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⇤ ← Revision 1 as of 2018-06-12 12:51:22
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| * Rupert Norman (RN: University of Nottingham) * Nicole Pearcy (NP: University of Nottingham) * Teresa Diaz Calvo (TDC: University of East Anglia) |
* Ela Al-Saidi (ES: Oxford Brookes University) * Kailash Adhikari (KA) |
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| ||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' || ||'''Thursdaay''' || ||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 || || || ||Tea/coffee || || || || || ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L2.pdf|Slides]] ||MP || || || ||P1. Computers: checking internet connectivity, software installation. ||[[Meetings/C1netWork4/ScrumPyInstall|Installation]] of !ScrumPy. ||DF, MP, TDC,NM || || || || || || || || || || || || || || || || || || || ||'''Friday''' || || || || || ||29/06/18 || ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L3.pdf|Slides]] ||MP || || || ||P2. Python and !ScrumPy ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM || || || ||Coffee/Tea || || || || || ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM || || || || || || || || || ||L4. Biotechnological applications of metabolic network analysis L4a. Elementary modes analysis of novel product synthesis. ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4.pdf|Slides]] [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4_NP_EMA.pdf|Slides]] ||DF, NP || || || ||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]] ||MP || || || ||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. ''Cupriavidus necator'' ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's slides]]; [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NP_GS.pdf|Nicole's slides]] ||NM, NP || || || || || || || || ||11:00 ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E coli''. ||[[Meetings/C1netWork4/Prac6|Prac 6 instructions]] ||All || || || || || || || || || ||L8 c. ''Clostridium autoethanogenum''. L9. Modelling metabolism of Non-Aureus Staphylococci ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_RN.pdf|Rupert's slides]]; [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L9_Maite.pdf|Maite's slides]] ||RN, TDC || || || ||P6 continued || ||All || || || ||Tea/Coffee || || || || || ||P7. Analysing a genome scale model ||[[Meetings/C1NetWork4/Prac7|Instructions]] ||All || || || ||Close || || || || || ||Dinner || || || || || || || || || ||'''Monday''' || ||Breakfast || || || ||02/07/18 || ||P7 continued || ||All || || || || || || || || || || || ||All || || || || || ||DF& MP || ||'''Tuesday'''|| || || || || ||03/07/18 || || || || || |
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| ||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' || ||'''Monday''' ||12:00 ||Registration opens at The Park Hotel || || || ||15/1/18 ||12:30 ||Lunch || || || || ||13:30 ||Opening and introductions || ||DF || || ||14:00 ||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 || || ||15:30 ||Tea/coffee || || || || ||16:00 ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L2.pdf|Slides]] ||MP || || ||17:00 ||P1. Computers: checking internet connectivity, software installation. ||[[Meetings/C1netWork4/ScrumPyInstall|Installation]] of !ScrumPy. ||DF, MP, TDC,NM || || ||18:00 ||Close and room registration (cont) || || || || ||19:00 ||Dinner (resident delegates only) || || || || || || || || || ||'''Tuesday''' ||08:00 ||Breakfast (resident delegates only) || || || ||16/1/18 ||09:00 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L3.pdf|Slides]] ||MP || || ||10:00 ||P2. Python and !ScrumPy ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM || || ||10:30 ||Coffee/Tea || || || || ||10:45 ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM || || ||12:30 ||Lunch || || || || ||13:30 ||L4. Biotechnological applications of metabolic network analysis L4a. Elementary modes analysis of novel product synthesis. ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4.pdf|Slides]] [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4_NP_EMA.pdf|Slides]] ||DF, NP || || ||14:30 ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/C1netWork4/Prac3|Prac 3 instructions]] ||All || || ||15:30 ||Tea/Coffee || || || || ||15:45 ||P3. Models, kernels, subsets and elementary modes (continued) || ||All || || ||17:30 ||Close || || || || ||19:00 ||Dinner || || || || || || || || || ||'''Wednesday''' ||08:00 ||Breakfast || || || ||17/1/18 ||09:00 ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L5.pdf|Slides]] ||MP || || ||10:00 ||L6. Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L6.pdf|Slides]] ||DF || || ||10:30 ||Coffee/Tea || || || || ||11:00 ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||DF, MP, TDC,NM || || ||12:30 ||Lunch || || || || ||13:30 ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L7.pdf|Slides]] ||MP || || ||14:30 ||P5. Building a !ScrumPy model from databases ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork4/Prac5|Prac 5 instructions]] ||All || || ||15:30 ||Tea/Coffee || || || || ||15:30 ||'''Free time (Hotel sports facilities/ Nottingham Castle?) ''' || || || || ||19:00 ||'''Workshop dinner (All participants)<<BR>>''' || || || || || || || || || ||'''Thursday''' ||08:00 ||Breakfast || || || ||18/1/18 ||09:00 ||L8. a, ''Acetobacterium woodii''. b. ''Cupriavidus necator'' ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's slides]]; [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NP_GS.pdf|Nicole's slides]] ||NM, NP || || ||10:30 ||Coffee/Tea || || || || ||11:00 ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E coli''. ||[[Meetings/C1netWork4/Prac6|Prac 6 instructions]] ||All || || ||12:30 ||Lunch || || || || ||13:30 ||L8 c. ''Clostridium autoethanogenum''. L9. Modelling metabolism of Non-Aureus Staphylococci ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_RN.pdf|Rupert's slides]]; [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L9_Maite.pdf|Maite's slides]] ||RN, TDC || || ||14:30 ||P6 continued || ||All || || ||15:30 ||Tea/Coffee || || || || ||16:00 ||P7. Analysing a genome scale model ||[[Meetings/C1NetWork4/Prac7|Instructions]] ||All || || ||17:30 ||Close || || || || ||19:00 ||Dinner || || || || || || || || || ||'''Friday''' ||08:00 ||Breakfast || || || ||19/1/18 ||09:00 ||P7 continued || ||All || || ||10:30 ||Coffee/Tea || || || || ||11:00 ||Discussion of results and prospective applications of modelling in attendees' projects || ||All || || ||12:00 ||Any questions? Closing remarks || ||DF& MP || || ||12:30 ||(Sandwich?) lunch and departure || || || || || || || || || |
!!! Page under construction - Ignore it!!!
Workshop on Metabolic Modelling
Introduction to Structural 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)
Course Timetable and Resources Index
Contents below are subject to modification, especially the links.
Day |
Time |
Activity |
Links |
Lecturer |
Thursdaay |
|
Admin & Registration |
|
|
28/06/18 |
|
Lunch |
|
|
|
|
Opening and introductions |
|
DF |
|
|
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 |
|
|
|
|
29/06/18 |
|
L3. Null space and elementary modes |
MP |
|
|
|
P2. Python and ScrumPy |
Prac2 instructions |
DF, MP, TDC,NM |
|
|
Coffee/Tea |
|
|
|
|
P2. Python and ScrumPy (continued) |
Prac2 instructions |
DF, MP, TDC,NM |
|
|
|
|
|
|
|
L4. Biotechnological applications of metabolic network analysis L4a. Elementary modes analysis of novel product synthesis. |
DF, NP |
|
|
|
P3. Models, kernels, subsets and elementary modes |
All |
|
|
|
|
|
|
|
15:45 |
P3. Models, kernels, subsets and elementary modes (continued) |
|
All |
|
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Close |
|
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|
|
|
Saturday |
|
|
|
|
30/06/18 |
|
L5. Linear Programming and Flux Balance Analysis |
MP |
|
|
|
L6. Sources of data for metabolic models |
DF |
|
|
|
Coffee/Tea |
|
|
|
|
P4. Structural analysis of the Calvin Cycle. |
DF, MP, TDC,NM |
|
|
|
|
|
|
|
|
L7. Building genome-scale metabolic networks |
MP |
|
|
|
P5. Building a ScrumPy model from databases |
All |
|
|
|
|
|
|
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|
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|
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Sunday |
|
|
|
|
01/07/18 |
09:00 |
L8. a, Acetobacterium woodii. b. Cupriavidus necator |
NM, NP |
|
|
|
|
|
|
|
11:00 |
P6. Flux Balance Analysis of fatty acid biosynthesis in E coli. |
All |
|
|
|
|
|
|
|
|
L8 c. Clostridium autoethanogenum. L9. Modelling metabolism of Non-Aureus Staphylococci |
RN, TDC |
|
|
|
P6 continued |
|
All |
|
|
Tea/Coffee |
|
|
|
|
P7. Analysing a genome scale model |
All |
|
|
|
Close |
|
|
|
|
Dinner |
|
|
|
|
|
|
|
Monday |
|
Breakfast |
|
|
02/07/18 |
|
P7 continued |
|
All |
|
|
|
|
|
|
|
|
|
All |
|
|
|
|
DF& MP |
Tuesday |
|
|
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|
03/07/18 |
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