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Workshop: Metabolic Modelling and its Applications
27 - 30 June 2016
Tribhuvan University, Kirtipur, Kathmandu, Nepal
- The workshop is organised by Tribhuvan University and the Society for Biological Applications Nepal (SBAN).
A brief introduction to the workshop is available on the website for the SBAN.
Tutors
- The course is presented by:
- Dr Mark Poolman
- Prof David Fell
- Kailash Adhikari, and
- Dipali Singh
- all of Oxford Brookes University, Oxford, UK.
Examples presented in the workshop will include results from their research, which has been funded by the EU via the AccliPhot project and the BBSRC (UK).
Application
To apply for the workshop, complete the registration form an the SBAN website. If the workshop is over-subscribed, successful applicants will be selected and notified.
Instructions for workshop attendees
You are required to bring a laptop to the workshop. The metabolic modelling package used in the course, !ScrumPy, will be made available to you. The two options for installing ScrumPy on your computer are to directly install the package on a suitable Linux operating system, or to run a virtual machine under other operating system. Instructions are here. (TO BE UPDATED)
Timetable
- To help plan your attendance, the provisional workshop timetable is given below. The precise content and order of topics may be changed - even during the workshop itself!
Day |
Time |
Room |
Activity |
Resources |
Who |
Mon 27th, AM |
10:30 |
|
Arrival and registration |
|
SBAN |
11:00 |
|
Welcome talks |
|
MP + TU |
|
11:30 |
|
Talk: Introductory theory |
MP |
||
12:30 |
|
Lunch |
|
All |
|
Mon 27th, PM |
14:00 |
|
Talk: Python, object-orientation and models. |
MP |
|
15:00 |
|
Practical 0: Checking ScrumPy Installation and familiarisation with the Python language. |
All |
||
17:30 |
|
Close |
|
|
|
Tue 28th, AM |
09:30 |
|
Talk: Structural analysis of small models. (+ break) |
DF |
|
11:00 |
|
Talk: Introduction to plant metabolism and its modelling |
Slides |
DS, KA and MP |
|
12:30 |
|
Lunch |
|
|
|
Tue 28th, PM |
14:00 |
|
Practical 1: Structural analysis of small models |
All |
|
17:00 |
|
Close |
|
|
|
Wed 29th, AM |
09:30 |
|
Talk: Sources of data for metabolic models |
DF |
|
10:15 |
|
Talk: Construction of Genome-Scale Models |
MP |
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11:15 |
|
Talk: Linear Programming and Flux Balance Analysis |
MP |
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Talk: Linear Programming and Flux Balance Analysis |
MP |
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12:30 |
|
Lunch |
|
|
|
Wed 29th, PM |
14:00 |
|
Practical 2a: Construction of a working ScrumPy model from databases |
All |
|
15:30 |
|
Practical 2a: Flux Balance Analysis of a simple model |
All |
||
17:00 |
|
Close |
|
|
|
Thur 30th, AM |
09:30 |
|
Talk: Biotechnological Applications of Metabolic Network Analysis |
DF |
|
10:30 |
|
Talk: Genome scale modelling of Arabidopsis |
tbp |
KA |
|
11:30 |
|
Talk: Genome scale modelling of a diatom for oil production |
tbp |
DS |
|
12:30 |
|
Lunch |
|
|
|
Thur 30th, PM |
14:00 |
|
Practical 3: GSM of Arabidopsis – metabolic phenotypes of mutants – metabolic responses to light intensity |
All |
|
16:30 |
|
Concluding remarks and presentation of certificates |
|
All |
|
17:00 |
|
Close of the Workshop |
|
|