Delhi Workshop on Metabolic Modelling 2013
This is an activity of the collaborative project Development of Metabolic Models to Support Systems Biology Approaches to Bioenergy Research
About the Workshop
This second workshop will cover kinetic modelling of metabolism and Metabolic Control Analysis, with an emphasis on their application to biotechnology and metabolic engineering.
Practical Sessions
Participants are invited to bring their own laptops to the practicals to supplement the available computing resources.
If you can bring a laptop, please follow these instructions to install ScrumPy on it before the workshop. If the files are too large for Windows users to download, at least try installing the VirtualBox software, and we will supply the ScrumPy virtual machine file at the workshop. We will also use the GnuPlot plotting package; this is included with the ScrumPy virtual machine, but Windows users can download it from this site, choosing the 'gp463-win32-setup.exe' option.
Provisional Timetable
Student Contributions
The last hour of the first four morning sessions will be given over to student presentations. Students will be informed later as to the exact timetabling of their talks.
Typical daily timetable
Mornings, 9:30 -12:30 (Monday 10:00 - 12:30); Lunch 12:1300 - 14:00; Afternoons, 14:00 - 17:00 (at the latest)
Time |
Activity |
Who |
Mon 7th, AM |
Session 1: Revision of mathematical representation of metabolic networks. Enzyme kinetics for modelling |
David Fell; Mark Poolman |
Mon 7th, PM |
Practical 1: Plotting enzyme kinetic functions; graphical soluton to a two enzyme system; rough time course calculation for an enzyme-catalysed reaction |
David Fell; Mark Poolman |
Tue 8th, AM |
Session 2: Building kinetic models of metabolism (? Model optimisation?) |
David Fell; Mark Poolman |
Tue 8th, PM |
Practical 2: Brief Python introduction; kinetic modelling with ScrumPy |
David Fell; Mark Poolman |
Wed 9th, AM |
Session 3: Metabolic control analysis - understanding the control of metabolic fluxes and metabolite concentrations |
David Fell; Mark Poolman |
Wed 9th, PM |
Practical 3: Kinetic modelling with ScrumPy continued, plus calculation of control coefficients |
David Fell; Mark Poolman |
Thu 10th, AM |
Session 4: Implications of metabolic control analysis for feedback inhibtion and enzyme over-expression. Case studies in biotechnology and metabolic engineering. |
David Fell; Mark Poolman |
Thu 10th, PM |
Practical 4: Simulation of pathway optimisation |
David Fell; Mark Poolman |
Fri 11th, AM |
Session 5: Review and Conclusion: choosing the appropriate metabolic modelling methodology for the problem. Close and presentation of certificates. |
David Fell; Mark Poolman |