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CSC8324 : Modelling Cellular Systems

  • Offered for Year: 2024/25
  • Module Leader(s): Dr Tim Rudge
  • Lecturer: Dr Harold Fellermann
  • Owning School: Computing
  • Teaching Location: Newcastle City Campus

Your programme is made up of credits, the total differs on programme to programme.

Semester 1 Credit Value: 10
ECTS Credits: 5.0
European Credit Transfer System


To understand how biological systems can be represented at different levels of abstraction.

To introduce a range of computational modelling approaches and to select an appropriate modelling strategy for a given biological domain and problem.

To understand how models may be used to represent cellular machinery at a systems level and how models can be used to generate biological hypotheses.

Outline Of Syllabus

- Introduction to modelling biochemical systems.
- Abstraction and levels of abstraction in modelling.
- Structural models: ER modelling and network models.
- Metabolic modelling using flux balance analysis.
- Dynamic modelling using continuous differential equations.
- Simulation.
- Modelling discrete stochastic systems.
- Parameter estimation and inference.
- Biological hypothesis generation.
- Model optimisation.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion14:004:00Formative assessment coursework.
Guided Independent StudyAssessment preparation and completion72:0014:00Coursework for summative assignment.
Structured Guided LearningLecture materials160:4512:00Revise lecture material.
Scheduled Learning And Teaching ActivitiesLecture161:0016:00Lectures online or pre-recorded
Scheduled Learning And Teaching ActivitiesPractical73:0021:00Asynchronous online lab practicals.
Scheduled Learning And Teaching ActivitiesPractical42:008:00In person practical sessions with demonstrators
Scheduled Learning And Teaching ActivitiesDrop-in/surgery41:004:00Drop-in tutorials (weeks 1-4)
Guided Independent StudyIndependent study211:0021:00Background reading.
Teaching Rationale And Relationship

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

Tutorials will be used to provide opportunities to clarify lecture material.

Practicals will be used to emphasise the learning material and its application to the solution of problems and exercises set as coursework, during which students will analyse problems as individuals.

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.

Assessment Methods

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

Other Assessment
Description Semester When Set Percentage Comment
Practical/lab report1M100Summative Assessment: A practical report on a more advanced modelling exercise. Max 2,000 words.
Formative Assessments

Formative Assessment is an assessment which develops your skills in being assessed, allows for you to receive feedback, and prepares you for being assessed. However, it does not count to your final mark.

Description Semester When Set Comment
Practical/lab report1MCompulsory formative assessment: A preliminary report on the model for a modelling exercise. Max 750 words
Assessment Rationale And Relationship

The coursework will assess the students’ ability to understand and apply the concepts of a range of a biological modelling theories and techniques to a given biological system. The first coursework component is a compulsory formative assessment which will assess the students growing knowledge of the field and provide feedback. The second component is a summative assessment testing the students’ ability to apply the theory they have learnt at the end of the module.

Reading Lists