Registry

Module Specifications

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

Module Title	Biocomputing
Module Code	CA658
School	School of Computing
Online Module Resources
Module Co-ordinator	Semester 1: Heather Ruskin Semester 2: Heather Ruskin Autumn: Ray Walshe
NFQ level	8	Credit Rating	7.5
Pre-requisite	None
Co-requisite	None
Compatibles	None
Incompatibles	None

Description

This module builds on the foundation courses, particularly in Data Analysis, incorporating complementary information on computational and analytical methods. Provided is an introduction to Python and its structure for purposes of biodata processing, simulation and modelling principles and an overview of database construction and function, together with a review of major bioinformatics resources. A case study, illustrating the elements of an investigation, incorporating these features, will also be discussed.

Learning Outcomes

1. 'demonstrate' that they understand Python simple command structure
2. 'demonstrate' that they understand how components of a database function/how queries are handled
3. 'demonstrate' that they appreciate the range of bioinfomatics resources
4. 'demonstrate' that they understand how basic models are formulated and simulation objectives
5. 'demonstrate' that they understand the steps involved in a formal investigation, based on a widely-used technology

Workload	Full-time hours per semester
*Type*	*Hours*	*Description*
Lecture	36	No Description
Laboratory	24	No Description
Assignment	55	of form describd
Independent learning	72.5	No Description
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

Introduction to Databases.
Definitions, hierarchy, DBMS, data Models and development, Common and current types. relationship definitions and classifications.

Relational databases - in depth.
Concepts, Constraints and types, Primary/foreign keys, SQL function and primer,Basic queries, clauses.

Bio Databases.
Primary, Secondary, compositeData types and stored informationExamples for sequence and structure.

Simple Alignments and Beyond.
Visual Methods and Similarity MeasuresScoring schemes and SubstitutionAutomating - Dynamic Programming & variantsHeuristics and h-methodsMSA/Algorithm outlines & tools and how it works - database search/alignmentExamplesSimple metrics to models for alignment - HMM /MarkovModel basis.

Structure.
Putting it together for predicting structureSimilarity scores and metricsProbabilistic models and simulation, MC,ANN, Homology models, MDResources and status quo on automation.

Assessment Breakdown
Continuous Assessment	25%	Examination Weight	75%

Course Work Breakdown
Type	Description	% of total	Assessment Date
Group assignment	Practical questions on biological database search and identification/alignment/classification/evolutionary tree generation, using different resources. Case study (cross-resource) on investigation, modelling and analysis of given data set or condition.	25%	Week 7

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 3

Indicative Reading List

Gibas G. and Jambeck P.: 2001, Developing Bioinformatics Computer Skills, O' Reilly & associates,
Bergeron B.: 2002, Bioinformatics Computing, Prentice-Hall,
Moorhouse M. and Barry P.: 2004, Bioinformatics, Biocomputing & Perl: An Introduction to Bioinformatics Computing Skills and Practice, John Wiley & Sons,

Other Resources

1646, Frosch C., 0, A Short introduction to Biocomputing, http://www.imib.med.uni-rostock.de/bc4s/example.html,

Relevant examples from the current literature will be selected for practical questions/illustrations.

Programme or List of Programmes

CAPD

CAPM

CAPT

EEPD