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Workshop on Metabolic Modelling
Introduction to Structural Modelling
Tutors
- David Fell (DF: Oxford Brookes University)
- Mark Poolman (MP: Oxford Brookes University)
- Noah Mesfin (NM: Oxford Brookes University)
- Ela Al-Saidi (ES: Oxford Brookes University)
- Kailash Adhikari (KA)
Course Timetable and Resources Index
Contents below are subject to modification, especially the links.
Day |
Time |
Activity |
Links |
Lecturer |
Thursdaay |
|
Admin & Registration |
|
|
28/06/18 |
|
Lunch |
|
|
|
|
Opening and introductions |
|
DF |
|
|
L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week |
DF |
|
|
|
Tea/coffee |
|
|
|
|
L2. Computational representation of metabolic networks |
MP |
|
|
|
P1. Computers: checking internet connectivity, software installation. |
Installation of ScrumPy. |
DF, MP, TDC,NM |
|
|
|
|
|
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Friday |
|
|
|
|
29/06/18 |
|
L3. Null space and elementary modes |
MP |
|
|
|
P2. Python and ScrumPy |
Prac2 instructions |
DF, MP, TDC,NM |
|
|
Coffee/Tea |
|
|
|
|
P2. Python and ScrumPy (continued) |
Prac2 instructions |
DF, MP, TDC,NM |
|
|
|
|
|
|
|
L4. Biotechnological applications of metabolic network analysis L4a. Elementary modes analysis of novel product synthesis. |
DF, NP |
|
|
|
P3. Models, kernels, subsets and elementary modes |
All |
|
|
|
|
|
|
|
15:45 |
P3. Models, kernels, subsets and elementary modes (continued) |
|
All |
|
|
Close |
|
|
|
|
|
|
|
|
|
|
|
|
Saturday |
|
|
|
|
30/06/18 |
|
L5. Linear Programming and Flux Balance Analysis |
MP |
|
|
|
L6. Sources of data for metabolic models |
DF |
|
|
|
Coffee/Tea |
|
|
|
|
P4. Structural analysis of the Calvin Cycle. |
DF, MP, TDC,NM |
|
|
|
|
|
|
|
|
L7. Building genome-scale metabolic networks |
MP |
|
|
|
P5. Building a ScrumPy model from databases |
All |
|
|
|
|
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|
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Sunday |
|
|
|
|
01/07/18 |
09:00 |
L8. a, Acetobacterium woodii. b. Cupriavidus necator |
NM, NP |
|
|
|
|
|
|
|
11:00 |
P6. Flux Balance Analysis of fatty acid biosynthesis in E coli. |
All |
|
|
|
|
|
|
|
|
L8 c. Clostridium autoethanogenum. L9. Modelling metabolism of Non-Aureus Staphylococci |
RN, TDC |
|
|
|
P6 continued |
|
All |
|
|
Tea/Coffee |
|
|
|
|
P7. Analysing a genome scale model |
All |
|
|
|
Close |
|
|
|
|
Dinner |
|
|
|
|
|
|
|
Monday |
|
Breakfast |
|
|
02/07/18 |
|
P7 continued |
|
All |
|
|
|
|
|
|
|
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|
All |
|
|
|
|
DF& MP |
Tuesday |
|
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|
|
03/07/18 |
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