|
Size: 4612
Comment:
|
Size: 4462
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 15: | Line 15: |
| Draft [[attachment:TimeTable.pdf]] (Will definitely change!) | . [[attachment:TimeTable.pdf]] (Subject to change!) |
| Line 21: | Line 21: |
| * David Fell (DF: Oxford Brookes University) * Yanica Said (YS: Oxford Brookes University) * Dipali Singh (DS: Quadram Institute, Norwhich) * Nicole Pearcy (NP: University of Nottingham) |
* David Fell (DF: Oxford Brookes University) * Yanica Said (YS: Oxford Brookes University) * Dipali Singh (DS: Quadram Institute, Norwich) * Nicole Pearcy (NP: University of Nottingham) |
| Line 27: | Line 27: |
| * Prof. John Wain (Quadram Institute, Norwhich) | * Prof. John Wain (JW: Quadram Institute, Norwich) |
| Line 30: | Line 30: |
| . A reading list for topics covered in the course is provided [[Meetings/Nepal2018/Reading|here]]. | . A reading list for topics covered in the course is provided [[Meetings/Nottingham2022/Reading|here]]. |
| Line 38: | Line 38: |
| ||' ||??? ||''Introductions. Each participant introduces themself in 2-3 sentences: name, place of study/work; what they do. '' ||''?? Do this or similar ??<<BR>>'' ||''Everyone '' || || || ||Welcome and introduction to the course. Outline of the week ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L0.pdf|Slides]] ||DF || || ||14:00 ||L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||DF || |
|| ||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. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||DF || |
| Line 42: | Line 42: |
| || || ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||MP || | || || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||MP || |
| Line 45: | Line 45: |
| ||Wednesday ''' ''' ||AM ''' ''' || || || || || ||09:30 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||NP || |
||Wednesday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||NP || |
| Line 52: | Line 52: |
| || ||PM ''' ''' ||L3b. Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF || | || ||PM ''' ''' ||L3b. Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF || |
| Line 59: | Line 59: |
| ||Thursday ''' ''' || || || || || | ||Thursday ''' ''' || || || || || |
| Line 66: | Line 66: |
| || ||PM ''' ''' ||L7. The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM || | || ||PM ''' ''' ||L7. The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM || |
| Line 69: | Line 69: |
| ||Friday ''' ''' ||AM ''' ''' || || || || || ||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 || |
||Friday ''' ''' ||AM ''' ''' || || || || || ||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 || |
Under Construction - Ignore !
Overview
TimeTable.pdf (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 |
L3. Null space and elementary modes |
NP |
|
|
|
Demo for Prac 2. |
|
MP |
|
|
P2. Python and ScrumPy (Part 1) |
All |
|
|
11:00 |
Break |
|
|
|
|
P2. Python and ScrumPy (Part 2) |
All |
|
|
13:00 |
Lunch |
|
|
|
PM |
L3b. Examples of Elementary Modes Analysis |
DF |
|
|
|
L4. Biotechnological applications of metabolic network analysis |
DF |
|
|
|
Demo for Prac 3 |
|
TBC |
|
|
P3. Models, kernels, subsets and elementary modes |
All |
|
|
|
Break |
|
|
|
|
P3. Models, kernels, subsets and elementary modes (continued) |
|
All |
|
16:45 |
Close |
|
|
Thursday |
|
|
|
|
|
09:30 |
Demo for Prac4 |
|
MP |
|
|
P4. Structural analysis of the Calvin Cycle. |
Prac 4 ***instructions |
ALL |
|
11:00 |
Break |
|
|
|
|
L5. Linear Programming and Flux Balance Analysis |
NM |
|
|
|
L6. Sources of data for metabolic models |
DF |
|
|
13:00 |
Lunch |
|
|
|
PM |
L7. The unique metabolism of Acetobacterium woodii |
NM |
|
|
|
P5. Flux Balance Analysis of alkane biosynthesis in E coli. |
All |
|
|
16:45 |
close |
|
|
Friday |
AM |
|
|
|
|
09:30 |
L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP |
MP, DF |
|
|
|
P5 Flux Balance Analysis of alkane biosynthesis in E coli. |
|
|
|
11:00 |
Break |
|
|
|
|
Practical 5 continues |
|
|
|
13:00 |
Lunch |
|
|
|
|
Conclusions |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|