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Workshop on Metabolic Modelling
Nottingham 2022
Tutors
- Mark Poolman (MP: Oxford Brookes University)
- David Fell (DF: Oxford Brookes University)
- Yanica Said (YS: Oxford Brookes University)
- Oliver Ebenhöh (OE: Heinrich-Heine-Universität, Dusseldorf)
- Dipali Singh (DS: Quadram Institute, Norwhich)
- Nicole Pearcy (NP: University of Nottingham)
Reading List
A reading list for topics covered in the course is provided here.
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Lecturer |
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Tuesday |
AM |
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03/04/22 |
09:00 |
Arrival, Admin & Registration |
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PM |
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13:00 |
Lunch |
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' |
??? |
Introductions. Each participant introduces themself in 2-3 sentences: name, place of study/work; what they do. |
?? Do this or similar ?? |
Everyone |
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Welcome and introduction to the course. Outline of the week |
DF |
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14:00 |
L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
DF |
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Tuesday AM 03/04/22 09:00 Arrival, Admin & Registration PM 13:00 Lunch ' ??? Introductions. Each participant introduces themself in 2-3 sentences: name, place of study/work; what they do. ?? Do this or similar ?? Everyone Welcome and introduction to the course. Outline of the week DF 14:00 L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. DF
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Tea/coffee L2. Computational representation of metabolic networks MP P1. Computers: checking internet connectivity, software installation. Installation of ScrumPy. All
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Close Wednesday AM
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Close Wednesday AM
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09:30 L3. Null space and elementary modes NM Demo for Prac 2. TBC P2. Python and ScrumPy (Part 1) All 11:00 Break P2. Python and ScrumPy (Part 2) All 13:00 Lunch PM L3b. Examples of Elementary Modes Analysis DF L4. Biotechnological applications of metabolic network analysis DF Demo for Prac 3 TBC P3. Models, kernels, subsets and elementary modes All Break P3. Models, kernels, subsets and elementary modes (continued) All 16:45 Close
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Thursday
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Thursday
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09:30 Demo for Prac4 MP P4. Structural analysis of the Calvin Cycle. Prac 4 ***instructions ALL 11:00 Break L5. Linear Programming and Flux Balance Analysis NM L6. Sources of data for metabolic models DF 13:00 Lunch PM L7. The unique metabolism of Acetobacterium woodii NM P5. Flux Balance Analysis of alkane biosynthesis in E coli. All 16:45 close
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Friday AM
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Friday AM
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09:30 L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP MP, DF P5 Flux Balance Analysis of alkane biosynthesis in E coli. 11:00 Break Practical 5 continues 13:00 Lunch 14:00 L9 Modelling photosynthesis in eukaryotes. KA L10 Beyond structural modelling EA Closing and Presentation of Certificates 16:45 Depart