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| || ||PM ''' ''' ||L3b. Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF || | || ||PM ''' ''' ||L3b. Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF || |
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| || ||PM ''' ''' ||L7. The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM || | || ||PM ''' ''' ||L7. The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM || |
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| ||Friday ''' ''' ||AM ''' ''' || || || || || ||09:30 ||L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||MP, DF || |
||Friday ''' ''' ||AM ''' ''' || || || || || ||09:30 ||L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||MP, DF || |
Under Construction - Ignore !
Overview
Draft TimeTable.pdf (Will definitely change!)
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)
- 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 |
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 Tea/coffee L2. Computational representation of metabolic networks MP P1. Computers: checking internet connectivity, software installation. Installation of ScrumPy. All Close Wednesday AM 09:30 L3. Null space and elementary modes NP Demo for Prac 2. MP 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 Thursday 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 Friday AM 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 Conclusions