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CS904 Computational Biology

CS904-15 Computational Biology

Academic year
20/21
Department
Computer Science
Level
Taught Postgraduate Level
Module leader
Till Bretschneider
Credit value
15
Module duration
10 weeks
Assessment
Multiple
Study location
University of Warwick main campus, Coventry
Introductory description

The module will cover topics on the acquisition of and analysis of large-scale data generated in biomedical sciences, particularly DNA/RNA sequences, live cell microscopy and multi-gigapixel pathology images. Students will be introduced to how these data are acquired, modern machine learning methods to process the data, and computational modelling approaches to help us better understand the complex phenomena underpinning biological processes. The module will be taught following an "algorithmic approach," demonstrating that addressing problems in computational biology requires a diverse range of theoretical concepts and algorithms, making it an exciting and rapidly evolving field for computer scientists.

Module aims

The module is designed to develop student research skills in the broad area of computational biology.

Outline syllabus

This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.

  • Molecular biology fundamentals;
  • Sequence alignments;
  • Phylogenetic Trees;
  • Dimensionality reduction and clustering;
  • Live cell microscopy fundamentals;
  • Image based modelling of single cell dynamics;
  • Introduction to tissue imaging and computational pathology;
  • Whole-slide image (WSI) handling and processing;
  • Recognising various kinds of cells in cancerous WSIs;
  • Advanced research topics in computational biology;
Learning outcomes

By the end of the module, students should be able to:

  • Have an understanding of how tissue slides are imaged with high throughput
  • Have a basic grasp of fundamental molecular biology concepts as relevant to this module
  • Understand some basic and commonly used algorithms in bioinformatics
  • Know algorithms to compute sequence alignments and how these are applied in current research
  • Understand basic problems in the processing and analysis of tissue images and some standard solutions to those
  • Be able to apply image analysis and machine learning to real-world computational pathology problems
  • Understand principles of fluorescence microscopy and image-based modelling of single cell dynamics
Indicative reading list

Zvelebil, M., and Baum, J.O., Understanding Bioinformatics. Garland Science, 2008;
Kremling, A., Systems Biology. CRC Press, 2014;
Pantanowitz, L., and Parwani, A., Digital Pathology. ASCP, 2017;
Alberts, B., et al., Essential cell biology: an introduction to the molecular biology of the cell (5/e). Garland, 2008.

Research element

Students need to develop and implement algorithms to address questions typically asked in current research projects. For example: Perform sequence analysis of homologous genes and construct phylogenetic trees, generate simulation data of gene regulatory networks and perform dimensionality reduction and clustering, develop models for cellular dynamics, analyze digital pathology images taken from real-world data.

Interdisciplinary

The module will cover a broad range of techniques used in biology, mathematics, and computer science.

Subject specific skills

By the end of the module, students will have acquired skills in:

  • Implementing fundamental bioinformatics algorithms for computing alignments and phylogenetic trees
  • Formulating and solving mathematical models of gene regulatory networks
  • Applying methods of dimensionality reduction and clustering
  • Formulating mathematical models of cellular dynamics
  • Handling and processing of whole-slide images (WSI) data
  • Recognising various kinds of cells in cancerous WSIs
Transferable skills

 Technical - Technological competence and staying current with knowledge
 Communication - Verbal, listening, writing, technical communication skills, using different medium for communicating
 Critical Thinking - Problem-solving, analysis of possible solutions etc
 Creativity - Ability to harnass creative ideas and turn them into tangible and strategic products/solutions

Study time

Type Required
Lectures 20 sessions of 1 hour (13%)
Supervised practical classes 10 sessions of 1 hour (7%)
Private study 120 hours (80%)
Total 150 hours
Private study description

Background reading of research papers, working through additional examples and improving coding skills, revision.

Costs

No further costs have been identified for this module.

You do not need to pass all assessment components to pass the module.

Students can register for this module without taking any assessment.

Assessment group C3
Weighting Study time
Assignment 1, Assignment 2, and Assignment 3 50%

3 assignments are given on the following topics, each having the given overall weighting:
Sequence analysis, phylogenetic trees and gene regulatory networks - 16.6%
Cellular dynamics - 16.7%
Digital pathology - 16.7%

CS904 Examination 50%

CS904 examination

~Platforms - AEP

Assessment group R
Weighting Study time
CS904 resit examination. 100%

CS904 resit examination.

~Platforms - AEP

Feedback on assessment

Written comments on coursework

Past exam papers for CS904

Courses

This module is Core optional for:

  • Year 1 of TBSA-C1P9 Postgraduate Taught Systems Biology

This module is Optional for:

  • TCOS-F3P6 Complex Systems Science (Erasmus Mundus)
    • Year 2 of F3P6 Complex Systems Science
    • Year 2 of F3PJ Complex Systems Science (Ecole Polytechnique/Chalmers University)
    • Year 2 of F3PK Complex Systems Science (Ecole Polytechnique/Gothenburg)
  • TCOS-F3P7 Complex Systems Science (Erasmus Mundus) (University of Warwick)
    • Year 2 of F3PH Complex Systems Science (Double Degree with Chalmers University)
    • Year 2 of F3PG Complex Systems Science (Double Degree with Ecole Polytechnique)
    • Year 2 of F3PJ Complex Systems Science (Ecole Polytechnique/Chalmers University)
    • Year 2 of F3PK Complex Systems Science (Ecole Polytechnique/Gothenburg)
    • Year 2 of F3P7 Complex Systems Science (University of Warwick)
  • TCYA-G5P5 MSc in Scientific Computing
    • Year 1 of G5P5 Scientific Computing
    • Year 2 of G5P5 Scientific Computing
  • TCSA-G5PD Postgraduate Taught Computer Science
    • Year 1 of G5PD Computer Science
    • Year 1 of G5PD Computer Science
  • Year 1 of TCSA-G5P8 Postgraduate Taught Computer Science and Applications
  • Year 1 of TMAA-G1PF Postgraduate Taught Mathematics of Systems
  • Year 1 of TBSA-C1P9 Postgraduate Taught Systems Biology

This module is Option list A for:

  • TCOS-F3P6 Complex Systems Science (Erasmus Mundus)
    • Year 1 of F3P6 Complex Systems Science
    • Year 1 of F3PJ Complex Systems Science (Ecole Polytechnique/Chalmers University)
    • Year 1 of F3PK Complex Systems Science (Ecole Polytechnique/Gothenburg)
  • TCOS-F3P7 Complex Systems Science (Erasmus Mundus) (University of Warwick)
    • Year 1 of F3PH Complex Systems Science (Double Degree with Chalmers University)
    • Year 1 of F3PG Complex Systems Science (Double Degree with Ecole Polytechnique)
    • Year 1 of F3PJ Complex Systems Science (Ecole Polytechnique/Chalmers University)
    • Year 1 of F3PK Complex Systems Science (Ecole Polytechnique/Gothenburg)
    • Year 1 of F3P7 Complex Systems Science (University of Warwick)
  • Year 1 of RMAA-G1PG Postgraduate Research Mathematics of Systems
  • Year 1 of TMAA-G1PF Postgraduate Taught Mathematics of Systems

This module is Option list B for:

  • Year 5 of UCSA-G504 MEng Computer Science (with intercalated year)
  • Year 4 of UCSA-G402 MEng Computing Systems
  • Year 5 of UCSA-G403 MEng Computing Systems (Intercalated Year)
  • Year 4 of UCSA-G503 Undergraduate Computer Science MEng

Further Information

Term 2

15 CATS

Online Material