Module Title

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Module Title

Introduction to programming for biologists

Module Code

MA170

Credits


5

Courses and year of study for which
module is designed

Biotechnology, 1
st

year

Semester(s) in which module is taught

1

Module Coordinator

Tim Downing

Date
submitted to LTA Committee

9 March 2012

Module Descriptor

Module Overview:

This module provides biology students with foundation programming skills in Perl and enables them
to perform core bioinformatic tasks. It will also introduce them to the scope for

further learning and
more advanced applications,

and allow them to appreciate that computer
-
based tools are
fundamental to modern biology and medicine.

General Aims:

To equip students with the capacity to perform basic data manipulation and analysis tasks

using a
high
-
level computer programming language.

Learning Outcomes:

On successful completion of this module, students should be able to



foundation programming skills in Perl and to perform core bioinformatic tasks



understand the
scope for further
learning and more advanced applications




appreciate that computer
-
based tools are fundamental to modern biology and medicine



Module Delivery:

The module will be delivered as a series of weekly 2
-
hour lectures based in computer labs for 1
semester (12x2=2
4 hours). 1 weekly 1 hour tutorial will help maintain progress for students who
struggle with material and also to allow keen students to enhance their learning (12x1=12 hours).
Lecture, assessment and class exercise notes will be listed on Blackboard. Stu
dent assignments for
continuous assessment will be completed individually, requiring 7 hours a week of independent
learning (12x5=84 hours).



Module Workload:



Activity

Time (hours)

Taught Periods

Taught Activities

36

Homework and Study

84

Total

120

Formal Examination
and Study Periods

Examinations and
Study

0


Overall Total

120

Module Assessment:

2


The module will be examined through continuous assessment focusing on applying programming to
simple biological problems, each of which will account for 1/12th of the overall module marks.
Assessment questions and assignment submission will be completed on

Blackboard or via email.


Overall scheme:

Sessions for each week (lecture and tutorial topics):

1.

oneliners; awk; bash vs c
-
shell; creating scripts; warnings

2.

printing; aliases; standard input/output; opening/closing files

3.

my variables; scalars; strings; ar
rays; die; if
-
else; and/or;

4.

undefined variables; while; for; unless; until

5.

pattern matching; motif searching; printf statements

6.

translating DNA/protein sequences; sequence processing

7.

homology searching using scripts to implement tools, accessing websites

8.

debugging; sub
-
routines; script structure

9.

example application: testing rates of molecular evolution in DNA (eg PAML)

10.

hashes


format, usage and applications

11.

example application: processing high
-
throughput DNA sequence data

12.

modular programming; online
resources; other languages


Example session assignments
:

1.

write Perl/awk/shell commands to denote columns in a fasta text file

2.

read in, sort based on user preference, and print to file a set of genes

3.

denote the amino acid length and present of stop codons i
n a DNA sequence

4.

do pairwise alignments for all possible sequences in a file

5.

determine species given unknown sequence

6.

guess likely function of gene using homology searches

7.

assess variation at the Mc1r gene in vertebrates

8.

use sub
-
routines to infer mutation
type in a protein sequence

9.

what primate species has the fastest evolving Foxp2 gene?

10.

compare hash
-

and array
-
based scripts on computer time taken

11.

determine origin of unknown high
-
throughput sequence library.

12.

incorporate simple BioPerl/CPAN module to execut
e homology searches