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| || || ||( Keynote DF online?) || || || || || ||Lecture: Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DF ?? || |
|| ||14:00 ||Lecture: Introduction to python and metabolic modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DF ?? || |
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| || || ||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 || || || || || || || |
|| ||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 || || || |
!! 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 |
|
|
|
09/12/2024 |
09:00 |
Arrival, Admin & Registration |
|
|
|
PM |
|
|
|
|
12:00 |
Lunch |
|
|
|
13:00 |
Welcome and introduction to the course. Outline of the week. |
|
MP et al |
|
14:00 |
Lecture: Introduction to python and metabolic modelling |
DF ?? |
|
|
|
Tea/coffee |
|
|
|
15:00 |
P1. Computers: checking internet connectivity, software installation.-> P2 |
Installation of ScrumPy. |
All |
|
|
P2. Introduction to python |
|
|
Tuesday |
AM |
|
|
|
|
09:00 |
P2. Python |
All |
|
|
|
Lecture: Null space, subsets and elementary modes |
CS |
|
|
11:00 |
Break |
|
|
|
|
P3. Null space, subsets and elementary modes |
All |
|
|
13:00 |
Lunch |
|
|
|
PM |
Lecture. Biotechnological applications of elementary modes analysis |
DF |
|
|
|
P4. Elementary Modes of the Woods-Ljungdahl Pathway |
All |
|
|
|
|
|
|
Wednesday |
|
|
|
|
|
09:00 |
Lecture: Linear programming and Flux Balance Analysis |
MP |
|
|
|
Lecture: Validation and construction of models |
TD |
|
|
11:00 |
Break |
|
|
|
|
Lecture: Determination of minimal media requirements for Campylobacter jejuni |
PV |
|
|
|
P5: Determination of minimal media requirements for Campylobacter jejuni |
All |
|
|
13:00 |
Lunch |
|
|
|
PM |
Lecture: Phaeodactylum tricornutm for biofuel synthesis |
DS |
|
|
|
P6. Identifying pathways for TAG synthesis in P. tricornutm |
All |
|
|
16:45 |
|
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Thursday |
AM |
|
|
|
|
09:00 |
Lecture. Cupriavadus necator |
NP |
|
|
|
P6 (ctd) P7: KOs for ethylene production in C. necator |
|
|
|
13:00 |
Lunch |
|
|
|
14:00 |
Practical or Lecture here (LPEMs ?? Reaction CCs ??) |
|
|
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|
Friday |
AM |
|
|
|
|
09:00 |
Complete unfinished practicals |
|
|
|
11:00 |
General discussion. AOB |
|
|
|
13:00 |
Lunch |
||
|
14:00 |
Go Home ! |