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| . A reading list for topics covered in the course is provided [[Meetings/Nottingham2022/Reading|here]] | . A reading list for topics covered in the course is provided [[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Reading|here]] |
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| ||Monday || ''' ''' || || || || |
||Monday ||AM ''' ''' || || || || |
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| || ||14:00 ||Lecture: Introduction to python ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||MP || | || || ||( Keynote DF online?) || || || || || ||Lecture: Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DF ?? || |
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| || ||15:00 ||P1. Computers: checking internet connectivity, software installation.-> P2 ||[[https://gitlab.com/MarkPoolman/scrumpy/-/wikis/Manual/Install|Installation]] of !ScrumPy. ||All || || || ||P2. Introduction to python ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All || ||Tuesday ''' ''' || ''' ''' || || || || || ||09:00 ||P2. Python continued ... ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All || || ||10: 00 ||Lecture: Introduction to metabolic modelling || ||DF || || ||11:00 ||Lecture: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||CS || |
|| || ||Python and computational representation of metabolic networks. +Minor updates ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||MP || || || ||P1. Computers: checking internet connectivity, software installation.-> P2 ||[[https://gitlab.com/MarkPoolman/scrumpy/-/wikis/Manual/Install|Installation]] of ScrumPy. ||All || || || || || || || ||Tuesday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||P2. Python ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All || || || ||Lecture: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||CS || || ||11:00 ||Break || || || || || ||P3. Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All || |
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| || ||14:00 ||P3. Null space, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac3]] ||All || || ||16:00 ||Lecture: Construction and curation of metabolic GSMs || ||TD/PV || |
|| ||PM ''' ''' ||Lecture. Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DF || || || ||P4. Elementary Modes of the Woods-Ljungdahl Pathway ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All || |
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| || ||9:00 ||P3 continued ... || || || || ||10:00 ||Lecture. Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DF || || ||11:00 ||P4. Elementary Modes of the Woods-Ljungdahl Pathway ||[[Meetings/Nottingham2022/Prac4|Prac4]] ||All || ---- /!\ '''Edit conflict - other version:''' ---- ---- /!\ '''Edit conflict - your version:''' ---- || ||11:00 ||P4. Elementary Modes of the Woods-Ljungdahl Pathway ||[[Meetings/Nottingham2022/Prac4|Prac4]] ||All || ---- /!\ '''End of edit conflict''' ---- |
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---- /!\ '''Edit conflict - other version:''' ---- ---- /!\ '''Edit conflict - your version:''' ---- ---- /!\ '''End of edit conflict''' ---- |
!! Under Construction - Contents Liable to Change !!
Workshop on Metabolic Modelling
Nottingham 2024
Tutors
- Mark Poolman (MP: Oxford Brookes University)
- Trunil Desai (DS: Oxford Brookes University)
- Pareena Verma (PV: Oxford Brookes University)
- Cristiana Sebu (CS: University of Malta)
- Prof. David Fell (DF: Oxford Brookes University ) - Online
Reading List
A reading list for topics covered in the course is provided here
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Lecturer |
Monday |
AM |
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|
|
09/12/2024 |
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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( Keynote DF online?) |
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Lecture: Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
DF ?? |
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|
Tea/coffee |
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Python and computational representation of metabolic networks. +Minor updates |
MP |
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P1. Computers: checking internet connectivity, software installation.-> P2 |
Installation of ScrumPy. |
All |
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Tuesday |
AM |
|
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09:00 |
P2. Python |
All |
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Lecture: Null space, subsets and elementary modes |
CS |
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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 |
|
|
|
PM |
Lecture. Biotechnological applications of elementary modes analysis |
DF |
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P4. Elementary Modes of the Woods-Ljungdahl Pathway |
All |
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Wednesday |
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09:00 |
Lecture: Linear programming and Flux Balance Analysis |
MP |
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Lecture: Validation and construction of models |
TD |
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11:00 |
Break |
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Lecture: Determination of minimal media requirements for Campylobacter jejuni |
PV |
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P5: Determination of minimal media requirements for Campylobacter jejuni |
All |
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13:00 |
Lunch |
|
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|
PM |
Lecture: Phaeodactylum tricornutm for biofuel synthesis |
DS |
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P6. Identifying pathways for TAG synthesis in P. tricornutm |
All |
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16:45 |
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Thursday |
AM |
|
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|
|
09:00 |
Lecture. Cupriavadus necator |
NP |
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P6 (ctd) P7: KOs for ethylene production in C. necator |
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13:00 |
Lunch |
|
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|
14:00 |
Practical or Lecture here (LPEMs ?? Reaction CCs ??) |
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Friday |
AM |
|
|
|
|
09:00 |
Complete unfinished practicals |
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11:00 |
General discussion. AOB |
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13:00 |
Lunch |
||
|
14:00 |
Go Home ! |