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Module Specifications

Current Academic Year 2012 - 2013
Please note that this information is subject to change.

Module Title Next Gen. Sequencing Techn. & Systems Biology
Module Code BET501
School School of Biotechnology
Online Module Resources

Module Co-ordinatorSemester 1: Michael Parkinson
Semester 2: Michael Parkinson
Autumn: Michael Parkinson
Module TeacherMichael Parkinson
NFQ level 8 Credit Rating 7.5
Pre-requisite None
Co-requisite None
Compatibles None
Incompatibles None
Description
This course will provide an introduction to the perl programming language and associated bioperl modules. The course will have two principal foci (1) How interact with the UNIX envirounment and automate computational tasks (e.g. using loops), and (2) provide the students with the programming skills necessary to handle, store and analyse biological data. Topics will cover: Proramming styles (Imperative versus Object Oriented programming), Control Flow (e.g. while, for, foreach loops, and if statements) data structures (scalars, arrays, hashes, and complex data structures – e.g. multidimensional arrays), handling I/Os, subroutines, perl packages, and bioperl.

Learning Outcomes
1. 1. Use the linux environment and file hierarchy.
2. 2. Create linux shell scripts for the repetitive analysis of large datasets.
3. 3. Program in the perl language: opening and closing files, read and write to files, use regular expressions and complex data structures.
4. 4. Develop bespoke perl programs for the analyses of biological datasets, and automate tasks in the UNIX envirounment.
5. 5. Effective and efficient use and applicaton of the Bioperl modules.
6. 6. Analyse biological datasets/problems and implement programming solutions.
7. 7. Design, implement and rigorously test bespoke software for sequence bioinformatics and be able to work alone on a defined project.
8. Note: This module entails hands on computer laboratory work.



Workload Full-time hours per semester
Type Hours Description
Lecture24giving all the theory, descriptions and worked examples for the students on Perl and Unix environments
Laboratory8.5Practical workshops: Hands on experience of writing code – supervised by lecturer. Students will be given small problems to solve during these sessions. They will be given time to design solutions and implement them. The lecturer will be on hand to discuss with them possible ways to improve their code, thereby providing immediate feedback. Using these sample codes they will then be given a larger related problem to solve for their continuous assessment.
Assignment100analysis of biological data for systems biology and next generation sequencing
Independent learning time55reading of supplied materials
Total Workload: 187.5

All module information is indicative and subject to change. For further information,students are advised to refer to the University's Marks and Standards and Programme Specific Regulations at: http://www.dcu.ie/registry/examinations/index.shtml

Indicative Content and Learning Activities
None
Assessment Breakdown
Continuous Assessment100% Examination Weight0%
Course Work Breakdown
TypeDescription% of totalAssessment Date
Assignmentcontinuous assessment project involving design of bespoke software for pattern finding in biological data.35%n/a
Reassessment Requirement
Resit arrangements are explained by the following categories;
1 = A resit is available for all components of the module
2 = No resit is available for 100% continuous assessment module
3 = No resit is available for the continuous assessment component
This module is category 1
Indicative Reading List
  • James D. Tisdall: 0, Beginning Perl for bioinformatics, 978-0-596-00080-6
  • Arnold Robbins and Nelson H. F. Beebe: 2005, Classic shell scripting, O'Reilly, Sebastopol, CA, 978-0-596-00595-5
Other Resources
None
Array
Programme or List of Programmes
MBIOMSc in Bioinformatics
Timetable this semester: Timetable for BET501
Date of Last Revision02-FEB-11
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