|
Size: 3868
Comment:
|
← Revision 68 as of 2024-12-06 14:46:49 ⇥
Size: 3534
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Under Construction - Contents Liable to Change = | === (Under Construction - Contents Liable to Change) === |
| Line 7: | Line 7: |
| * Pareena Verma (PV: Oxford Brookes University) | |
| Line 9: | Line 8: |
| * Prof. David Fell (DF: Oxford Brookes University ) - Online | |
| Line 11: | Line 11: |
| . A reading list for topics covered in the course is provided [[Meetings/Nottingham2022/Reading|here]] (updated). | . A reading list for topics covered in the course is provided [[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Reading|here]] |
| Line 15: | Line 15: |
| ||Tuesday ||AM ''' ''' || || || || ||03/04/22 ||09:00 ||Arrival, Admin & Registration || || || |
||Monday ||AM ''' ''' || || || || ||09/12/2024 ||09:00 ||Arrival, Admin & Registration || || || |
| Line 19: | Line 19: |
| || ||13:00 ||Welcome and introduction to the course. Outline of the week. || ||MP et al || || || ||Lecture 1: Young microbiologists need models not critics ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||JW || || || ||Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DF || |
|| ||13:00 ||Welcome and introduction to the course. Outline of the week. || ||MP ''et al '' || || ||14:00 ||'''L1''': Introduction to python and metabolic modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L1.pdf|Slides]] ||MP || |
| Line 23: | Line 22: |
| || || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||MP || || || ||P1. Computers: checking internet connectivity, software installation. ||[[Meetings/Nottingham2022/ScrumPyInstall|Installation]] of !ScrumPy. ||All || || || ||Close || || || ||Wednesday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||P2. Python and !ScrumPy ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All || || || ||Lecture 4: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||MP || || ||11:00 ||Break || || || || || ||P3. Null space, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac3]] ||All || |
|| ||15:00 ||'''P1''': Computers: checking internet connectivity, software installation.-> P2 ||[[Meetings/Nottingham2024/Installation|Installing ScrumPy]]. ||All || || ||16:00 ||'''P2''': Introduction to Python ||[[Meetings/Nottingham2024/Prac2|Prac2]] ||All || ||Tuesday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||'''P2''': Introduction to Python ''(continued) '' ||[[Meetings/Nottingham2024/Prac2|Prac2-(ctd)]] ||All || || ||10:00 ||'''L2:''' Introduction to metabolic modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L2.pdf|Slides]] ||DF || || ||11:00 ||'''L3:''' Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L3.pdf|Slides]] ||CS || |
| Line 32: | Line 29: |
| || ||PM ''' ''' ||Lecture 5. Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DF || || || ||P4. Elementary Modes of the Woods-Ljungdahl Pathway ||[[Meetings/Nottingham2022/Prac4|Prac4]] ||All || ||Thursday ''' ''' || || || || || || ||09:00 ||Lecture 6: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||MP || || || ||Lecture 7 : Validation and construction of models ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] ||DS || || ||11:00 ||Break || || || || || ||Lecture 8: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]] ||DS || || || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||DS || |
|| ||14:00 ||'''P3:''' Basic Model Properties ||[[Meetings/Nottingham2024/Prac3|Prac3]] [[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/P3.pdf|Slides]] ||All / MP || || ||16:00 ||'''L4: '''Construction and Curation of GSMs ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L4.pdf|Slides]] ||TD || || || || || || || ||Wednesday ''' ''' || || || || || || ||09:00 ||'''P3:''' ''(continued)'' || ||All || || ||10:00 ||'''L5:''' Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L5.pdf|Slides]] ||DF || || ||11:00 ||'''P4.''' Elementary Modes of the Woods-Ljungdahl Pathway ||[[Meetings/Nottingham2024/Prac4|Prac4]] ||All || |
| Line 41: | Line 37: |
| || ||PM ''' ''' ||Lecture 9: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||DS || || || ||P6. Identifying pathways for TAG synthesis in ''P. tricornutm'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P6|Prac6]] ||All || || ||16:45 ||close || || || ||Friday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||Lecture 10. ''Cupriavadus necator'' ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L10.pdf|Slides]] ||NP || || || ||P6 (ctd) P7: KOs for ethelene production in ''C. necator'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P7|Prac7]] || || |
|| ||14:00 ||'''L6:''' Linear programming and flux balance analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L6.pdf|Slides]] ||MP || || ||15:00 ||'''L7: ''' ''Phaeodactylum tricornutum'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L7.pdf|Slides]] ||MP || || || ||'''P5: '''TAG synthesis in''' '''''P. tricornutum'' ||[[Meetings/Nottingham2024/Prac5|Prac5]] ||All || || || || || || || ||Thursday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||'''P5:''''' (continued) '' ||[[Meetings/Nottingham2024/Prac5|Prac5]] ||- || || ||10:00 ||'''L8:''' Reaction Correlation Coefficients and LPEMs ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L8.pdf|Slides]] ||CS || |
| Line 48: | Line 45: |
| || ||14:00 ||Concluding remarks, discussion, feedback || || || | || ||14:00 ||'''P6:''' Elementary Modes in the'' A. woodii ''model ||[[Meetings/Nottingham2024/Prac6|Prac6]] ||All || |
| Line 50: | Line 47: |
| || || || || | ||Friday ||AM || || || || || ||09:00 ||Discussion || ||All || || ||12:00 ||Lunch || || ||14:00 ||Go Home ! || |
(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)
- 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 |
L1: Introduction to python and metabolic modelling |
MP |
|
|
|
Tea/coffee |
|
|
|
15:00 |
P1: Computers: checking internet connectivity, software installation.-> P2 |
All |
|
|
16:00 |
P2: Introduction to Python |
All |
|
Tuesday |
AM |
|
|
|
|
09:00 |
P2: Introduction to Python (continued) |
All |
|
|
10:00 |
L2: Introduction to metabolic modelling |
DF |
|
|
11:00 |
L3: Null space, subsets and elementary modes |
CS |
|
|
13:00 |
Lunch |
|
|
|
14:00 |
P3: Basic Model Properties |
All / MP |
|
|
16:00 |
L4: Construction and Curation of GSMs |
TD |
|
|
|
|
|
|
Wednesday |
|
|
|
|
|
09:00 |
P3: (continued) |
|
All |
|
10:00 |
L5: Biotechnological applications of elementary modes analysis |
DF |
|
|
11:00 |
P4. Elementary Modes of the Woods-Ljungdahl Pathway |
All |
|
|
13:00 |
Lunch |
|
|
|
14:00 |
L6: Linear programming and flux balance analysis |
MP |
|
|
15:00 |
L7: Phaeodactylum tricornutum |
MP |
|
|
|
P5: TAG synthesis in P. tricornutum |
All |
|
|
|
|
|
|
Thursday |
AM |
|
|
|
|
09:00 |
P5: (continued) |
- |
|
|
10:00 |
L8: Reaction Correlation Coefficients and LPEMs |
CS |
|
|
13:00 |
Lunch |
|
|
|
14:00 |
P6: Elementary Modes in the A. woodii model |
All |
|
|
|
|
|
|
Friday |
AM |
|
|
|
|
09:00 |
Discussion |
|
All |
|
12:00 |
Lunch |
||
|
14:00 |
Go Home ! |