|
Size: 4091
Comment:
|
Size: 4075
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 52: | Line 52: |
| || || ||P4. Elementary Modes of the Woods-Ljungdahl Pathway ||[[Meetings/Nottingham2022/Prac4|Prac4]]||All || | || || ||P4. Elementary Modes of the Woods-Ljungdahl Pathway ||[[Meetings/Nottingham2022/Prac4|Prac4]] ||All || |
| Line 54: | Line 54: |
| || ||09:00 ||L5: Linear programming and Flux Balance Analysis || ||MP || || || ||L6: Validation and construction of models || ||MP|DS|| |
|| ||09:00 ||L5: Linear programming and Flux Balance Analysis || ||DS|MP || || || ||L6: Validation and construction of models '''(Naming Conventions)''' || ||MP|DS || |
| Line 57: | Line 57: |
| || || ||L7: ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||NM || || || ||L6. Sources of data for metabolic models ||[[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/L5.pdf|Slides]] ||DS || || || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||DF || |
| Line 60: | Line 60: |
| || ||PM ''' ''' ||L7. The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM || || || ||P5. Flux Balance Analysis of alkane biosynthesis in ''E coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] ||All || |
|| ||PM ''' ''' ||L8: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM || || || ||P6. Identifying pathways for TAG synthesis in ''P. tricornutm'' ||[[Meetings/Nepal2018/Prac5|Prac 5]] ||All || |
| Line 64: | Line 64: |
| || ||09:30 ||L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||MP, DF || || || ||P5 Flux Balance Analysis of alkane biosynthesis in ''E coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] || || || ||11:00 ||Break || || || || || ||Practical 5 continues || || || |
|| ||09:00 ||L8. ''Cupriavadus necator'' ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||NP || || || ||P6 (ctd) P7: KOs for ethelene production in ''C. necator'' ||[[Meetings/Nepal2018/Prac5|Prac 5]] || || |
| Line 69: | Line 67: |
| || || ||Conclusions || || || | || ||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 |
|
|
|
03/04/22 |
09:00 |
Arrival, Admin & Registration |
|
|
|
PM |
|
|
|
|
12:00 |
Lunch |
|
|
|
13:00 |
Welcome and introduction to the course. Outline of the week. |
' |
MP et al |
|
|
Lecture 1: Title TBC |
|
JW |
|
|
Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
DF |
|
|
|
Tea/coffee |
|
|
|
|
Lecture 3: Python and computational representation of metabolic networks. |
MP |
|
|
|
P1. Computers: checking internet connectivity, software installation. |
Installation of ScrumPy. |
All |
|
|
Close |
|
|
Wednesday |
AM |
|
|
|
|
09:00 |
P2. Python and ScrumPy |
All |
|
|
|
L3. Null space, subsets and elementary modes |
MP |
|
|
11:00 |
Break |
|
|
|
|
P3. Null space, subsets and elementary modes |
All |
|
|
13:00 |
Lunch |
|
|
|
PM |
L4. A. woodii and the elementary modes of the Woods-Ljungdahl Pathway |
DF |
|
|
|
P4. Elementary Modes of the Woods-Ljungdahl Pathway |
All |
|
Thursday |
|
|
|
|
|
09:00 |
L5: Linear programming and Flux Balance Analysis |
|
DS|MP |
|
|
L6: Validation and construction of models (Naming Conventions) |
|
MP|DS |
|
11:00 |
Break |
|
|
|
|
L7: Determination of minimal media requirements for Campylobacter jejuni |
DS |
|
|
|
P5: Determination of minimal media requirements for Campylobacter jejuni |
DF |
|
|
13:00 |
Lunch |
|
|
|
PM |
L8: Phaeodactylum tricornutm for biofuel synthesis |
NM |
|
|
|
P6. Identifying pathways for TAG synthesis in P. tricornutm |
All |
|
|
16:45 |
close |
|
|
Friday |
AM |
|
|
|
|
09:00 |
L8. Cupriavadus necator |
NP |
|
|
|
P6 (ctd) P7: KOs for ethelene production in C. necator |
|
|
|
13:00 |
Lunch |
|
|
|
14:00 |
Concluding remarks, discussion, feedback |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|