Module Specification
The information contained in this module specification was correct at the time of publication but may be subject to change, either during the session because of unforeseen circumstances, or following review of the module at the end of the session. Queries about the module should be directed to the member of staff with responsibility for the module.
Title PROGRAMMING FOR LIFE SCIENCES
Code LIFE733
Coordinator Dr AC Darby
Functional and Comparative Genomics
Alistair.Darby@liverpool.ac.uk
Year CATS Level Semester CATS Value
Session 2016-17 Level 7 FHEQ Second Semester 15

Pre-requisites before taking this module (other modules and/or general educational/academic requirements):
Students should have a 2:2 in a Life sciences undergraduate degree or related subject. I background in bioinformatics and/or computational biology would be helpful but not required. 

Modules for which this module is a pre-requisite:
 

Co-requisite modules:
 

Linked Modules:
 

Teaching Schedule
  Lectures Seminars Tutorials Lab Practicals Fieldwork Placement Other TOTAL
Study Hours 11
lectures to introduce key concepts
        44
Workshops
55
Timetable (if known)              
Private Study 95
TOTAL HOURS 150

Assessment
EXAM Duration Timing
(Semester)		 % of
final
mark		 Resit/resubmission
opportunity		 Penalty for late
submission		 Notes
             
CONTINUOUS Duration Timing
(Semester)		 % of
final
mark		 Resit/resubmission
opportunity		 Penalty for late
submission		 Notes
Coursework  1 week   semester 2  10  No reassessment opportunity  Standard UoL penalty applies  Project work - Summative assessment of the course material There is no reassessment opportunity,  
Coursework  1 week  semester 2  10    Standard UoL penalty applies  Project work - Summative assessment of the course material  
Coursework  1 week   semester 2  10  No reassessment opportunity  Standard UoL penalty applies  Project work - Summative assessment of the course material There is no reassessment opportunity,  
Coursework  4 week  semester 2  30  No reassessment opportunity  Standard UoL penalty applies  Team-working assignment There is no reassessment opportunity,  
Coursework  4 weeks  semester 2  40  Yes  Standard UoL penalty applies  Individual scripting project Notes (applying to all assessments) Notes (applying to all assessments) Assessment 1-3 Summative assessment of the course material providing an opportunity to use knowledge gained. Assessment 1-3 basics of python - A 1 Strings (DNA), maths and conditionals Learning outcomes 1 and 2 Assessment 2 - Arrays, hashes and command line arguments Learning outcomes 1 and 2 Assessment 3 - Regular expressions, working with files, controlling other programs (BLAST) Biopython and graphics Learning outcomes 1-5 Assessment 5 – Individual large scripting project to produce an analyses. Assessment 4 - Team-working assignment Learning outcomes 1-5, 7 and 8 Students must assign tasks of the project to different team members. The students will give a demonstration of the software in a presentation style (10%) and submit individual reports describing the software design and functions (10%). 

Aims

To provide a broad overview of the use of a scripting language for performing basic tasks in the biological sciences, with examples demonstrated through the use of  Python . 

Learning Outcomes

Use Python for basic scripting

Understand data structures in python and how to apply them to biological data

Use regular expressions for manipulating biological data

Use Python for manipulating files and controlling the running of external programs

Design and build simple relational databases

Teaching and Learning Strategies

Lecture - lectures to introduce key concepts

Large Group Learning - Workshops

Syllabus
1 

- Using Python for basic scripting

  1. - Data structures in Python and how to apply them to biological data
  2. - Regular expressions for manipulating biological data
  3. - Using  Python for manipulating files and controlling the running of external programs
  4. - Object oriented techniques
  5. - Designing and building simple relational databases

Recommended Texts
Reading lists are managed at readinglists.liverpool.ac.uk. Click here to access the reading lists for this module.
Explanation of Reading List: