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| This is an activity of the collaborative project [[UKIPA|Development of Metabolic Models to Support Systems Biology Approaches to Bioenergy Research]] | |
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| == About the Workshop == Why here? Why now? See the [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/intro.pdf|introductory slides]]. |
'''ICGEB, 7-11 October 2013''' |
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| This second workshop will cover kinetic modelling of metabolism and Metabolic Control Analysis, with an emphasis on their application to biotechnology and metabolic engineering. | This was an activity of the collaborative project [[UKIPA|Development of Metabolic Models to Support Systems Biology Approaches to Bioenergy Research]] |
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| == Practical Sessions == Participants are invited to bring their own laptops to the practicals to supplement the available computing resources. |
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| === Software Requirements === If you can bring a laptop, please follow [[Meetings/Riga2013/Practicals/ScrumPyVM|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 [[http://gnuplot.info/|GnuPlot]] plotting package; this is included with the ScrumPy virtual machine, but Windows users can download it from [[http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.3/|this site]], choosing the 'gp463-win32-setup.exe' option. |
The [[Programme]] and instructions are now on their own page. |
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| === Model Files === The model files we will be using, and referred to in the instructions below, can be found [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Models/|here.]] |
== Workshop Group Photos == |
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| == 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. |
{{attachment:Group1_small.jpg|alt Group photo1}} |
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| ==== 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: [[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, PM ||[[Meetings/Delhi2013/Practicals/Practical_1|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: [[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.|| || ||Tue 8th, PM ||[[Meetings/Delhi2013/Practicals/Practical_2|Practical 2]]: Brief Python introduction; kinetic modelling with {{{ScrumPy}}} ||David Fell; Mark Poolman; Amar Ghaisas || ||Wed 9th, AM ||Session 3: [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_mca1.pdf|Understanding the control of metabolism]], [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_mca2.pdf|Applications of metabolic control analysis]] ||David Fell; Mark Poolman || || ||Student presentations: Ritu Som, Kamran Jawed, Trunil Desai, Asish Sharma. || || ||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 || ||Thu 10th, AM ||Session 4: [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Slides/wshop2_mca3.pdf|Case studies in biotechnology and metabolic engineering]]. ||David Fell; Mark Poolman || || ||Student presentations: Jaya Anand Gupta, 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 || |
{{attachment:Group2_small.jpg|alt Group photo2}} Full quality versions of these can be downloaded: [[attachment:Group1.jpg|Group photo1]] and [[attachment:Group2.jpg|Group photo2]] Not exactly on the workshop timetable, but see if you can spot two of us [[https://www.facebook.com/nagalandk?rf=123263314424845|here]]. |
Delhi Workshop on Metabolic Modelling 2013
ICGEB, 7-11 October 2013
This was an activity of the collaborative project Development of Metabolic Models to Support Systems Biology Approaches to Bioenergy Research
The Programme and instructions are now on their own page.
Workshop Group Photos
Full quality versions of these can be downloaded: Group photo1 and Group photo2
Not exactly on the workshop timetable, but see if you can spot two of us here.