C1net Workshop 4 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
The venue for the course is the Regent Suite, The Park Hotel.
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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