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| ||<height="38px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">17:00 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">P1. Computers: checking internet connectivity, software installation ||<style="text-align:left;vertical-align:top">[[Meetings/C1netWork1/Prac1|Instructions]] ||<style="text-align:left;vertical-align:top">DF, MP, DS, KA,TK || | ||<height="38px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">17:00 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">P1. Computers: checking internet connectivity, software installation. Enzyme and metabolism databases. ||<style="text-align:left;vertical-align:top">[[http://mudshark.brookes.ac.uk/Meetings/Riga2013/Practicals/ScrumPyVM|Installation]] of ScrumPy. [[Meetings/C1netWork1/Prac1|Database Instructions]] ||<style="text-align:left;vertical-align:top">DF, MP, DS, KA,TK || |
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| ||<height="38px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P2. Python and ScrumPy ||<style="text-align:left;vertical-align:top">Instructions ||<style="text-align:left;vertical-align:top">MP, DF, DS, TK || | ||<height="38px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P2. Python and !ScrumPy ||<style="text-align:left;vertical-align:top">[[http://mudshark.brookes.ac.uk/AccliPhot/WorkshopOne/prac1|Instructions]] ||<style="text-align:left;vertical-align:top">MP, DF, DS, TK || |
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| ||<height="38px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P3. Null space analysis with ScrumPy ||<style="text-align:left;vertical-align:top">Instructions ||<style="text-align:left;vertical-align:top">DF, HH, DS, TK || | ||<height="38px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P3. Null space analysis with !ScrumPy ||<style="text-align:left;vertical-align:top">As P2 plus these [[http://mudshark.brookes.ac.uk/Meetings/Riga2013/Practicals/Practical_2/ScrumPyIntro|instructions]] ||<style="text-align:left;vertical-align:top">DF, HH, DS, TK || |
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| ||<height="56px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P4. Elementary modes of a simple model ||<style="text-align:left;vertical-align:top">Instructions ||<style="text-align:left;vertical-align:top">MP, DF, KA || | ||<height="56px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P4. Elementary modes of a simple model ||<style="text-align:left;vertical-align:top">[[http://mudshark.brookes.ac.uk/AccliPhot/WorkshopOne/prac2|Instructions]] ||<style="text-align:left;vertical-align:top">MP, DF, KA || |
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| ||<height="56px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P5. Building models from !MetaCyc with ScrumPy – group work ||<style="text-align:left;vertical-align:top">[[../Prac5|Instructions]] ||<style="text-align:left;vertical-align:top">MP, DF, HH, KA || | ||<height="56px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P5. Building models from !MetaCyc with ScrumPy – group work ||<style="text-align:left;vertical-align:top">[[Meetings/C1netWork1/Prac5|Instructions]] ||<style="text-align:left;vertical-align:top">MP, DF, HH, KA || |
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| ||<height="20px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P6. Flux Balance Analysis of a simple model ||<style="text-align:left;vertical-align:top">Instructions ||<style="text-align:left;vertical-align:top">DF, KA, DS || | ||<height="20px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P6. Flux Balance Analysis of a simple model ||<style="text-align:left;vertical-align:top">[[http://mudshark.brookes.ac.uk/AccliPhot/WorkshopOne/prac3|Instruction]] ||<style="text-align:left;vertical-align:top">DF, KA, DS || |
C1Net Workshop on Metabolic Modelling
Course Timetable and Resources Index (Provisional)
Day |
Time |
Place |
Activity |
Links |
Lecturer |
Monday |
13:00 |
|
Room registration opens at St Anne's Lodge |
|
|
15/12/14 |
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 |
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. Enzyme and metabolism databases. |
DF, MP, DS, KA,TK |
|
|
18:30 |
|
Room registration (cont) |
|
|
|
19:00 |
S9 |
Opening reception |
|
|
|
19:30 |
S9 |
Dinner |
|
|
|
|
|
|
|
|
Tuesday |
08:00 |
Hall |
Breakfast |
|
|
16/12/14 |
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 |
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 |
As P2 plus these 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 |
|
|
|
19:00 |
S9 |
Dinner |
|
|
|
|
|
|
|
|
Wednesday |
08:00 |
Hall |
Breakfast |
|
|
17/12/14 |
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 |
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 |
MP, DF, HH, KA |
|
|
15:30 |
S9 |
Tea/Coffee |
|
|
|
16:00 |
S8 |
P5 continued |
|
MP, DF, HH, KA |
|
17:30 |
|
Close |
|
|
|
19:00 |
UCR |
Dinner (Upper Common Room) |
|
|
|
|
|
|
|
|
Thursday |
08:00 |
Hall |
Breakfast |
|
|
18/12/14 |
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 |
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 |
|
|
|
18:30 |
S9 |
Pre-dinner drinks |
|
|
|
19:00 |
S9 |
Workshop dinner with cash bar |
|
|
|
|
|
|
|
|
Friday |
08:00 |
Hall |
Breakfast |
|
|
19/12/14 |
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 |
|
|