Workshop on Metabolic 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)
Reading List
A reading list for topics covered in the course is provided here.
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Lecturer |
Thursday |
AM |
|
|
|
28/06/18 |
09:00 |
Admin & Registration |
|
|
|
10:00 |
Opening Ceremony |
|
|
|
10:30 |
Introductions. Each participant introduces themself in 2-3 sentences: name, place of study/work; what they do. |
|
Everyone |
|
11:00 |
Tea |
|
|
|
11:30 |
Welcome and introduction to the course |
DF |
|
|
13:00 |
Lunch |
|
|
|
PM |
|
|
|
|
14:00 |
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. |
All |
|
!6:45 |
Close |
|
|
Friday |
AM |
|
|
|
|
09:30 |
L3. Null space and elementary modes |
NM |
|
|
|
Demo for Prac 2. |
|
TBC |
|
|
P2. Python and ScrumPy (Part 1) |
All |
|
|
11:00 |
Break |
|
|
|
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P2. Python and ScrumPy (Part 2) |
All |
|
|
13:00 |
Lunch |
|
|
|
PM |
L3b. Examples of Elementary Modes Analysis |
DF |
|
|
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L4. Biotechnological applications of metabolic network analysis |
DF |
|
|
|
Demo for Prac 3 |
|
TBC |
|
|
P3. Models, kernels, subsets and elementary modes |
All |
|
|
|
Break |
|
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P3. Models, kernels, subsets and elementary modes (continued) |
|
All |
|
16:45 |
Close |
|
|
Monday |
|
|
|
|
|
09:30 |
Demo for Prac4 |
|
MP |
|
|
P4. Structural analysis of the Calvin Cycle. |
Prac 4 ***instructions |
ALL |
|
11:00 |
Break |
|
|
|
|
L5. Linear Programming and Flux Balance Analysis |
NM |
|
|
|
L6. Sources of data for metabolic models |
DF |
|
|
13:00 |
Lunch |
|
|
|
PM |
L7. The unique metabolism of Acetobacterium woodii |
NM |
|
|
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P5. Flux Balance Analysis of alkane biosynthesis in E coli. |
All |
|
|
16:45 |
close |
|
|
Tuesday |
AM |
|
|
|
|
09:30 |
L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP |
MP, DF |
|
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P5 Flux Balance Analysis of alkane biosynthesis in E coli. |
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|
|
11:00 |
Break |
|
|
|
|
Practical 5 continues |
|
|
|
13:00 |
Lunch |
|
|
|
14:00 |
L9 Modelling photosynthesis in eukaryotes. |
KA |
|
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L10 Beyond structural modelling |
|
EA |
|
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Closing and Presentation of Certificates |
|
|
|
16:45 |
Depart |
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