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| a | = Innotargets: Introduction to Metabolic Modelling = == Barcelona 2023 == == Tutors == * Dr Mark Poolman (MP: Oxford Brookes University) * Dr Anu Raghunathan (AR: NCL, Pune) * Dr Dipali Singh (DS: Quadram Institute, Norwich) * Pareena Verma (PV: Oxford Brookes University) * Dr Trunil Desai (TD: Oxford Brookes University) == Guest Speaker == * TBD == Course Timetable and Resources == ||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' || ||Day 1 - Tues(17/09) || || || || || ||AM ||09:00 ||Arrival, Admin & Registration etc || || || || ||12:00 ||Lunch || || || || || || || || || ||PM ||13:00 ||Welcome and introduction to the course - why do modelling? || ||M, AR || || ||13:30||Lecture 1: Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||TBD || || ||15:00 ||Tea/coffee || || || || ||15:30||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L2.pdf|Slides]] ||TBD || || ||16:30||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona2023/ScrumPyInstall|Prac1]] ||All || || || ||P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All || || || ||Close || || || || || || || || || ||Day 2 - Wed (18/09) || || || || || ||AM ||09:00 ||Lecture 3: Null space, elementary modes and conserved cycles ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||TBD || || ||10:00||P3. Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona/Prac3|Prac3]] ||All || || ||11:00 ||tea/coffee || || || || ||11:30||P3 continues || ||All|| || || ||Lunch || || || || || || || || || ||PM ||13:00 ||Guest lecture || ||Sudip? || || ||14:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]]||TBD || || ||15:00||tea/coffe|| || || || ||15:30||P4: LP - maybe?|| || || || ||16:00||FBA - Title to be added by Anu|| ||AR|| || || || || || || ||Day 3 Thurs (19/09) || || || || || ||AM ||09:00 || || || || || || ||Lecture 5: Response to varying ATP demand in a metabolic model of '' Salmonella typhimurium'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L5.pdf|Slides]] ||MP || || ||10:30 ||Break || || || || || ||P4 Central metabolism of ''S. epidermidis'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] ||YS/DS || || || || || || || || ||13:00 ||Lunch || || || || || ||Lecture 6: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L6.pdf|Slides]] ||DS || || || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All || || || || || || || ||Friday || || || || || ||AM ||09:00 ||Lecture 7: construction and validation ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.pdf|Slides]] ||DS || || || ||Finish practicals/General discussion/Something else ||[[https://mudshark.brookes.ac.uk/Meetings/C1NetWork1/Prac7|Prac6]] ||(Optional if time allows) || || ||13:00 ||Lunch || || || || || ||Go home! || || || |
Innotargets: Introduction to Metabolic Modelling
Barcelona 2023
Tutors
- Dr Mark Poolman (MP: Oxford Brookes University)
- Dr Anu Raghunathan (AR: NCL, Pune)
- Dr Dipali Singh (DS: Quadram Institute, Norwich)
- Pareena Verma (PV: Oxford Brookes University)
- Dr Trunil Desai (TD: Oxford Brookes University)
Guest Speaker
- TBD
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Lecturer |
Day 1 - Tues(17/09) |
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|
AM |
09:00 |
Arrival, Admin & Registration etc |
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|
12:00 |
Lunch |
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|
|
|
|
|
PM |
13:00 |
Welcome and introduction to the course - why do modelling? |
|
M, AR |
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13:30 |
Lecture 1: Introduction to metabolic modelling. |
TBD |
|
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15:00 |
Tea/coffee |
|
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|
15:30 |
Lecture 2: Python and computational representation of metabolic networks. |
TBD |
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16:30 |
P1. Computers: checking internet connectivity, software installation. |
All |
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P2. Python and ScrumPy |
All |
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Close |
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Day 2 - Wed (18/09) |
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AM |
09:00 |
Lecture 3: Null space, elementary modes and conserved cycles |
TBD |
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10:00 |
P3. Null space, subsets and elementary modes |
All |
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11:00 |
tea/coffee |
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11:30 |
P3 continues |
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All |
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Lunch |
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PM |
13:00 |
Guest lecture |
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Sudip? |
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14:00 |
Lecture 4. Linear programming and Flux Balance Analysis |
TBD |
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15:00 |
tea/coffe |
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15:30 |
P4: LP - maybe? |
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16:00 |
FBA - Title to be added by Anu |
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AR |
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Day 3 Thurs (19/09) |
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AM |
09:00 |
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Lecture 5: Response to varying ATP demand in a metabolic model of Salmonella typhimurium |
MP |
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10:30 |
Break |
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P4 Central metabolism of S. epidermidis |
YS/DS |
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13:00 |
Lunch |
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Lecture 6: Determination of minimal media requirements for Campylobacter jejuni |
DS |
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P5: Determination of minimal media requirements for Campylobacter jejuni |
All |
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Friday |
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AM |
09:00 |
Lecture 7: construction and validation |
DS |
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Finish practicals/General discussion/Something else |
(Optional if time allows) |
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13:00 |
Lunch |
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Go home! |
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