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| || || ||P2. Python and !ScrumPy (Part 1) ||[[Meetings/Nepal2018/Prac2|Prac2]] ***instructions ||All || | || || ||P2. Python and !ScrumPy (Part 1) ||[[Meetings/Nepal2018/Prac2|Prac2]] ||All || |
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| || || ||P2. Python and !ScrumPy (Part 2) ||[[Meetings/Nepal2018/Prac2|Prac2]] ***instructions ||All || | || || ||P2. Python and !ScrumPy (Part 2) ||[[Meetings/Nepal2018/Prac2|Prac2]] ||All || |
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| || || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nepal2018/Prac3|Prac 3]] ***instructions ||All || | || || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nepal2018/Prac3|Prac 3]] ||All || |
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| || ||09:30 ||Demo for Prac4 (??) || || || | || ||09:30 ||Demo for Prac4 || ||MP|| |
| Line 47: | Line 47: |
| || ||'''PM''' ||L7. Building genome-scale metabolic networks **Swap with L8** ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] ||MP || || || ||P5. Flux Balance Analysis of fatty acid biosynthesis in ''E coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] ***instructions ||All || |
|| ||'''PM''' ||L7. The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] ||NM || || || ||P5. Flux Balance Analysis of alkane biosynthesis in ''E coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] ***instructions ||All || |
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| || ||09:30 ||L8. '''a''': The unique metabolism of ''Acetobacterium woodii''. **Swap With L7** '''b''': Beyond Structural Modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L8.pdf|Noah's slides]]; ||NM, EA || | || ||09:30 ||L8. '''a''': .Building genome-scale metabolic networks '''b''': Beyond Structural Modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L8.pdf|Slides]]; ||MP, EA || |
Workshop on Metabolic Modelling - Provisional Timetable
This timetable is not yet finalised. Both timings and content are liable to change, but the material here represents what will be covered in the talks.
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
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 |
|
|
|
|
P2. Python and ScrumPy (Part 2) |
All |
|
|
13:00 |
Lunch |
|
|
|
PM |
L3b. Examples of Elementary Modes Analysis |
DF |
|
|
|
L4. Biotechnological applications of metabolic network analysis |
DF |
|
|
|
Demo for Prac 3 |
|
TBC |
|
|
P3. Models, kernels, subsets and elementary modes |
All |
|
|
|
Break |
|
|
|
|
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 |
|
|
|
P5. Flux Balance Analysis of alkane biosynthesis in E coli. |
Prac 5 ***instructions |
All |
|
16:45 |
close |
|
|
Tuesday |
AM |
|
|
|
|
09:30 |
L8. a: .Building genome-scale metabolic networks b: Beyond Structural Modelling. |
MP, EA |
|
|
|
Intro to P6 - *** demonstrate datasets*** |
|
MP |
|
|
P6. Analysing a genome scale model |
Prac 6 ***instructions |
All |
|
11:00 |
Break |
|
|
|
|
L8 Modelling photosynthesis in eukaryotes (title TBC) |
**Need link to slides** |
KA |
|
13:00 |
Lunch |
|
All |
|
14:00 |
P6 ctd. |
|
All |
|
|
Closing remarks |
|
|
|
|
Certificates |
|
|
|
16:45 |
Depart |
|
|