MEIN40240 Systems Biology

Academic Year 2023/2024

This module gives an overview of systems biology and its applications, with a particular focus on the mathematical and computational approaches used in modelling biochemical reaction pathways in cell biology.



Course outline: Introduction to systems biology (basic concepts), Overview of the relevant mathematical background: differential equations, nonlinear dynamics; Overview of mathematical software: MATLAB, xppaut; Dynamical models of biochemical reactions: law of mass action, reaction networks, enzyme kinetics; Dynamical control in signal transduction networks: protein modification cycles, signaling cascades, positive and negative feedback, switches and bistability, bifurcations and oscillations; Advanced topics in modelling: Combinatorial domain interactions, Rule based modelling (BioNetGen), Modelling of cell populations; Perspectives on systems medicine.



The course will provide a guided tour of the relevant systems biology research literature, discussions of the underlying theoretical concepts, practical experience with some popular computational tools available, and a discussion of applications to systems medicine.

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Curricular information is subject to change

Learning Outcomes:

On completion of this module students will:
1. be familiar with the research literature in systems biology and be able to understand mathematical and computational modelling approaches used in systems biology.
2. be able to formulate mathematical models based on differential equations for biological reaction pathways.
3. be familiar with the key concepts of nonlinear dynamical systems the use of mathematical approaches to analyse reaction pathway models
4. be able to use computational software tools to simulate and analyse biochemical reaction pathways (Matlab, xppaut, BioNetGen)

Indicative Module Content:

Course outline: Introduction to systems biology (basic concepts), Overview of the relevant mathematical background: differential equations, nonlinear dynamics; Overview of mathematical software: MATLAB, xppaut; Dynamical models of biochemical reactions: law of mass action, reaction networks, enzyme kinetics; Dynamical control in signal transduction networks: protein modification cycles, signaling cascades, positive and negative feedback, switches and bistability, bifurcations and oscillations; Advanced topics in modelling: Combinatorial domain interactions, Rule based modelling (BioNetGen), Modelling of cell populations; Perspectives on systems medicine.

Student Effort Hours: 
Student Effort Type Hours
Lectures

20
Specified Learning Activities

20
Autonomous Student Learning

60
Total

100
Approaches to Teaching and Learning:
Lectures - mostly chalk and talk - to learn about mathematical modelling and analysis (theory)
Tutorials - computer based - to learn how to simulate / analyse biological systems in (praxis)
Student based activities - examples - lectures are interspiked with student-based activities using examples to reinforce the learned theoretical concepts
Reading assignments - lecture notes, research articles - 
Requirements, Exclusions and Recommendations

Not applicable to this module.


Module Requisites and Incompatibles
Not applicable to this module.
 
Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade
Continuous Assessment: Small assignments throughout the course of the module. Varies over the Trimester n/a Graded Yes

100

Carry forward of passed components
No
 
Remediation Type Remediation Timing
In-Module Resit Prior to relevant Programme Exam Board
Please see Student Jargon Buster for more information about remediation types and timing. 
Feedback Strategy/Strategies

• Feedback individually to students, post-assessment
• Group/class feedback, post-assessment

How will my Feedback be Delivered?

Not yet recorded.

Timetabling information is displayed only for guidance purposes, relates to the current Academic Year only and is subject to change.
 

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