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SOFT9018 - Appln Dev for Biosciences 1

Title:Appln Dev for Biosciences 1
Long Title:Application Development for Biosciences 1
Module Code:SOFT9018
Credits: 5
NFQ Level:Expert
Field of Study: Computer Software
Valid From: Semester 1 - 2013/14 ( September 2013 )
Module Delivered in 1 programme(s)
Module Coordinator: Donna OShea
Module Author:  
Module Description: This module teaches software development techniques relevant to computational biology. The emphasis is on assessing software development technologies and techniques suitable for processing data in an efficient and effective manner. Students will be able to apply best principles and practice in creating their software applications.
Learning Outcomes
On successful completion of this module the learner will be able to:
LO1 Evaluate different software development techniques suitable for computational biology.
LO2 Analyze a bioscience problem and synthesize an algorithm for that problem or a class of related problems.
LO3 Provide a synthesis of various programming elements and libraries to solve a set problem or class of problems in biosciences.
Pre-requisite learning
Module Recommendations
This is prior learning (or a practical skill) that is strongly recommended before enrolment in this module. You may enrol in this module if you have not acquired the recommended learning but you will have considerable difficulty in passing (i.e. achieving the learning outcomes of) the module. While the prior learning is expressed as named CIT module(s) it also allows for learning (in another module or modules) which is equivalent to the learning specified in the named module(s).
No recommendations listed
Incompatible Modules
These are modules which have learning outcomes that are too similar to the learning outcomes of this module. You may not earn additional credit for the same learning and therefore you may not enrol in this module if you have successfully completed any modules in the incompatible list.
No incompatible modules listed
Co-requisite Modules
No Co-requisite modules listed

This is prior learning (or a practical skill) that is mandatory before enrolment in this module is allowed. You may not enrol on this module if you have not acquired the learning specified in this section.


Module Content & Assessment

Indicative Content
High Level Language Basics
Types, variables, functions, development tools, functional languages, object oriented languages, dynamic programming languages, scripting.
Programming Types and Constructs
Scalar values and expressions, complex types; declarations and statements; selection and repeated computation; arrays and strings; procedural abstraction, parameter passing; threading and parallel processing constructs.
Classes, Responsibilities, Collaboration and Inheritance
Classes and objects, messages, encapsulation interfaces; behaviours; collaborating classes, extending classes.
Exception handling
Basic constructs - try.. catch.., exception propagation, throwing and declaring exceptions, standard exception types, contracts.
User Interfaces
Building basic GUIs, declaring and handling events.
Assessment Breakdown%
Course Work100.00%
Course Work
Assessment Type Assessment Description Outcome addressed % of total Assessment Date
Project Build an application that processes a large biological data set using appropriate technologies, complete with report. 1,2,3 50.0 Week 8
Other In Class Assessments 1,2,3 50.0 Every Second Week
No End of Module Formal Examination
Reassessment Requirement
Coursework Only
This module is reassessed solely on the basis of re-submitted coursework. There is no repeat written examination.

The institute reserves the right to alter the nature and timings of assessment


Module Workload

Workload: Full Time
Workload Type Workload Description Hours Frequency Average Weekly Learner Workload
Lecture Lecture 2.0 Every Week 2.00
Lab Lab 2.0 Every Week 2.00
Independent & Directed Learning (Non-contact) No Description 3.0 Every Week 3.00
Total Hours 7.00
Total Weekly Learner Workload 7.00
Total Weekly Contact Hours 4.00
This module has no Part Time workload.

Module Resources

Recommended Book Resources
  • Mark Lutz 2006, Programming Python, O'Reilly [ISBN: 0596009259]
  • M .L. Model 2008, Bioinformatics Programming Using Python: Practical Programming for Biological Data, O'Reilly [ISBN: 059615450X]
Supplementary Book Resources
  • Jason Kinser 2009, Python for bioinformatics, Jones and Bartlett Publishers Sudbury, Mass. [ISBN: 0763751863]
  • James D. Tisdall 2001, Beginning Perl for bioinformatics, 1 Ed., O'Reilly Media; California, USA [ISBN: 978-0596000806]
This module does not have any article/paper resources
Other Resources
  • http://www.biotechtools.org: BioTech Resource
  • http://www.bioinf.org/: Bioinformatics Resource

Module Delivered in

Programme Code Programme Semester Delivery
CR_SCMPB_9 Master of Science in Computational Biology 1 Elective

Cork Institute of Technology
Rossa Avenue, Bishopstown, Cork

Tel: 021-4326100     Fax: 021-4545343
Email: help@cit.edu.ie