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| || || ||P1. Computers: checking internet connectivity, software installation. ||[[Meetings/Nottingham2022/ScrumPyInstall|Installation]] of !ScrumPy. ||All || | || || ||P1. Computers: checking internet connectivity, software installation. ||[[Meetings/Nottingham2022/ScrumPyInstall|Installation]] of !ScrumPy. ||All || |
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| || ||09:00 ||P2. Python and !ScrumPy (Part 1) || ||<tablewidth="60px" tableheight="24px">[[Meetings/Nottingham2022/Prac2|Prac2]] || ||All || || || ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]]||MP || || || || || || || |
|| ||09:00 ||P2. Python and !ScrumPy ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All || || || ||L3. Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||MP || |
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| || || ||P2. Python and !ScrumPy (Part 2) ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All || | || || ||P3. Null space, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac3]] ||All || |
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| || ||PM ''' ''' ||L3b. Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF || || || ||L4. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||DF || || || ||Demo for Prac 3 || ||TBC || || || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac 3]] ||All || || || ||Break || || || || || ||P3. Models, kernels, subsets and elementary modes (continued) || ||All || || ||16:45 ||Close || || || |
|| ||PM ''' ''' ||L4. A. woodii and the elementary modes of the Woods-Ljungdahl Pathway ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF || || || ||P4. Elementary Modes of the Woods-Ljungdahl Pathway ||[[Meetings/Nottingham2022/Prac4|Prac4]]||All || |
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| || ||09:30 ||Demo for Prac4 || ||MP || || || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/Nottingham2022/Prac4|Prac 4]] ***instructions ||ALL || |
|| ||09:00 ||L5: Linear programming and Flux Balance Analysis || ||MP || || || ||L6: Validation and construction of models || ||MP|DS|| |
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| || || ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||NM || | || || ||L7: ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||NM || |
Under Construction - Ignore !
Overview
Timetable overview (Subject to 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, Norwich)
- Nicole Pearcy (NP: University of Nottingham)
Guest Speaker
- Prof. John Wain (JW: Quadram Institute, Norwich)
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 |
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03/04/22 |
09:00 |
Arrival, Admin & Registration |
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PM |
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12:00 |
Lunch |
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13:00 |
Welcome and introduction to the course. Outline of the week. |
' |
MP et al |
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Lecture 1: Title TBC |
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JW |
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Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
DF |
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Tea/coffee |
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Lecture 3: Python and computational representation of metabolic networks. |
MP |
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P1. Computers: checking internet connectivity, software installation. |
Installation of ScrumPy. |
All |
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Close |
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Wednesday |
AM |
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09:00 |
P2. Python and ScrumPy |
All |
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L3. Null space, subsets and elementary modes |
MP |
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11:00 |
Break |
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P3. Null space, subsets and elementary modes |
All |
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13:00 |
Lunch |
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PM |
L4. A. woodii and the elementary modes of the Woods-Ljungdahl Pathway |
DF |
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P4. Elementary Modes of the Woods-Ljungdahl Pathway |
All |
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Thursday |
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09:00 |
L5: Linear programming and Flux Balance Analysis |
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MP |
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L6: Validation and construction of models |
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MP|DS |
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11:00 |
Break |
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L7: |
NM |
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L6. Sources of data for metabolic models |
DF |
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13:00 |
Lunch |
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PM |
L7. The unique metabolism of Acetobacterium woodii |
NM |
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P5. Flux Balance Analysis of alkane biosynthesis in E coli. |
All |
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16:45 |
close |
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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 |
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P5 Flux Balance Analysis of alkane biosynthesis in E coli. |
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11:00 |
Break |
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Practical 5 continues |
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13:00 |
Lunch |
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Conclusions |
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