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| == DRAFT/UNDER CONSTRUCTION - STUDENTS PLEASE IGNORE == | |
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| Guest Speaker ?? * TBA ?? |
== Guest Speaker == * Dr. Rodriguez-Caso (University of Malaga) |
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| || || || || || ||AM||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || || |
||AM ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || || |
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| ||PM ||14:00 ||Welcome and introduction to the course - why do modelling? ||[[https://mudsharkstatic.brookes.ac.uk/Barcelona2023/L0.pdf|Slides]] ||MP ('''Not Yet Created''') || || || ||Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||YS (Cut down and align w/ L3) || |
||PM ||14:00 ||Welcome and introduction to the course - why do modelling? || ||MP || || || ||Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||YS || |
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| || || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona2023/ScrumPyInstall|Installing ScrumPy]] ||All ('''Not Yet Created''') || || || ||P2. Python and ScrumPy ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All (Review) || |
|| || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona2023/ScrumPyInstall|Prac1]] ||All || || || ||P2. Python and ScrumPy ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All || |
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| ||AM || || || || || || || || || || || || ||09:00 ||Lecture 3: Null space and elementary modes and conserved cycles (? keep the latter ? something else ?) ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||OE (review - ensure alligned w/ L2 and P3) || || || ||P3. Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All (review - do we need more?) || |
||AM ||09:00 ||Lecture 3: Null space, elementary modes and conserved cycles ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||OE || || || ||P3. Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona/Prac3|Prac3]] ||All || |
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| ||Thursday || || ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] || || || ||09:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||OE || || || ||Lecture 5: S. typhim model ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L5.pdf|Slides]] ||MP || || || ||Break || || || || || ||S.typhim prac ||[[http://mudshark.brookes.ac.uk/Barcelona2023/PracStyphim|Prac4]] ||All (Styphim ? to big a jump from P3?) || || || ||Lunch || || || |
||Thursday || || || || || ||AM ||09:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||OE || || || ||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 || || || |
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| ||Friday || ||Lecture 7: construction and validation ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.pdf|Slides]] ||DS || || || ||Finish practicals/General discussion/Something else || || || |
|| || || || || || ||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) || |
Innotargets: Introduction to Metabolic Modelling
Barcelona 2023
Tutors
- Mark Poolman (MP: Oxford Brookes University)
- Oliver Ebenhoeh (OE: Heinrich Heine University, Dusseldorf)
- Yanica Said (YS: Oxford Brookes University)
- Dipali Singh (DS: Quadram Institute, Norwich)
Guest Speaker
- Dr. Rodriguez-Caso (University of Malaga)
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Lecturer |
30/05/23 Tuesday |
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AM |
09:00 |
Arrival, Admin & Registration Hotel check-in etc |
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13:00 |
Lunch |
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PM |
14:00 |
Welcome and introduction to the course - why do modelling? |
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MP |
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Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
YS |
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15:30 |
Tea/coffee |
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Lecture 2: Python and computational representation of metabolic networks. |
MP |
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P1. Computers: checking internet connectivity, software installation. |
All |
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P2. Python and ScrumPy |
All |
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1800 |
Close |
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Wednesday |
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AM |
09:00 |
Lecture 3: Null space, elementary modes and conserved cycles |
OE |
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P3. Null space, subsets and elementary modes |
All |
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10:30 |
tea/coffee |
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P3 continues |
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13:00 |
Lunch |
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PM |
14:00 |
Guest lecture - Synthetic Biology: Uncovering principles of biological design applying math and experiments. |
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Dr. Rodriguez-Caso |
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15:00 |
Depart social activity |
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All |
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Thursday |
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AM |
09:00 |
Lecture 4. Linear programming and Flux Balance Analysis |
OE |
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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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