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| ||Mon 7th, AM ||Session 1: [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_1.pdf|Revision]] of mathematical representation of metabolic networks. [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_2.pdf|Enzyme kinetics for modelling]]||David Fell; Mark Poolman || | ||Mon 7th, AM ||Session 1: [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_1.pdf|Revision]] of mathematical representation of metabolic networks. [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_2.pdf|Enzyme kinetics for modelling]] ||David Fell; Mark Poolman || |
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| ||Tue 8th, AM ||Session 2: [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_3.pdf|Enzyme kinetics for model building]]; [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/Tues_am_Mark.pdf | Building kinetic models with ScrumPy]]||David Fell; Mark Poolman || ||Tue 8th, PM ||[[Meetings/Delhi2013/Practicals/Practical_2|Practical 2]]: Brief Python introduction; kinetic modelling with {{{ScrumPy}}} ||David Fell; Mark Poolman || |
||Tue 8th, AM ||Session 2: [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_3.pdf|Enzyme kinetics for model building]]; [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/Tues_am_Mark.pdf|Building kinetic models with ScrumPy]] ||David Fell; Mark Poolman || || ||Student presentations: Anu Jose Mattam, Zia Fatma, Nandita Pasari, Neetu Tyagi, Ritu Som.|| || ||Tue 8th, PM ||[[Meetings/Delhi2013/Practicals/Practical_2|Practical 2]]: Brief Python introduction; kinetic modelling with {{{ScrumPy}}} ||David Fell; Mark Poolman; Amar Ghaisas || |
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| ||Wed 9th, PM ||[[Meetings/Delhi2013/Practicals/Practical_3|Practical 3]]: Kinetic modelling with {{{ScrumPy}}} continued, plus calculation of control coefficients ||David Fell; Mark Poolman || | || ||Student presentations: Neha Munjal, Mohd Kamran, Trunil Desai, Asish Sharma, Jaya Anand Gupta|| || ||Wed 9th, PM ||[[Meetings/Delhi2013/Practicals/Practical_3|Practical 3]]: Kinetic modelling with {{{ScrumPy}}} continued, plus calculation of control coefficients ||David Fell; Mark Poolman; Amar Ghaisas || |
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| ||Thu 10th, PM ||[[Meetings/Delhi2013/Practicals/Practical_4|Practical 4]]: Simulation of pathway optimisation. Close and presentation of certificates ||David Fell; Mark Poolman || | || ||Student presentations: Nidhi Adlaka, Tabinda Shakeel, Ahmad Ahmad, Deepti Mann|| || ||Thu 10th, PM ||[[Meetings/Delhi2013/Practicals/Practical_4|Practical 4]]: Simulation of pathway optimisation. Close and presentation of certificates ||David Fell; Mark Poolman; Amar Ghaisas || |
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
Why here? Why now? See the introductory slides.
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.
Software Requirements
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 on USB memory sticks. 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.
Model Files
The model files we will be using, and referred to in the instructions below, can be found here.
Provisional Timetable
Student Contributions
The last hour of the morning sessions will be given over to student presentations. Students will be informed later as to the exact timetabling of their talks. Plan on a 10 minute talk with 5 to 6 slides.
Typical daily timetable
Mornings, 9:30 -12:30 (Monday 10:00 - 12:30); Lunch 12:30 - 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 solution to a two enzyme system; rough time course calculation for an enzyme-catalysed reaction |
David Fell; Mark Poolman |
Tue 8th, AM |
Session 2: Enzyme kinetics for model building; Building kinetic models with ScrumPy |
David Fell; Mark Poolman |
|
Student presentations: Anu Jose Mattam, Zia Fatma, Nandita Pasari, Neetu Tyagi, Ritu Som. |
|
Tue 8th, PM |
Practical 2: Brief Python introduction; kinetic modelling with ScrumPy |
David Fell; Mark Poolman; Amar Ghaisas |
Wed 9th, AM |
Session 3: Understanding the control of metabolism, Applications of metabolic control analysis |
David Fell; Mark Poolman |
|
Student presentations: Neha Munjal, Mohd Kamran, Trunil Desai, Asish Sharma, Jaya Anand Gupta |
|
Wed 9th, PM |
Practical 3: Kinetic modelling with ScrumPy continued, plus calculation of control coefficients |
David Fell; Mark Poolman; Amar Ghaisas |
Thu 10th, AM |
Session 4: for feedback inhibtion and enzyme over-expression. Case studies in biotechnology and metabolic engineering. |
David Fell; Mark Poolman |
|
Student presentations: Nidhi Adlaka, Tabinda Shakeel, Ahmad Ahmad, Deepti Mann |
|
Thu 10th, PM |
Practical 4: Simulation of pathway optimisation. Close and presentation of certificates |
David Fell; Mark Poolman; Amar Ghaisas |