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March '08 issue of the Bioinformatics.Org Newslette

March '08 issue of the Bioinformatics.Org Newslette

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Published by A Roy
---------------------------------------------------------------------
March '08 issue of the Bioinformatics.Org Newsletter is now available
Submitted by J.W. Bizzaro; posted on Monday, March 31, 2008
---------------------------------------------------------------------
The newsletter includes some of the best of our various online forums and details some of our internal (and external) activities.

IN THIS ISSUE:
- Unveiling Pipet (part two)
- Project spotlight: Molekel
- Job search highlight
- Upcoming events
---------------------------------------------------------------------
March '08 issue of the Bioinformatics.Org Newsletter is now available
Submitted by J.W. Bizzaro; posted on Monday, March 31, 2008
---------------------------------------------------------------------
The newsletter includes some of the best of our various online forums and details some of our internal (and external) activities.

IN THIS ISSUE:
- Unveiling Pipet (part two)
- Project spotlight: Molekel
- Job search highlight
- Upcoming events

More info:

Published by: A Roy on Apr 01, 2008
Copyright:Attribution Non-commercial

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Unveiling Pipet (part two)
 J.W. Bizzaro
Unveiling Pipet(part two)
............................Page 1
Project spotlight
............................Page 2
 Job search
............................Page 3
 Upcoming events
............................Page 4
Copyright © 2008Bioinformatics Org., Inc.
Vol. 1 No. 2February 2008
In this issue
We’ve been revealing the unique aspectsof the Pipet collaborative research envi-ronment in this multipart article. Thismonth, we’ll delve into the declaration
and denition of Pipet cells, a generic
container for graphical user interface(GUI) and command-line interface (CLI)components.Pipet can work something like a wikisystem in which “templates” have beenreplaced by “cells.” So, interacting withcells can be easy. For instance, the soft-ware behind Wikipedia.org (MediaWiki)uses the following directive to add thecontents of one page (the template) toanother:
{{templatename|parname1=parvalue1|parname2=parvalue2|...}}
 And it’s the same in Pipet: the directivecalls a cell and inserts the cell’s con-tents in its place. Parameters can alsobe used, separated by vertical bars (
|
).This works a lot like adding a functioncall to a print statement in a commonprogramming language. As an example,suppose we have a cell named “
List
”,previously created for the ubiquitousUnix “
ls
” command. We could then en-ter the following in a new, empty cell:
Here are the contents of the FTP directory:{{List|Directory=/ftp/pub}}
Here, a call is made to the cell,passing along the parameter
Directory=/ftp/pub
”. By default, thiscell contains an XML description of thecommand “
ls -l ./
”, which containsthree arguments: (0)
ls
, (1)
-l
, and (2)
./
(see Figure 1).
Figure 1: The Unix command for list-ing a directory, as described by thePipet Cell Markup Language (sans at-tributes). The command characters (inred) are oriented vertically to matchtheir respective XML elements.
For the uninitiated, the rst argument
in the command—programmaticallynumbered 0 and commonly consideredthe command itself—is a program thatlists the contents of a directory. The Li-nux manual entry actually says, “List
 F e b r u a
 r y
Continued on page 2.
 
- 2 -
Molekel is an open-source(GPL) multiplatform molecu-lar visualization programbeing developed at theSwiss National Supercom-puting Centre (CSCS). Some of the features avail-able inlude: Multiplatform: Mac OS X, Windows,Linux Visualization of residues (ribbon or schematic)
y
Complete control over the generation of mo-
y
lecular surfaces (bounding box and resolution) Visualization of the following surfaces:
y
Orbitals
Iso-surface from density matrix
Iso-surface from Gaussian cube grid data
SAS
SES
 Van der Waals
 Animation of molecular surfaces
y
Export to PostScript
y
Export animation
y
Plane widget to visualize a scalar eld: the
y
plane can be freely moved in 3d space and thepoints on the plane surface will be colored accord-
ing to the value of the scalar eld: a cursor can
be moved on the plane surface to show the exact
 value of the eld at a specic point in space.
Molekel has been hosted at Bioinformatics.Org since2006 and is available at http://bifx.org/molekel/.
Project spotlight:
Molekel
information about the [specied] les (the current
directory by default).” So, skipping over to argumentnumber 2,
./
is our specied directory, the current
directory (since this is the default, it is in fact redun-dant, but let’s keep it in for this example).
In-between the program name and the specied di
-rectory is an option,
-l
. This option species that
the output is to be printed in “long format,” with ad-ditional details. Figure 2 is an example of what thiswould look like from the Bioinformatics.Org FTP di-rectory. Had other options been used instead of, or inaddition to,
-l
, the output would be different. (On aUnix/Linux computer, type
man ls
for more informa-tion on this command and its options.)
Figure 2: Wiki-formatted text, including the out-put returned by a hypothetical “
List
” cell.
In a similar fashion, Pipet Cell Markup Language con-tains “
<command>
” elements, which contain a num-ber of “
<argument>
” elements, and they in turn con-tain text (or character data) denoted by “
<value>
elements. Furthermore, in Figure 3, you’ll see thatall of the elements can be contained within a single
<cell>
” element (where
key=”List”
). Recall that acell is a generic container.
Continued from page 1.Continued on page 3.
 
- 3 -
 Job search
Looking for a job inthe bioinformatics
eld?
The USDA, Agricultural Re-search Service, Bovine Func-tional Genomics Labora-tory in Beltsville, Maryland(Metropolitan Washington DC),is seeking a POSTDOCTORALRESEARCH ASSOCIATE, (Re-search Bioinformaticist/Computational Biologist)for a TWO YEAR APPOINTMENT. Salary is commen-surate with experience ($55,706 - $72,421 per an-
num) plus benets. Citizenship restrictions apply.
  As a member of a multidisciplinary team of physi-ologist, molecular biologists, and computational bi-ologists, the incumbent will be working on a rumen
metagenomics project. The incumbent¡¯s specic re
-sponsibilities will include, but not limited to, the fol-lowing: (1) Implementing algorithms for clustering,alignment, annotation, and gene prediction from meta-genomic sequence data. (2) Optimizing sequence as-sembly algorithms and protocols for short reads, and(3) Developing models to characterize rumen microor-ganism dynamics in response to nutritional changes.Full announcement:http://bifx.org/forums/forum.php?forum_id=6338Figure 3: The Unix command for listing a direc-tory, including two cells.
Being a container, a cell also has a key-value rela-tionship with whatever character data it contains, atany level of nesting. Within Pipet, our hypothetical
List
” cell becomes a variable that is declared via
XML. Its default denition (without the execution of 
the command) is the sum of the character data in the<value> elements, which is “
ls -l ./
”. In fact, our
Directory=/ftp/pub
” parameter is also represent-ed by a cell (see Figure 3), and passing this param-
eter along to the cell replaces the default denition.
If we were to continue to add cells with addition-al commands to the XML, we would form a scriptwhere one or more command arguments can appearas options to be set by a Web user.In next month’s installment, we’ll look into cell com-pilation and its affect on the GUI. If you have anyquestions or would like to get involved in Pipet,please contact jeff@bioinformatics.org.
Other9%
Which operating system do you mostfrequently use for bioinformatics R&D?
2515 total responses
Windows/DOS variantMacOS (OSX)Linux variant15%22%54%
Continued from page 2.

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