Module Catalogue 2017/18

CSC8313 : Bioinformatics Theory and Practice

  • Offered for Year: 2017/18
  • Module Leader(s): Dr Jaume Bacardit
  • Lecturer: Professor Anil Wipat
  • Teaching Assistant: Dr Jennifer Warrender
  • Other Staff: Dr Simon Cockell
  • Owning School: Computing
  • Teaching Location: Newcastle City Campus
Semesters
Semester 1 Credit Value: 20
ECTS Credits: 10.0
Pre Requisites
Pre Requisite Comment

None.

Co Requisites
Co Requisite Comment

None.

Aims

To introduce the data that arises from studies in molecular biology.
To reinforce the theory underlying the concepts and techniques of sequence analysis and post-genomic bioinformatics.
An understanding of the distributed and available resources for bioinformatics analyses.

This module provides an understanding of the basic theory behind bioinformatics analyses and experience in practically applying that theory. The module introduces basic concepts of molecule biology, sequence analysis and genomic era biology. It introduces a number of many different tools and their usage, as well as the analysis algorithms behind some of them including BLAST and dynamic programming. Later parts of the module introduces the concepts behind modern postgenomic bioinformatics including material of biological pathways and networks.

Outline Of Syllabus

Basic concepts of molecular biology: genomes, transcripomes, proteomes.
Sequence analysis: genome annotation, sequence alignment, multiple sequence alignment.
Phylogenetic analysis.
Protein families.
Database searching tools.
Appropriate tools for performing the above.
Post genomic analysis: Gene and genomic comparison, protein structure, proteomics. Gene networks.
Human computer interaction for bioinformatics

Learning Outcomes

Intended Knowledge Outcomes

To be able to describe and discuss:
- genomes, genome sequencing, genomic structure and comparison.
- the fundamental theory of genome and post genomic analysis.
- the data arising from such studies.
- the application of computing and statistics to predictive biology.
- the technology for studies in modern post-genomic biology and the data that is generated by such studies.
- the advantages and shortcomings of various bioinformatics software tools.
- the appropriate application of a range of bioinformatics software.

Intended Skill Outcomes

The ability to demonstrate the use of much of the existing software for the analysis of genomic data.
The ability to apply knowledge of specific computational, mathematical and statistical techniques to the storage and analysis of biological data.
The ability to select the most appropriate bioinformatics tools for a given analysis.

Graduate Skills Framework

Graduate Skills Framework Applicable: Yes
  • Cognitive/Intellectual Skills
    • Critical Thinking : Assessed
    • Data Synthesis : Assessed
    • Active Learning : Present
    • Numeracy : Present
    • Literacy : Assessed
    • Information Literacy
      • Source Materials : Assessed
      • Synthesise And Present Materials : Assessed
      • Use Of Computer Applications : Assessed
  • Self Management
    • Self Awareness And Reflection : Present
    • Planning and Organisation
      • Goal Setting And Action Planning : Present
      • Decision Making : Present
    • Personal Enterprise
      • Innovation And Creativity : Present
      • Initiative : Assessed
      • Independence : Assessed
      • Problem Solving : Assessed
      • Adaptability : Present
  • Application
    • Occupational Awareness : Present

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion400:3020:00Revision for end of Semester exam & exam duration
Guided Independent StudyAssessment preparation and completion361:0036:00Lecture follow-up
Scheduled Learning And Teaching ActivitiesLecture361:0036:00Lectures
Scheduled Learning And Teaching ActivitiesPractical122:0024:00Practicals
Guided Independent StudyProject work122:0024:00Coursework
Guided Independent StudyIndependent study601:0060:00Background reading
Total200:00
Teaching Rationale And Relationship

Lectures will be used to introduce the learning material and for demonstrating the key concepts by example. Students are expected to follow-up lectures within a few days by re-reading and annotating lecture notes to aid deep learning.

This is a very practical subject, and it is important that the learning materials are supported by hands-on opportunities provided by practical classes. Students are expected to spend time on coursework outside timetabled practical classes.

Students aiming for 1st class marks are expected to widen their knowledge beyond the content of lecture notes through background reading.

Students should set aside sufficient time to revise for the end of semester exam.

Reading Lists

Assessment Methods

The format of resits will be determined by the Board of Examiners

Exams
Description Length Semester When Set Percentage Comment
Written Examination601A30N/A
Other Assessment
Description Semester When Set Percentage Comment
Essay1M20Max 2000 words
Report1M50Max 4000 words
Assessment Rationale And Relationship

The examination will assess the students knowledge of the fundamental theories of genome and post genomic
analysis and is an appropriate technique for assessing this work.
The practical component will assess the students ability to apply theory in the a practical setting and will be assessed as an essay and practical report, which are suitable methods for assessing
the use of bioinformatics software.

Study abroad students may request to take their exam before the semester 1 exam period, in which case the length of the exam may differ from that shown in the MOF.

N.B. This module has both “Exam Assessment” and “Other Assessment” (e.g. coursework). If the total mark for either assessment falls below 40%, the maximum mark returned for the module will normally be 40%.

Timetable

Past Exam Papers

General Notes

N/A

Disclaimer: The information contained within the Module Catalogue relates to the 2017/18 academic year. In accordance with University Terms and Conditions, the University makes all reasonable efforts to deliver the modules as described. Modules may be amended on an annual basis to take account of changing staff expertise, developments in the discipline, the requirements of external bodies and partners, and student feedback. Module information for the 2017/18 entry will be published here in early-April 2017. Queries about information in the Module Catalogue should in the first instance be addressed to your School Office.