4. Select the required report template
The report template is opened and ready for use. The Select Data and Select Well filters update
accordingly.
To Select the Data Channels and Wells on which to Report:

The entire data set can be reported on or filters can be set to limit the data reported on to a subset of
the whole data set.
1. Select which data channels to include in the report by checking the appropriate check box. A
tick denotes the data channel is selected for inclusion.
2. Select which wells to include in the report by clicking on the tree view nodes to show the
wells selected within each group. Select the groups and wells to include in the report by
inclusion.
Page 378 of 381

To View the Report:
1. To view the report based on the loaded data set and any applied data filters, click Refresh
on the Report Viewer toolbar.
The Report Viewer updates to display the report
To Adjust the Report Viewer Settings:

The Report Viewer window displays the report and the toolbar provides numerous tools to aid viewing,
copying, exporting and printing.
Sidebar Toggle Click to reveal report page thumbnails. Click on a

page thumbnail to display the page
Print Click to launch the print dialogue to print the report
(See Print for more information)
Export Click to select the data export format. Choose from
Word, Excel, PDF, HTML, RTF, text and TIFF (see
Export for more information)
Galley mode Click to view the galley proof of the report. Page
breaks are removed in this viewing mode
Copy Places selected text on the clipboard (see Selection
Mode below)
Find Click to launch the textual search dialogue
Zoom Out Click to reduce the zoom level
Zoom In Click to increase the zoom level
Zoom Value Click on the arrow to select a zoom level or type the
required zoom level value in the edit field
Fit Width Click to adjust the display properties so the full width
of each page of the report is displayed
Fit Page Click to adjust the display properties so the each page
of the report is displayed in full
Single Page View Click to display a single page. To view other pages,
use the Page Controls (see below)
Continuous Page Click to view pages using the scroll bar to scroll
View through the pages or by using the Page Controls (see
below)
Page Controls Click on the arrows to view the first page, previous
page, next page and last page respectively
Backward Displays the last viewed page (once clicked, the
Forward button is enabled)
Forward Displays the last viewed page before the Backward
button was clicked
Pan Click to use pan navigation control
Selection Mode Click to allow content to be selected (see Copy above)
Snapshot Click to enable selection of a region that can be

pasted into an external application as an image
Page 379 of 381

To Print the Report:
1. Load the data on which to report on
2. Load and Open the report template from which to produce the report
3. Set the data channels and wells on which to report
4. View the report
5. Click Print in the Report Viewer toolbar
6. Select the printer from the Print dialogue and click OK
To Export the Report to other Formats:

Measurement, instrument and manipulated data can be exported to several data formats, including:
o Microsoft Word
o Microsoft Excel
o PDF
o HTML
o Rich text format (RTF)
o Text
o TIFF
The reporting capability of Galapagos provides data export options.
To Export Data to a File:

1. Load the data on which to report on
2. Load and Open the report template from which to produce the report
3. Set the data channels and wells on which to report
4. View the report
5. Click on Export from the Report Viewer toolbar and select the required export format
Page 380 of 381

6. Enter the file name and location and click Save
The files are stored in Public Documents/Biochrom/Galapagos/[User]
Page 381 of 381

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Galapagos

Model Wavelength Selection Variant

1.2 General Safety

Standards to which conformity is declared include:

1.3 Warnings and Hazards

Use of PCs for Controlling Software

Lifting and Carrying

1.5 Equipment Ratings

Consumption 250VA 80VA 80VA 20VA 65VA

1.8 Powering up the EZ Read Microplate Reader

1.9 Performing a Quick Measurement

5. Click ‘Start’ to begin acquisition

6. Raw absorbances are displayed in the wells:

PROBLEM POSSIBLE CAUSE

2.1 Cleaning and Disinfecting the Instrument

2.2 Emergency Instructions

2.3 Safe Disposal of the Instrument

2.4 Regular Maintenance

Online Help Topics

To show online help:

Keyboard shortcut: Press ALT, H, H

Keyboard shortcut: Press ALT, H, M

2. Click on the Manual icon

To show the application 'About' dialog:

2. Click on the About icon

Logged in user is 'Rob'

Database is not connected, working offline

The File tab is shown by selecting File or pressing Alt, F

The Setup tab contains the following:

The Methods tab is shown by selecting Methods or by pressing Alt, M

The Methods tab contains the following:

The Help tab contains the following:

Data Window Overview

To Select which File is Displayed:

2. Click on the close button

To View the Method Properties of the Current Results File:

3. Click on the pin to keep the pane in view.

To View the Plate Layout Groups of the Current Results File:

3. Click on the pin to keep the pane in view.

Note: It is not possible to edit or delete information in the Groups view

To View a Well's Chart data for the Current Results File:

4. Click on the pin to keep the pane in view.

4. Click on the pin to keep the pane in view.

Exiting the Application

1. Click the close in the upper-right corner of the application window.

To initiate a new method:

Galapagos data can be opened from either a database or disk file.

To open a data source from file:

Galapagos data can be stored in a database or saved to disk file.

Storing data in a database:

Galapagos offers a default name in the format: Measurement [YYYYMMDDHHMMSS] [Computer

Galapagos offers a default name in the format: Quick Measurement [YYYYMMDDHHMMSS]

Database Connection and Management

This topic contains the following sub-topics:

Connecting to a database for the first time:

The Methods tab is displayed

Galapagos connects to the database and displays the Methods tab

Note: If it is not possible to connect to the database, a warning dialog is displayed

Select Work Offline to save data as disk files

The Methods tab is displayed

1. Click on the Setup tab

2. Click on Work Offline

Galapagos disconnects from the database and works offline

Connecting to the last used database