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| = Overview = . [[attachment:TimeTable.pdf]] (Subject to change!) |
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| * David Fell (DF: Oxford Brookes University) * Yanica Said (YS: Oxford Brookes University) * Oliver Ebenhöh (OE: Heinrich-Heine-Universität, Dusseldorf) * 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) == Guest Speaker == * Prof. John Wain (JW: Quadram Institute, Norwich) |
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| . 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]]. |
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''' ||Tuesday ||AM ''' ''' || || || || |
||Tuesday ||AM ''' ''' || || || || |
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| || ||13:00 ||Lunch || || || ||' ||??? ||''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 || |
|| ||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. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||DF || |
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| || || ||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 || |
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| ||Wednesday ''' ''' ||AM ''' ''' || || || || || ||09:30 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||NM || || || ||Demo for Prac 2. || ||TBC || |
||Wednesday ''' ''' ||AM ''' ''' || || || || || ||09:00 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||NP || || || ||Demo for Prac 2. || ||MP || |
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| || ||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 || |
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| ||Thursday ''' ''' || || || || || | ||Thursday ''' ''' || || || || || |
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| || ||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 || |
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| ||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 || |
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| || ||14:00 ||L9 Modelling photosynthesis in eukaryotes. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||KA || || || ||L10 Beyond structural modelling || ||EA || || || ||Closing and Presentation of Certificates || || || || ||16:45 ||Depart || || || |
|| || ||Conclusions || || || || || || || || || || || || || || || || || || || || || |
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| ''' | ''' ''' |
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 |
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03/04/22 |
09:00 |
Arrival, Admin & Registration |
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PM |
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12:00 |
Lunch |
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13:00 |
Welcome and introduction to the course. Outline of the week. |
' |
MP et al |
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Lecture 1: Title TBC |
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JW |
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Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
DF |
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Tea/coffee |
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Lecture 3: Python and computational representation of metabolic networks. |
MP |
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P1. Computers: checking internet connectivity, software installation. |
Installation of ScrumPy. |
All |
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Close |
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Wednesday |
AM |
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09:00 |
L3. Null space and elementary modes |
NP |
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Demo for Prac 2. |
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MP |
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P2. Python and ScrumPy (Part 1) |
All |
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11:00 |
Break |
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P2. Python and ScrumPy (Part 2) |
All |
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13:00 |
Lunch |
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PM |
L3b. Examples of Elementary Modes Analysis |
DF |
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L4. Biotechnological applications of metabolic network analysis |
DF |
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Demo for Prac 3 |
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TBC |
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P3. Models, kernels, subsets and elementary modes |
All |
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Break |
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P3. Models, kernels, subsets and elementary modes (continued) |
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All |
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16:45 |
Close |
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Thursday |
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09:30 |
Demo for Prac4 |
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MP |
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P4. Structural analysis of the Calvin Cycle. |
Prac 4 ***instructions |
ALL |
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11:00 |
Break |
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L5. Linear Programming and Flux Balance Analysis |
NM |
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L6. Sources of data for metabolic models |
DF |
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13:00 |
Lunch |
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PM |
L7. The unique metabolism of Acetobacterium woodii |
NM |
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P5. Flux Balance Analysis of alkane biosynthesis in E coli. |
All |
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16:45 |
close |
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Friday |
AM |
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09:30 |
L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP |
MP, DF |
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P5 Flux Balance Analysis of alkane biosynthesis in E coli. |
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11:00 |
Break |
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Practical 5 continues |
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13:00 |
Lunch |
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Conclusions |
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