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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)
- Rupert Norman (RN: University of Nottingham)
- Nicole Pearcy (NP: University of Nottingham)
- Teresa Diaz Calvo (TDC: University of East Anglia)
Course Timetable and Resources Index
Contents below are subject to modification, especially the links.
Day |
Time |
Activity |
Links |
Lecturer |
Monday |
12:00 |
Registration opens at The Park Hotel |
|
|
15/1/18 |
12:30 |
Lunch |
|
|
|
13:30 |
Opening and introductions |
|
DF |
|
14:00 |
L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week |
DF |
|
|
15:30 |
Tea/coffee |
|
|
|
16:00 |
L2. Computational representation of metabolic networks |
MP |
|
|
17:00 |
P1. Computers: checking internet connectivity, software installation. |
Installation of ScrumPy. |
DF, MP, TDC,NM |
|
18:00 |
Close and room registration (cont) |
|
|
|
19:00 |
Dinner (resident delegates only) |
|
|
|
|
|
|
|
Tuesday |
08:00 |
Breakfast (resident delegates only) |
|
|
16/1/18 |
09:00 |
L3. Null space and elementary modes |
MP |
|
|
10:00 |
P2. Python and ScrumPy |
Prac2 instructions |
DF, MP, TDC,NM |
|
10:30 |
Coffee/Tea |
|
|
|
10:45 |
P2. Python and ScrumPy (continued) |
Prac2 instructions |
DF, MP, TDC,NM |
|
12:30 |
Lunch |
|
|
|
13:30 |
L4. Biotechnological applications of metabolic network analysis L4a. Elementary modes analysis of novel product synthesis. |
DF, NP |
|
|
14:30 |
P3. Models, kernels, subsets and elementary modes |
All |
|
|
15:30 |
Tea/Coffee |
|
|
|
15:45 |
P3. Models, kernels, subsets and elementary modes (continued) |
|
All |
|
17:30 |
Close |
|
|
|
19:00 |
Dinner |
|
|
|
|
|
|
|
Wednesday |
08:00 |
Breakfast |
|
|
17/1/18 |
09:00 |
L5. Linear Programming and Flux Balance Analysis |
MP |
|
|
10:00 |
L6. Sources of data for metabolic models |
DF |
|
|
10:30 |
Coffee/Tea |
|
|
|
11:00 |
P4. Structural analysis of the Calvin Cycle. |
DF, MP, TDC,NM |
|
|
12:30 |
Lunch |
|
|
|
13:30 |
L7. Building genome-scale metabolic networks |
MP |
|
|
14:30 |
P5. Building a ScrumPy model from databases |
All |
|
|
15:30 |
Tea/Coffee |
|
|
|
15:30 |
Free time (Hotel sports facilities/ Nottingham Castle?) |
|
|
|
19:00 |
Workshop dinner (All participants) |
|
|
|
|
|
|
|
Thursday |
08:00 |
Breakfast |
|
|
18/1/18 |
09:00 |
L8. a, Acetobacterium woodii. b. Cupriavidus necator |
NM, NP |
|
|
10:30 |
Coffee/Tea |
|
|
|
11:00 |
P6. Flux Balance Analysis of fatty acid biosynthesis in E coli. |
All |
|
|
12:30 |
Lunch |
|
|
|
13:30 |
L8 c. Clostridium autoethanogenum. L9. Modelling metabolism of Non-Aureus Staphylococci |
RN, TDC |
|
|
14:30 |
P6 continued |
|
All |
|
15:30 |
Tea/Coffee |
|
|
|
16:00 |
P7. Analysing a genome scale model |
All |
|
|
17:30 |
Close |
|
|
|
19:00 |
Dinner |
|
|
|
|
|
|
|
Friday |
08:00 |
Breakfast |
|
|
19/1/18 |
09:00 |
P7 continued |
|
All |
|
10:30 |
Coffee/Tea |
|
|
|
11:00 |
Discussion of results and prospective applications of modelling in attendees' projects |
|
All |
|
12:00 |
Any questions? Closing remarks |
|
DF& MP |
|
12:30 |
(Sandwich?) lunch and departure |
|
|
|
|
|
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