BIOL2013

Bioinformatics and DNA technology

ACADEMIC YEAR 2018/19

SEMESTER 2

7.5 ECTS

MODULE COORDINATORS: Dr James Dillon

E-MAIL: jcd@soton.ac.uk
ABOUT THIS MODULE
The aim of this course is to provide an understanding of techniques and applications
that exploit genetic processes at the molecular level. Over the past few decades,
molecular biology and bioinformatic approaches have been applied to almost every area
of biological science and medicine and, in many cases, have revolutionised the ways in
which research is carried out. Many of the key advances stem from a detailed study of
fundamental cellular processes and knowledge of these processes is still indispensable
for an in-depth understanding of modern molecular biology. The topics covered on this
course include recombinant DNA techniques ('genetic engineering') involving the use of
diverse cloning systems, DNA sequence determination and bioinformatic analysis, and
applications of these techniques, e.g. methods to track down genes involved in disease
processes. Lectures are complemented by a five week bioinformatics project. Many of
the tools and topics covered in this course will be used by those of you taking the
Bioinformatics and Systems Biology (BIOL3063) next year.

Lectures: Lectures will be held on Mondays 09:00-11:00 (54/5027). Lectures

start on the hour. Please be punctual - latecomers disturb not only the
lecturer but also your fellow students.

Project: All students will have a bioinformatics research project that will be
introduced in week 1. The objective of this project is to expose students to a
number of the bioinformatics tools and techniques that are used in many
fields of biology and medicine. Each student will work individually on their
own project. Full instructions will be provided, and students will be able to
work on projects at their own pace. Assessment will be in the form of two
submitted documents: (1) A technical assessment consisting of a workflow
file uploaded through Blackboard; (2) A written project summary to be
submitted via a turnitin link on Blackboard. The project will be worth 25%
in total.

Workshop: There will be a drop-in workshop to help with your projects. The
workshop will be Tuesday 26th Feb 16:00-18:00 in 44/1061. Please
save your questions for this session. Demonstrators will be available to
help troubleshoot any problems you have with the bioinformatics project.

TEACHING STAFF
Name Email
Dr Jane Gibson (JG) J.Gibson@soton.ac.uk
Dr James Dillon (JCD) J.C.Dillon@soton.ac.uk
Dr Christopher Bell (CB) C.G.Bell@soton.ac.uk
Dr Paul J Skipp (PJS) pjss@soton.ac.uk
 ASSESSMENT
1. A two hour unseen examination at the end of the semester consisting of two
compulsory computer based sections and one essay question from a
choice of three. All have equal weighting.
2. Bioinformatics project.

ASSESSMENT WEIGHTING
1. Written examination: 75%
2. Bioinformatics project: 25%

TIMETABLE: Please note that this guide may be updated, should

circumstances demand.

Wk Date Time Room Staff Lectures & workshop Coursework

28th Jan 0900 54/5027 JG Intro to Bioinformatics Intro
1 (18)
1000 54/5027 JG/JD Intro to Project
4th Feb 0900 54/5027 JG Sequence determination
2(19)
1000 54/5027 JG Sequence determination
11th Feb 0900 54/5027 JG Genomics and the ‘omics revolution
3(20)
1000 54/5027 JG Genomics and the ‘omics revolution
18th Feb 0900 54/5027 CGB Epigenomics
4(21)
1000 54/5027 CGB Epigenomics
25th Feb 1000 54/5027 CGB Epigenomics
5(22) 26th Feb 1600 44/1061 Demonstrators Computer room session for project
1700 44/1061 Demonstrators Computer room session for project
4th Mar 0900 54/5027 PJS Sequence alignment
6(23)
1000 54/5027 PJS Sequence alignment
11th Mar 1000 54/5027 PJS Sequence alignment
7(24)

18th Mar 0900 54/5027 JCD Recombinant DNA techniques & applications
8(25)
1000 54/5027 JCD Recombinant DNA techniques & applications
25th Mar 0900 54/5027 JCD Recombinant DNA techniques & applications Deadline
9(30)
1000 54/5027 JCD Recombinant DNA techniques & applications 29 th March

EASTER
29th Apr 0900 54/5027 JCD Recombinant DNA techniques & applications
10(31)
1000 54/5027 JCD Recombinant DNA techniques & applications
6th May Bank Holiday
11(32)

13th May 0900 54/5027 Revision sessions

12(33)
1000 54/5027
LECTURE MATERIALS
Lecture slides will be made available on Blackboard before the lecture. It is your
responsibility to check Blackboard for handouts ahead of a lecture and print if required.
Panopto lecture recordings will be made available after the lectures.

TEXTBOOKS
A general reading list is available on Blackboard. Other recommended reading will be
highlighted in lectures.

ASSIGNMENT SUBMISSION DATES

Assignment name Deadline Hand-in location
Bioinformatics Project 14:00 29th March 2018 BIOL2013 Blackboard site

IMPORTANT INFORMATION

RECORDED SESSIONS: By default, all lectures by BioSci academics in BIOL-coded modules will be recorded via
the University’s Panopto system. These recordings will be available via the module’s Blackboard site; they are solely
for personal use and must never be distributed or shared with anyone else. Panopto recordings are meant as an extra
revision aid and are not to be considered an alternative for attending a lecture. Lack of a lecture recording (e.g. as a
result of a technical failure) can never be used as ground for extenuating circumstances.

FEEDBACK: Feedback will be provided via written comments on module assignments, tests, quizzes on Blackboard
and verbal comments from module staff. Feedback on examination performance should be sought from your Personal
Tutor in the first instance. Second and third year students will be able to review their semester 1 exam scripts towards
the end of February/beginning of March. You will be advised of the exact dates nearer the time. Past exam papers for
all modules are also available from SUSSED.

FACULTY STUDENT RECEPTION DESK: The Faculty Student Reception Desk is located in building 85 on Level
2. The administrative support team are available to offer general advice. The Reception Desk is open from 09:00 –
17:00 Mon to Fri. You can also email them on sobiol@soton.ac.uk. Do not forget the answer to your question might
already be available on the ‘Biological Sciences Undergraduate Information Site’ on Blackboard which is full of useful
information.

BLACKBOARD: Further information is available on the Blackboard site for this module, including module aims,
learning outcomes and (where appropriate) past exam papers. You should ensure you have read all the information
and check the site regularly for updates. Go to http://blackboard.soton.ac.uk/ and use your email login and
password.
ACADEMIC INTEGRITY: Failure to follow the rules for academic integrity will result in penalties varying from a
reduction in the mark awarded to termination of programme. You should pay special attention to the following
examples of possible academic integrity breaches:
Plagiarism is the reproduction or paraphrasing, without acknowledgement, from public or private (ie:
unpublished) material (including material downloaded from the internet) attributable to, or which is the
intellectual property of, another including the work of students.
Cheating is any action before, during or after an assessment or examination which seeks to gain unfair advantage or
assists another student to do so.
Falsification is any attempt to present fictitious or distorted data, evidence, references, experimental results or
other material and/or knowingly to make use of such material.
Recycling is where a piece of work which has already been used in one context is used again (without declaration) in
another context.
It is your responsibility to understand and adhere to these regulations as set out in
http://www.calendar.soton.ac.uk/sectionIV/academic-integrity-statement.html

LATE WORK
The University penalty for submission of late work is

University Working Days Mark

late
1 (final agreed mark) * 0.9
2 (final agreed mark) * 0.8
3 (final agreed mark) * 0.7
4 (final agreed mark) * 0.6
5 (final agreed mark) * 0.5
More than 5 Zero

Extensions for Late Submission of Work

A student may request an extension using a deadline extension form available from the Biological Sciences teaching
office in advance of the submission deadline date.
The deadline for all work is 14:00 (2pm).