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| || ||13:00 ||Welcome and introduction to the course. Outline of the week. ||'''' ''' ||MP et al || | || ||13:00 ||Welcome and introduction to the course. Outline of the week. || ||MP et al || |
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| || || ||Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||DF || | || || ||Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DF || |
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| || || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||MP || | || || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||MP || |
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| || ||PM ''' ''' ||L4. A. woodii and the elementary modes of the Woods-Ljungdahl Pathway ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF || | || ||PM ''' ''' ||L4. A. woodii and the elementary modes of the Woods-Ljungdahl Pathway ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||DF || |
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| || ||09:00 ||L5: Linear programming and Flux Balance Analysis || ||DS|MP || || || ||L6: Validation and construction of models '''(Naming Conventions)''' || ||MP|DS || |
|| ||09:00 ||L5: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DS|MP || || || ||L6: Validation and construction of models '''(Naming Conventions)''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||MP|DS || |
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| || || ||L7: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DS || || || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||DF || |
|| || ||L7: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] ||DS || || || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' || ||DF || |
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| || ||PM ''' ''' ||L8: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM || | || ||PM ''' ''' ||L8: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM || |
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| || ||09:00 ||L8. ''Cupriavadus necator'' ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||NP || | || ||09:00 ||L8. ''Cupriavadus necator'' ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||NP || |
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| || ||14:00||Concluding remarks, discussion, feedback || || || | || ||14:00 ||Concluding remarks, discussion, feedback || || || |
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 |
|
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 |
DS|MP |
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L6: Validation and construction of models (Naming Conventions) |
MP|DS |
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11:00 |
Break |
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L7: Determination of minimal media requirements for Campylobacter jejuni |
DS |
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P5: Determination of minimal media requirements for Campylobacter jejuni |
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DF |
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13:00 |
Lunch |
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PM |
L8: Phaeodactylum tricornutm for biofuel synthesis |
NM |
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P6. Identifying pathways for TAG synthesis in P. tricornutm |
All |
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16:45 |
close |
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Friday |
AM |
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09:00 |
L8. Cupriavadus necator |
NP |
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P6 (ctd) P7: KOs for ethelene production in C. necator |
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13:00 |
Lunch |
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14:00 |
Concluding remarks, discussion, feedback |
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