|
Size: 4009
Comment:
|
Size: 3524
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 9: | Line 9: |
| * Prof. David Fell (DF: Oxford Brookes University ) - Online | |
| Line 11: | Line 12: |
| . 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]] |
| Line 20: | Line 21: |
| || || ||Lecture 1: ( Keynote DF online?) ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] || || || || ||Lecture 2: 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]] ||MP || |
| Line 23: | Line 23: |
| || || ||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 || |
|| ||15:00 ||P1. Computers: checking internet connectivity, software installation.-> P2 ||[[https://gitlab.com/MarkPoolman/scrumpy/-/wikis/Manual/Install|Installation]] of [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]]. ||All || || ||16:00 ||P2. Introduction to python || ||All || ||Tuesday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||P2. Pythoncontinued ... ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All || || ||10:00 ||Lecture Intruction to metabolic modelling || ||DF || || ||11:00 ||Lecture: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||CS || || ||13:00 ||Lunch || || || || ||14:00 ||P3. practicalsame as india P3 ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All || || ||16:00 ||Lecture: Construction and curation of GSMs ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] ||TD/PV || |
| Line 26: | Line 33: |
| ||Tuesday ''' ''' ||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]] ||CS || || ||11:00 ||Break || || || || || ||P3. Null space, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac3]] ||All || |
||Wednesday ''' ''' || || || || || || ||09:00 ||P3 continued || ||All || || ||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 ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All || |
| Line 33: | Line 38: |
| || ||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 || ||Wednesday ''' ''' || || || || || || ||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]] ||TD || || ||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]] ||All || || ||13:00 ||Lunch || || || || ||PM ''' ''' ||Lecture 9: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||DS || |
|| ||14:00 ||Lecture: Linear programming and flux balance analysis ||Slides ||MP || || ||15:00 ||Lecture: ''Phaeodactylum tricornutm'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||PV || || || ||P5: ''Phaeodactylum tricornutm'' ||Prac5 ||All || || ||PM ''' ''' ||Lecture: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||DS || |
| Line 47: | Line 45: |
| ||Thursday ''' ''' ||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]] || || |
||Thursday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||P5 continued ||- ||- || || ||10:00 ||Lecture: Correlation coefficients and LPEMs ||Slides ||CS || |
| Line 52: | Line 49: |
| || ||14:00 ||Practical or Lecture here (LPEMs ?? Reaction CCs ??) || || || | || ||14:00 ||P7. LPEM? || ||All || |
| Line 54: | Line 51: |
| ||Friday||AM|| || || || || ||09:00||Complete unfinnished practicals|| || || || ||11:00||General discussion. AOB|| || || || ||13:00||Lunch|| || ||14:00||Go Home !|| |
||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)
- 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 |
MP |
|
|
|
Tea/coffee |
|
|
|
15:00 |
P1. Computers: checking internet connectivity, software installation.-> P2 |
Installation of ScrumPy. |
All |
|
16:00 |
P2. Introduction to python |
|
All |
Tuesday |
AM |
|
|
|
|
09:00 |
P2. Pythoncontinued ... |
All |
|
|
10:00 |
Lecture Intruction to metabolic modelling |
|
DF |
|
11:00 |
Lecture: Null space, subsets and elementary modes |
CS |
|
|
13:00 |
Lunch |
|
|
|
14:00 |
P3. practicalsame as india P3 |
All |
|
|
16:00 |
Lecture: Construction and curation of GSMs |
TD/PV |
|
|
|
|
|
|
Wednesday |
|
|
|
|
|
09:00 |
P3 continued |
|
All |
|
10:00 |
Lecture. Biotechnological applications of elementary modes analysis |
DF |
|
|
11:00 |
P4. Elementary Modes of the Woods-Ljungdahl Pathway |
All |
|
|
13:00 |
Lunch |
|
|
|
14:00 |
Lecture: Linear programming and flux balance analysis |
Slides |
MP |
|
15:00 |
Lecture: Phaeodactylum tricornutm |
PV |
|
|
|
P5: Phaeodactylum tricornutm |
Prac5 |
All |
|
PM |
Lecture: Phaeodactylum tricornutm for biofuel synthesis |
DS |
|
|
|
P6. Identifying pathways for TAG synthesis in P. tricornutm |
All |
|
|
16:45 |
|
|
|
|
|
|
|
|
Thursday |
AM |
|
|
|
|
09:00 |
P5 continued |
- |
- |
|
10:00 |
Lecture: Correlation coefficients and LPEMs |
Slides |
CS |
|
13:00 |
Lunch |
|
|
|
14:00 |
P7. LPEM? |
|
All |
|
|
|
|
|
Friday |
AM |
|
|
|
|
09:00 |
Discussion |
|
All |
|
12:00 |
Lunch |
||
|
14:00 |
Go Home ! |