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| = !!! Page under construction - Ignore it!!! = = Workshop on Metabolic Modelling = == Introduction to Structural Modelling == __'''Note: **Items** in the timetable in represent new material.'''__ |
= 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 talk. |
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| == Course Timetable and Resources Index == Contents below are subject to modification, especially the links. |
== Course Timetable and Resources == |
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| ||'''Thursday''' || ||Admin & Registration || || || ||28/06/18 || ||Lunch || || || || || ||Opening and introductions || ||DF || || || ||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''' ||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 || |
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| ||'''Friday''' ||'''AM''' ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3.pdf|Slides]] ||NM || || || ||P2. Python and !ScrumPy ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM || || || ||Break || || || || || ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM || || || ||Lunch || || || || ||'''PM''' ||L4. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4.pdf|Slides]] ||DF || || || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/C1netWork4/Prac3|Prac 3 instructions]] ||All || || || ||Break || || || || || ||P3. Models, kernels, subsets and elementary modes (continued) || ||All || |
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| ||'''Monday''' ||'''AM''' ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L5.pdf|Slides]] ||NM || || || ||L6. Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L6.pdf|Slides]] ||DF || || || ||Break || || || || || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||ALL || || || ||Lunch || || || || ||'''PM''' ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] ||MP || || || ||P5. Building a !ScrumPy model from databases ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork4/Prac5|Prac 5 instructions]] ||All || ||*******||******||I think we should scrap P5 - we don't do any LP/FBA practicals until the last day||******||*******|| |
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| ||'''Friday''' || || || || || ||29/06/18 || ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3.pdf|Slides]] ||NM || || || ||P2. Python and !ScrumPy ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM || || || || || || || || || ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM || || || || || || || || || ||L4. Biotechnological applications of metabolic network analysis L4a.**L4 B need something else (was Nicole)** ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4.pdf|Slides]] ||DF, ** ?? ** || || || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/C1netWork4/Prac3|Prac 3 instructions]] ||All || || || || || || || || ||15:45 ||P3. Models, kernels, subsets and elementary modes (continued) || ||All || || || ||Close || || || || || || || || || || || || || || || ||'''Saturday''' || || || || || ||30/06/18 || ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L5.pdf|Slides]] ||NM || || || ||L6. Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L6.pdf|Slides]] ||DF || || || ||Coffee/Tea || || || || || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||DF, MP, TDC,NM || || || || || || || || || ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L7.pdf|Slides]] ||MP || || || ||P5. Building a !ScrumPy model from databases ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork4/Prac5|Prac 5 instructions]] ||All || || || || || || || || || || || || || || || || || || || || || || || || || ||'''Sunday''' || || || || || ||01/07/18 ||09:00 ||L8. a, ''Acetobacterium woodii''. b.''** Need soething else (was Nicole) **'' ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's slides]]; ||NM, **??** || || || || || || || || ||11:00 ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E coli''. ||[[Meetings/C1netWork4/Prac6|Prac 6 instructions]] ||All || || || || || || || || || ||L8 ** what to do here? Was Rupert and Maite's talks (Ask Kailash)** || ||**?KA?** || |
||'''Tuesday''' || ||L8. a, ''Acetobacterium woodii''. b.''** Need soething else ?? Mark or Ela ?? (was Nicole) **'' ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's slides]]; ||NM, **??** || || || ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E coli''. ||[[Meetings/C1netWork4/Prac6|Prac 6 instructions]] ||All || || || ||L8 Modelling photosynthesis in eukaryotes (title TBC) ||**Need link to slides** ||KA || |
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| ||'''Monday''' || ||Breakfast || || || ||02/07/18 || ||P7 continued || ||All || || || || || || || || || || || ||All || || || || || ||DF& MP || ||'''Tuesday''' || || || || || ||03/07/18 || || || || || |
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 talk.
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 |
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 |
DF |
|
|
|
Tea/coffee |
|
|
|
|
L2. Computational representation of metabolic networks |
MP |
|
|
|
P1. Computers: checking internet connectivity, software installation. |
Installation of ScrumPy. |
DF, MP, TDC,NM |
|
|
|
|
|
Friday |
AM |
L3. Null space and elementary modes |
NM |
|
|
|
P2. Python and ScrumPy |
Prac2 instructions |
DF, MP, TDC,NM |
|
|
Break |
|
|
|
|
P2. Python and ScrumPy (continued) |
Prac2 instructions |
DF, MP, TDC,NM |
|
|
Lunch |
|
|
|
PM |
L4. Biotechnological applications of metabolic network analysis |
DF |
|
|
|
P3. Models, kernels, subsets and elementary modes |
All |
|
|
|
Break |
|
|
|
|
P3. Models, kernels, subsets and elementary modes (continued) |
|
All |
|
|
|
|
|
Monday |
AM |
L5. Linear Programming and Flux Balance Analysis |
NM |
|
|
|
L6. Sources of data for metabolic models |
DF |
|
|
|
Break |
|
|
|
|
P4. Structural analysis of the Calvin Cycle. |
ALL |
|
|
|
Lunch |
|
|
|
PM |
L7. Building genome-scale metabolic networks |
MP |
|
|
|
P5. Building a ScrumPy model from databases |
All |
|
******* |
****** |
I think we should scrap P5 - we don't do any LP/FBA practicals until the last day |
****** |
******* |
|
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|
Tuesday |
|
L8. a, Acetobacterium woodii. b.** Need soething else ?? Mark or Ela ?? (was Nicole) ** |
NM, **??** |
|
|
|
P6. Flux Balance Analysis of fatty acid biosynthesis in E coli. |
All |
|
|
|
L8 Modelling photosynthesis in eukaryotes (title TBC) |
**Need link to slides** |
KA |
|
|
P6 continued |
|
All |
|
|
Tea/Coffee |
|
|
|
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P7. Analysing a genome scale model |
All |
|
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Close |
|
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|
|
Dinner |
|
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