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== Course Plan and Resources Index == ||'''Day'''||'''Time''' ||'''Activity''' ||'''Resources'''||'''Who''' || ||Mon 15|| 13:30 ||[[Meetings/Delhi2012/Lectures/Session1|Session 1]]: Introduction to metabolic modelling. Mathematical representation of metabolic networks. Null space and its significance.|| A link.||David Fell; Mark Poolman || ||Mon 15|| PM ||[[Meetings/Delhi2012/Practicals/Practical_1|Practical 1]]: Familiarisation with pathway and enzyme databases. || ||Hassan Hartman || ||Tue 16|| AM ||[[Meetings/Delhi2012/Lectures/Session2|Session 2]]: Applications of elementary modes to real systems.|| ||David Fell; Sudip Kundu || ||Tue 16|| PM ||[[Meetings/Delhi2012/Practicals/Practical_2|Practical 2]]: Brief Python introduction; Null space and elementary modes analysis with {{{ScrumPy}}}|| ||Hassan Hartman; Sudip Kundu || ||Wed 17|| AM ||[[Meetings/Delhi2012/Lectures/Session3|Session 3]]: Linear Programming and Flux Balance Analysis. Building genome-scale metabolic models: data sources and issues.|| ||Mark Poolman; Oliver Ebenhoeh || ||Wed 17|| PM ||[[Meetings/Delhi2012/Practicals/Practical_3|Practical 3]]: Introduction to linear programming and Flux Balance Analysis with {{{ScrumPy}}}|| ||Hassan Hartman; Sudip Kundu || ||Thu 18|| AM ||[[Meetings/Delhi2012/Lectures/Session4|Session 4]]: Applications of genome-scale modelling.|| ||Mark Poolman; Oliver Ebenhoeh; Sudip Kundu || ||Thu 18|| PM ||[[Meetings/Delhi2012/Practicals/Practical_4|Practical 4]]: FBA continued|| ||Hassan Hartman; Sudip Kundu || ||Fri 19|| AM ||[[Meetings/Delhi2012/Lectures/Session5|Session 5]]: 1. Metabolic scope 2. Review and Conclusions|| ||Oliver Ebenhoeh; All || |
== Course Timetable and Resources Index (Provisional) == ||<height="23px">'''Date''' ||'''Day''' ||'''Time''' ||'''Place''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' || ||<height="23px">15/12/14 ||Monday ||13:00 || ||Room registration opens at St Anne's Lodge || || || ||<height="23px"> || ||13:30 ||S8 ||Workshop registration opens. || ||DF, DS, KA || ||<height="23px"> || ||14:00 ||S8 ||Opening and introductions || ||DF || ||<height="53px"> || ||14:30 ||S8 ||L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week ||Slides ||DF || ||<height="23px"> || ||15:30 ||S9 ||Tea/coffee || || || ||<height="23px"> || ||16:00 ||S8 ||L2. Sources of data for metabolic models ||Slides ||DF || ||<height="38px"> || ||17:00 ||S9 ||P1. Computers: checking internet connectivity, software installation ||Instructions ||DF, MP, DS, KA,TK || ||<height="23px"> || ||18:30 || ||Room registration (cont) || || || ||<height="23px"> || ||19:00 ||S9 ||Opening reception || || || ||<height="23px"> || ||19:30 ||S9 ||Dinner || || || ||<height="23px"> || || || || || || || ||<height="23px">16/12/14 ||Tuesday ||08:00 ||Hall ||Breakfast || || || ||<height="23px"> || ||09:00 ||S8 ||L3. Null space and elementary modes ||Slides ||DF || ||<height="36px"> || ||10:00 || ||L4. Computational representation of metabolic networks ||Slides ||MP || ||<height="23px"> || ||10:30 ||S9 ||Coffee/Tea || || || ||<height="36px"> || ||11:00 ||S8 ||P2. Python and ScrumPy ||Instructions ||MP, DF, DS, TK || ||<height="23px"> || ||12:30 ||S9 ||Lunch || || || ||<height="36px"> || ||13:30 ||S8 ||L5. Biotechnological applications of metabolic network analysis ||Slides ||DF || ||<height="36px"> || ||14:30 ||S8 ||P3. Null space analysis with ScrumPy ||Instructions ||DF, HH, DS, TK || ||<height="23px"> || ||15:30 ||S9 ||Tea/Coffee || || || ||<height="36px"> || ||16:00 ||S8 ||L6. Linear Programming and Flux Balance Analysis ||Slides ||HH || ||<height="23px"> || ||17:00 ||S8 ||P2 and P3 continued || || || ||<height="23px"> || ||17:30 || ||Close || || || ||<height="23px"> || ||19:30 ||S9 ||Dinner || || || ||<height="23px"> || || || || || || || ||<height="23px">17/12/14 ||Wednesday ||08:00 ||Hall ||Breakfast || || || ||<height="36px"> || ||09:00 ||S8 ||L7. Building genome-scale metabolic networks ||Slides ||MP || ||<height="23px"> || ||10:30 ||S9 ||Coffee/Tea || || || ||<height="53px"> || ||11:00 ||S8 ||P4. Elementary modes of a simple model ||Instructions ||MP, DF, KA || ||<height="23px"> || ||12:30 ||S9 ||Lunch || || || ||<height="36px"> || ||13:30 ||S8 ||L8. Examples of analyzing genome scale metabolic models ||Slides ||MP or DF || ||<height="53px"> || ||14:30 ||S8 ||P5. Building models from !MetaCyc with ScrumPy – group work ||Instructions ||MP, DF, HH, KA || ||<height="23px"> || ||15:30 ||S9 ||Tea/Coffee || || || ||<height="53px"> || ||16:00 ||S8 ||P5 continued || || || ||<height="23px"> || ||17:30 || ||Close || || || ||<height="23px"> || ||19:30 ||UCR ||Dinner (Upper Common Room) || || || ||<height="23px"> || || || || || || || ||<height="23px">18/12/14 ||Thursday ||08:00 ||Hall ||Breakfast || || || ||<height="19px"> || ||09:00 ||S8 ||L9. Examples of genome scale modelling ||Slides ||DS KA || ||<height="23px"> || ||10:30 ||S9 ||Coffee/Tea || || || ||<height="23px"> || ||11:00 ||S8 ||P6. Flux Balance Analysis of a simple model ||Instructions ||DF, KA, DS || ||<height="23px"> || ||12:30 ||S9 ||Lunch || || || ||<height="36px"> || ||13:30 ||S8 ||L10. Modelling energy metabolism in Salmonella ||Slides ||HH || ||<height="23px"> || ||14:30 ||S8 ||P7. FBA mini-projects (Group work) ||Instructions ||DF, MP, DS, KA || ||<height="23px"> || ||15:30 ||S9 ||Tea/Coffee || || || ||<height="23px"> || ||16:00 ||S8 ||P7 continued || ||DF, MP, DS, KA || ||<height="23px"> || ||17:30 || ||Close || || || ||<height="19px"> || ||19:30 ||S9 ||'''Workshop dinner with cash bar''' || || || ||<height="23px"> || || || || || || || ||<height="23px">19/12/14 ||Friday ||08:00 ||Hall ||Breakfast || || || ||<height="23px"> || ||09:00 ||S8 ||P7 continued || ||DF, MP, HH, DS, KA || ||<height="23px"> || ||10:30 ||S9 ||Coffee/Tea || || || ||<height="23px"> || ||11:00 ||S8 ||Reports from groups || ||DF, MP, HH, DS, KA || ||<height="23px"> || ||12:00 ||S8 ||Any questions? Closing remarks || ||DF || ||<height="23px"> || ||12:30 ||S9 ||Sandwich lunch (packed) || || || ||<height="23px"> || ||13:30 || ||Departure || || || |
C1Net Workshop on Metabolic Modelling
Course Timetable and Resources Index (Provisional)
Date |
Day |
Time |
Place |
Activity |
Links |
Lecturer |
15/12/14 |
Monday |
13:00 |
|
Room registration opens at St Anne's Lodge |
|
|
|
|
13:30 |
S8 |
Workshop registration opens. |
|
DF, DS, KA |
|
|
14:00 |
S8 |
Opening and introductions |
|
DF |
|
|
14:30 |
S8 |
L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week |
Slides |
DF |
|
|
15:30 |
S9 |
Tea/coffee |
|
|
|
|
16:00 |
S8 |
L2. Sources of data for metabolic models |
Slides |
DF |
|
|
17:00 |
S9 |
P1. Computers: checking internet connectivity, software installation |
Instructions |
DF, MP, DS, KA,TK |
|
|
18:30 |
|
Room registration (cont) |
|
|
|
|
19:00 |
S9 |
Opening reception |
|
|
|
|
19:30 |
S9 |
Dinner |
|
|
|
|
|
|
|
|
|
16/12/14 |
Tuesday |
08:00 |
Hall |
Breakfast |
|
|
|
|
09:00 |
S8 |
L3. Null space and elementary modes |
Slides |
DF |
|
|
10:00 |
|
L4. Computational representation of metabolic networks |
Slides |
MP |
|
|
10:30 |
S9 |
Coffee/Tea |
|
|
|
|
11:00 |
S8 |
P2. Python and ScrumPy |
Instructions |
MP, DF, DS, TK |
|
|
12:30 |
S9 |
Lunch |
|
|
|
|
13:30 |
S8 |
L5. Biotechnological applications of metabolic network analysis |
Slides |
DF |
|
|
14:30 |
S8 |
P3. Null space analysis with ScrumPy |
Instructions |
DF, HH, DS, TK |
|
|
15:30 |
S9 |
Tea/Coffee |
|
|
|
|
16:00 |
S8 |
L6. Linear Programming and Flux Balance Analysis |
Slides |
HH |
|
|
17:00 |
S8 |
P2 and P3 continued |
|
|
|
|
17:30 |
|
Close |
|
|
|
|
19:30 |
S9 |
Dinner |
|
|
|
|
|
|
|
|
|
17/12/14 |
Wednesday |
08:00 |
Hall |
Breakfast |
|
|
|
|
09:00 |
S8 |
L7. Building genome-scale metabolic networks |
Slides |
MP |
|
|
10:30 |
S9 |
Coffee/Tea |
|
|
|
|
11:00 |
S8 |
P4. Elementary modes of a simple model |
Instructions |
MP, DF, KA |
|
|
12:30 |
S9 |
Lunch |
|
|
|
|
13:30 |
S8 |
L8. Examples of analyzing genome scale metabolic models |
Slides |
MP or DF |
|
|
14:30 |
S8 |
P5. Building models from MetaCyc with ScrumPy – group work |
Instructions |
MP, DF, HH, KA |
|
|
15:30 |
S9 |
Tea/Coffee |
|
|
|
|
16:00 |
S8 |
P5 continued |
|
|
|
|
17:30 |
|
Close |
|
|
|
|
19:30 |
UCR |
Dinner (Upper Common Room) |
|
|
|
|
|
|
|
|
|
18/12/14 |
Thursday |
08:00 |
Hall |
Breakfast |
|
|
|
|
09:00 |
S8 |
L9. Examples of genome scale modelling |
Slides |
DS KA |
|
|
10:30 |
S9 |
Coffee/Tea |
|
|
|
|
11:00 |
S8 |
P6. Flux Balance Analysis of a simple model |
Instructions |
DF, KA, DS |
|
|
12:30 |
S9 |
Lunch |
|
|
|
|
13:30 |
S8 |
L10. Modelling energy metabolism in Salmonella |
Slides |
HH |
|
|
14:30 |
S8 |
P7. FBA mini-projects (Group work) |
Instructions |
DF, MP, DS, KA |
|
|
15:30 |
S9 |
Tea/Coffee |
|
|
|
|
16:00 |
S8 |
P7 continued |
|
DF, MP, DS, KA |
|
|
17:30 |
|
Close |
|
|
|
|
19:30 |
S9 |
Workshop dinner with cash bar |
|
|
|
|
|
|
|
|
|
19/12/14 |
Friday |
08:00 |
Hall |
Breakfast |
|
|
|
|
09:00 |
S8 |
P7 continued |
|
DF, MP, HH, DS, KA |
|
|
10:30 |
S9 |
Coffee/Tea |
|
|
|
|
11:00 |
S8 |
Reports from groups |
|
DF, MP, HH, DS, KA |
|
|
12:00 |
S8 |
Any questions? Closing remarks |
|
DF |
|
|
12:30 |
S9 |
Sandwich lunch (packed) |
|
|
|
|
13:30 |
|
Departure |
|
|