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CSC8324 : Modelling Cellular Systems

  • Offered for Year: 2021/22
  • Module Leader(s): Dr Paolo Zuliani
  • Owning School: Computing
  • Teaching Location: Newcastle City Campus
Semester 1 Credit Value: 10
ECTS Credits: 5.0


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.
Modelling discrete stochastic systems.
Parameter estimation and inference.
Biological hypothesis generation.
Model optimisation.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Structured Guided LearningLecture materials61:006:00Asynchronous online lecture material.
Guided Independent StudyAssessment preparation and completion101:0010:00Coursework for summative assignment.
Guided Independent StudyAssessment preparation and completion12:002:00Formative assessment coursework.
Scheduled Learning And Teaching ActivitiesLecture61:006:00PIP teaching lectures
Scheduled Learning And Teaching ActivitiesPractical64:0024:00Asynchronous online lab practicals.
Guided Independent StudyDirected research and reading241:0024:00Lecture follow up.
Scheduled Learning And Teaching ActivitiesDrop-in/surgery21:002:00Tutorial for summative assessment (week 3 and 4). PiP
Guided Independent StudyIndependent study221:0022:00Background reading.
Scheduled Learning And Teaching ActivitiesScheduled on-line contact time22:004:00Online sessions with demonstrators.
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 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 and in teams.

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
Description Semester When Set Comment
Practical/lab report1MCompulsory formative assessment: A preliminary report on the model for a modelling exercise. Max 500 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