Module Catalogue 2019/20

CSC8317 : Introductory Programming for Biologists

  • Offered for Year: 2019/20
  • Module Leader(s): Dr Jennifer Warrender
  • Owning School: Computing
  • Teaching Location: Newcastle City Campus
Semesters
Semester 1 Credit Value: 10
ECTS Credits: 5.0
Pre Requisites
Pre Requisite Comment

None.

Co Requisites
Co Requisite Comment

None.

Aims

To introduce the concept of computer programming.
To explain what is meant by an algorithm.
To teach students how to devise algorithms and approaches to tackle biological problems.
To provide a grounding in program design and implementation, programming environments and introduce practical exercises in writing bioinformatics software using a specific programming language.

The ability to write computer programs is a skill that is essential for working in fields that lie at the interface between computing and biology. An understanding of how to program is also a skill that is becoming increasingly useful for biologists as biology becomes more of a data-rich science. This module places an emphasis on clear design and development of programs, teaching how to break problems down to provide simpler and easier to use solutions; biological examples are used where-ever possible. You will apply your skills at a practical level with a commonly used bioinformatics programming language. The basic skills learnt here can be applied to any programming language.

Outline Of Syllabus

What is programming?
The building blocks and structure of computer programs.
Tackling a biological problem.
Algorithms and some examples.
Introduction to a programming language for bioinformatics.
Methods and data structures for nucleotide and protein sequence handling and analysis.

Learning Outcomes

Intended Knowledge Outcomes

To be able to describe and discuss:
- what is meant by programming a computer.
- how to break down a problem into a form suitable for solving with a program.
- what algorithms are and how to devise them.
- how to design, implement, test and debug software.
- the application of computer programming to biological problems.

Intended Skill Outcomes

To be be able to:
- formulate a systematic computational approach to biological problems.
- devise a programmatic approach to computational problems in biology.
- implement programs using a programming language.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion280:3014:00Revision for end of Semester exam & exam duration
Guided Independent StudyAssessment preparation and completion121:0012:00Coursework
Guided Independent StudyAssessment preparation and completion241:0024:00Lecture follow-up
Scheduled Learning And Teaching ActivitiesLecture241:0024:00Lectures
Scheduled Learning And Teaching ActivitiesPractical121:0012:00Practicals
Guided Independent StudyIndependent study141:0014:00Background reading
Total100:00
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 Examination901A30Open book exam
Other Assessment
Description Semester When Set Percentage Comment
Practical/lab report1M70Programmatic code. (20 hours)
Assessment Rationale And Relationship

The examination will assess the students’ understanding of program and algorithm design, basic programming concepts and the use of an object oriented language. The coursework will assess the students’ ability to use this understanding in a practical setting.

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 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.