Biochemistry Honours 2025

BCH714: Computational Systems Biology Minicourse

17 March – 15 April 2025

Prof Johann Rohwer, Prof Jacky Snoep & Dr Dawie van Niekerk
Laboratory for Molecular Systems Biology, Dept. of Biochemistry, Stellenbosch University

Course schedule

• Face-to-face lectures will take place in the Biochemistry Seminar Room (A111).
• Face-to-face computer practicals and data analysis will take place in the computer lab (JC Smuts B215, departmental computers or own laptops).
• Practical enzyme kinetics experiments will take place in the molecular systems biology lab (JC Smuts B203A).

Course material

• MSB book (PDF)
• Biochem 323 Notes (PDF)

Lectures (slides and supplementary materials)

• Lecture 1 (PDF)
• Data for Exercise 2
• Lecture 1: Answers to problems (PDF)
• Lecture 2 (PDF)
• Lecture 2: Answers to problems (PDF)
• Lecture 3 (PDF)
• Lecture 3: Answers to problems (PDF)
• Lecture 4 (PDF)
• Lecture 5 (PDF)
• Research Lecture (Rohwer) (PDF)

Tutorials and Computer sessions

• Memos will be provided in the Download section after each tutorial.
• Tutorial 2: Chemical kinetics and energetics (PDF)
• Data files available in Download section.
• Tutorial 3: Enzyme-catalysed reactions (PDF)
• Data files available in Download section.
• Tutorial 4: Structural analysis of reaction networks (PDF)
• Tutorial 5: The kinetic model (PDF)
• Tutorial 6: Metabolic control analysis (PDF)
• Skeleton notebook available in Download section.

Assessments

Assessment 1 — Tutorial test

Instructions available here.
Answer the questions in a Mathematica notebook. Hand in the notebook via the dedicated assignment link on STEMLearn.
Time: 2.5 hours (150 minutes)

Practical

Data analysis programme and Assessment

Schedule, groups and instructions

Kinetic mechanisms for rate equations

Reports

Your group's report in PDF format should be submitted via SUNLearn.
• Deadline: Tuesday 15 April 2025 at 23:59.
• On the first page, be sure to include:
• Your group number (e.g. 2B).
• Names and student numbers of your group members.
• NB: Only one report to be submitted per group! Any one of the group members can submit via STEMLearn.

File Downloads

• Download section

Mathematica resources

• Download Mathematica trial here
• Create a Wolfram ID to download. Use your SU email address.
• Hands-on Start to Mathematica
• An Elementary Introduction to the Wolfram Language
• Click on "Read Online"
• Same course in interactive video format here. You will need a Wolfram ID to gain access.
• Pay special attention to Chapters 1 - 11, 24, 28, 30 - 31
• Consult the extensive and searchable Help documentation of Mathematica once installed.
• Getting started with Mathematica