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| 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 talk. | 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. |
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| ||'''Thursday''' ||'''AM''' ||Admin & Registration || || || ||28/06/18 || ||Opening Ceremony || || || || || ||Welcome and introduction to the course || ||DF || || || ||Lunch || || || || ||'''PM''' ||L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L1.pdf|Slides]] ||DF || |
||'''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 ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L0.pdf|Slides]] ||DF || || ||13:00 ||Lunch || || || || ||'''PM''' || || || || || ||14:00 ||L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L1.pdf|Slides]] ||DF || |
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| || || || || || || ||'''Friday''' ||'''AM''' ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3.pdf|Slides]] ||NM || || || ||Demo for Prac 2.|| ||TBC|| || || ||P2. Python and !ScrumPy (Part 1) ||[[Meetings/Nepal2018/Prac2|Prac2]] ***instructions ||All || || || ||Break || || || || || ||P2. Python and !ScrumPy (Part 2) ||[[Meetings/Nepal2018/Prac2|Prac2]] ***instructions ||All || || || ||Lunch || || || || ||'''PM''' ||L4. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4.pdf|Slides]] ||DF || || || ||Demo for Prac 3|| ||TBC|| || || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/C1netWork4/Prac3|Prac 3 instructions]] ||All || |
|| ||!6:45 ||Close || || || ||'''Friday''' ||'''AM''' || || || || || ||09:30 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3.pdf|Slides]] ||NM || || || ||Demo for Prac 2. || ||TBC || || || ||P2. Python and !ScrumPy (Part 1) ||[[Meetings/Nepal2018/Prac2|Prac2]] ||All || || ||11:00 ||Break || || || || || ||P2. Python and !ScrumPy (Part 2) ||[[Meetings/Nepal2018/Prac2|Prac2]] ||All || || ||13:00 ||Lunch || || || || ||'''PM''' ||L3b. Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3b.pdf|Slides]] ||DF || || || ||L4. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4.pdf|Slides]] [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||DF || || || ||Demo for Prac 3 || ||TBC || || || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nepal2018/Prac3|Prac 3]] ||All || |
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| || || ||<<BR>> ||<<BR>> || || ||'''Monday'''||'''AM'''||Demo for Prac4 (??)|| || || || || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||ALL || || || ||Break || || || |
|| ||16:45 ||Close || || || ||'''Monday''' || || || || || || ||09:30 ||Demo for Prac4 || ||MP || || || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/Nepal2018/Prac4|Prac 4]] ***instructions ||ALL || || ||11:00 ||Break || || || |
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| || || ||L6. Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L6.pdf|Slides]] ||DF || || || ||Lunch || || || || ||'''PM''' ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] ||MP || || || ||P5. Flux Balance Analysis of fatty acid biosynthesis in ''E coli''. ||[[Meetings/C1netWork4/Prac6|Prac 5 instructions]] ||All || || || || || || || ||'''Tuesday''' || ||L8. '''a''': The unique metabolism of ''Acetobacterium woodii''. '''b''': Beyond Structural Modelling. ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's slides]]; ||NM, EA || || || ||P6. Analysing a genome scale model ||[[Meetings/C1NetWork4/Prac7|Instructions]] ||All || || || ||Break || || || |
|| || ||L6. Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L6.pdf|Slides]] ||DF || || ||13:00 ||Lunch || || || || ||'''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 || || ||16:45 ||close || || || ||'''Tuesday''' ||'''AM''' || || || || || ||09:30 ||L8. '''a''': .Building genome-scale metabolic networks '''b''': Beyond Structural Modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L8.pdf|Slides]]; ||MP, EA || || || ||Intro to P6 - *** demonstrate datasets*** || ||MP || || || ||P6. Analysing a genome scale model ||[[Meetings/Nepal2018/Prac6|Prac 6]] ***instructions ||All || || ||11:00 ||Break || || || |
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| || || ||Lunch || ||All || || || ||P6 ctd. || ||All || |
|| ||13:00 ||Lunch || ||All || || ||14:00 ||P6 ctd. || ||All || |
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| || || || || || || | || ||16:45 ||Depart || || || |
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 |
|
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