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| https://mudsharkstatic.brookes.ac.uk/Nottingham2022/DraftTT.pdf |
Under Construction - Ignore !
Overview
https://mudsharkstatic.brookes.ac.uk/Nottingham2022/DraftTT.pdf
Workshop on Metabolic Modelling
Nottingham 2022
Tutors
- Mark Poolman (MP: Oxford Brookes University)
- David Fell (DF: Oxford Brookes University)
- Yanica Said (YS: Oxford Brookes University)
- Dipali Singh (DS: Quadram Institute, Norwich)
- Nicole Pearcy (NP: University of Nottingham)
Guest Speaker
- Prof. John Wain (JW: Quadram Institute, Norwich)
Reading List
A reading list for topics covered in the course is provided here.
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Lecturer |
Tuesday |
AM |
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|
03/04/22 |
09:00 |
Arrival, Admin & Registration |
|
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PM |
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12:00 |
Lunch |
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13:00 |
Welcome and introduction to the course. Outline of the week. |
' |
MP et al |
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Lecture 1: Title TBC |
|
JW |
|
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Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
DF |
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Tea/coffee |
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Lecture 3: Python and computational representation of metabolic networks. |
MP |
|
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P1. Computers: checking internet connectivity, software installation. |
Installation of ScrumPy. |
All |
|
|
Close |
|
|
Wednesday |
AM |
|
|
|
|
09:00 |
L3. Null space and elementary modes |
NP |
|
|
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Demo for Prac 2. |
|
MP |
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P2. Python and ScrumPy (Part 1) |
All |
|
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11:00 |
Break |
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P2. Python and ScrumPy (Part 2) |
All |
|
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13:00 |
Lunch |
|
|
|
PM |
L3b. Examples of Elementary Modes Analysis |
DF |
|
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L4. Biotechnological applications of metabolic network analysis |
DF |
|
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Demo for Prac 3 |
|
TBC |
|
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P3. Models, kernels, subsets and elementary modes |
All |
|
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Break |
|
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P3. Models, kernels, subsets and elementary modes (continued) |
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All |
|
16:45 |
Close |
|
|
Thursday |
|
|
|
|
|
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 |
|
|
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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 |
|
|
Friday |
AM |
|
|
|
|
09:30 |
L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP |
MP, DF |
|
|
|
P5 Flux Balance Analysis of alkane biosynthesis in E coli. |
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|
|
11:00 |
Break |
|
|
|
|
Practical 5 continues |
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|
|
13:00 |
Lunch |
|
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Conclusions |
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