Module Catalogue 2019/20

CSC8311 : Advanced Programming for Biologists

  • Offered for Year: 2019/20
  • Module Leader(s): Dr Jennifer Warrender
  • Owning School: Computing
  • Teaching Location: Newcastle City Campus
Semesters
Semester 2 Credit Value: 10
ECTS Credits: 5.0
Pre Requisites
Code Title
CSC8317Introductory Programming for Biologists
Pre Requisite Comment

CSC8317 or appropriate programming experience.

Co Requisites
Co Requisite Comment

None

Aims

To enhance scientific programming skills to a more advanced level.
To examine the scientific programming ecosystem.
To understand the importance of reproducible computational analysis.

This module aims to introduce more advanced concepts in programming that are essential for scientific programming. We will investigate further the many libraries in our chosen environment. We will examine scientific programming in practice, in a number of its different forms.

Outline Of Syllabus

Advanced issues in Programming
Libraries for Scientific Data analysis.
Tools for reproducible software engineering.
Case studies in software development within a scientific context.

Learning Outcomes

Intended Knowledge Outcomes

To be able to define and discuss:
- software for biomedical data analysis,
- the use of common libraries for biomedical data analysis
- the tools and methodology for reproducible software

Intended Skill Outcomes

The ability to demonstrate:
- the use and application of advanced tools, in support of software development within a group.
- communication of software designs within a group.
- the use and application of programming for manipulating biological data

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion351:0035:00Coursework
Scheduled Learning And Teaching ActivitiesPractical271:0027:00Practicals
Guided Independent StudyIndependent study381:0038:00Background reading
Total100:00
Teaching Rationale And Relationship

Scheduled learning and teaching activities will be used to introduce new concepts in Scientific Programming. We will investigate how to store and access data, to use software to build computational models, and to perform analysis over it, using state-of-the-art library support within our chosen software environment.

Other scheduled learning and teaching activities will be used to reinforce and expand the material presented in the scheduled learning and teaching activities and to discuss the findings of literature surveys on aspects of the technology introduced. A large practical component will help to build skills in scientific programming and large-scale data analysis.

Reading Lists

Assessment Methods

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

Other Assessment
Description Semester When Set Percentage Comment
Practical/lab report1M10030 hours
Assessment Rationale And Relationship

The practical and the subsequent report will test the students' enhanced understanding and ability to develop scientific programs, to make appropriate use of software enginneering tools, enabling reproducibility.

Timetable

Past Exam Papers

General Notes

Original Handbook text:

Disclaimer: The information contained within the Module Catalogue relates to the 2019/20 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 2020/21 entry will be published here in early-April 2019. Queries about information in the Module Catalogue should in the first instance be addressed to your School Office.