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| ||AM || ''' ''' || || || || |
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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) || || ||15:30||Tea/coffee || || || |
||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) || || ||15:30 ||Tea/coffee || || || |
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| || || ||P2. Python and ScrumPy||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]]||All (Review)|| || ||1800||Close || || || |
|| || ||P2. Python and ScrumPy ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All (Review) || || ||1800 ||Close || || || |
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| ||Wednesday ''' ''' || ''' ''' || || || || ||AM|| || || || || |
||Wednesday || || || || || ||AM || || || || || |
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| || ||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) || | || ||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) || |
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| || ||10:30||tea/coffee|| || || || || ||P3 continues|| || || |
|| ||10:30 ||tea/coffee || || || || || ||P3 continues || || || |
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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|| |
||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 || |
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''' ''' |
Innotargets: Introduction to Metabolic Modelling
DRAFT/UNDER CONSTRUCTION - STUDENTS PLEASE IGNORE
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 ??
- TBA ??
Reading List ??
- Suggestions ?
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Lecturer |
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30/05/23 Tuesday |
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AM |
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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? |
MP (Not Yet Created) |
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Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
YS (Cut down and align w/ L3) |
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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 (Not Yet Created) |
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P2. Python and ScrumPy |
All (Review) |
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1800 |
Close |
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Wednesday |
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AM |
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09:00 |
Lecture 3: Null space and elementary modes and conserved cycles (? keep the latter ? something else ?) |
OE (review - ensure alligned w/ L2 and P3) |
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P3. Null space, subsets and elementary modes |
All (review - do we need more?) |
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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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09:00 |
Lecture 4. Linear programming and Flux Balance Analysis |
OE |
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Lecture 5: S. typhim model |
MP |
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Break |
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S.typhim prac |
All (Styphim ? to big a jump from P3?) |
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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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Lecture 7: construction and validation |
DS |
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Finish practicals/General discussion/Something else |
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13:00 |
Lunch |
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Go home! |
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