Instructor: Matthieu Bultelle, Geoff Baldwin.
Room: Biochemistry building, 310.
- This is the OWW page dedicated to the 2009 Synbio Computer Modelling Tutorials
- This page is still a work in progress. It will be complemented as the course progresses.
- Please come back often!
Regarding the Coursework
- The practical details are still to be finalised but you can expect the following
- One piece of coursework is to be handed in to your departmental secretary
- Departmental rules regarding deadlines will apply
- A paper and an electronic version are to be submitted
- Deadline for BioEngineers: 5pm 6th Feb
- We expect you to submit a coursework that is clear,concise and well presented. Here are a few tips:
- Reply to the questions in order
- Indicate clearly what question you reply to
- Indicate clearly what your answer is.
- Do not forget to label your simulations...
- Please keep your answers short
- But not too short of course: you still have to detail your reasoning and how you have come up to your answer
- Your coursework should be written in English.
- This may sound obvious but it means it should be easy to read
- This also means that equations are a means to an end! Use them to support your argumentation but do not forget to explain what they mean.
- Relevant simulations should be included and commented.
Computer Lab Overview
- Short Presentation: "All the models are wrong, but some of them are useful", George Box.
- Short Presentation: CellDesigner Crash Course (Thank you vincent)
- Features and GUI
- Kinetic Simulations
- Hands-on: Build your first kinetic models.
Practical 2: Enzymatic Reactions(2h)
- Description and Simulation of a standard Enzymatic reaction
- The Steady State Approximation
Practical 3: Gene Expression Modelling (2h)
- Constitutive Gene Expression
- Activated and Repressed Gene Expression
- Mystery Circuit
- 30th January: It has been brought to my attention that the questions regarding the reressilator were not explicit enough. I have therefore changed them a bit. Hope it is better now
- March the 9th: I would like to remind the life-scientists that for them the section on the mystery circuit is not compulsory for their coursework. However, I strongly advise them to have a look at it as it is very useful for the rest of the course.