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| = This web page under is under construction. = = Innotargets: Introduction to Metabolic Modelling = == India 2024 == |
= Metabolic Modelling: Tools, Techniques, and Applications in Research = == Nepal 2024 == |
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| TBD ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">'''Day''' ||<style=""text-align:left;vertical-align:bottom"">'''Time''' ||<style=""text-align:left;vertical-align:bottom"">'''Activity''' ||<style=""text-align:left;vertical-align:bottom"">'''Links''' ||<style=""text-align:left;vertical-align:bottom"">'''Tutor''' || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">Day 1 – Monday ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">AM ||<style=""text-align:right;vertical-align:bottom"">09:30:00 ||<style=""text-align:left;vertical-align:bottom"">Arrival, Admin etc ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot" ;&quot""> ||<style=""text-align:right"">10:00:00 ||<style=""text-align:left"">Welcome and introduction to the course - why do modelling? ||<style=""text-align:left""> ||<style=""text-align:left"">MP || ||<height=""" style=""text-align:left; 17px& quot" ;&quot""> ||<style=""text-align:right"">10:30:00 ||<style=""text-align:left;vertical-align:bottom"">Lecture 1: Introduction to metabolic modelling. ||<style=""text-align:left""> ||<style=""text-align:left"">TBD || ||<height=""" style=""text-align:left; 17px& quot" ;&quot""> ||<style=""text-align:left""> ||<style=""text-align:left;vertical-align:bottom"">Lecture 2: Python and computational representation of metabolic networks. ||<style=""text-align:left""> ||<style=""text-align:left"">TBD || ||<height=""" style=""text-align:left; 17px& quot" ;&quot""> ||<style=""text-align:left""> ||<style=""text-align:left;vertical-align:bottom"">P1. Computers: checking internet connectivity, software installation. ||<style=""text-align:left""> ||<style=""text-align:left"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">12:00:00 ||<style=""text-align:left;vertical-align:bottom"">Lunch ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">PM ||<style=""text-align:right;vertical-align:bottom"">13:00:00 ||<style=""text-align:left;vertical-align:bottom"">P1. Contd. ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">13:30:00 ||<style=""text-align:left"">P2. Python and ScrumPy ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">17:00:00 ||<style=""text-align:left;vertical-align:bottom"">Close ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot" ;&quot""> ||<style=""text-align:left""> ||<style=""text-align:left""> ||<style=""text-align:left""> ||<style=""text-align:left""> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">Day 2 – Tuesday ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">AM ||<style=""text-align:right;vertical-align:bottom"">10:00:00 ||<style=""text-align:left;vertical-align:bottom"">Lecture 3: Null space, elementary modes and conserved cycles ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">TBD || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">P3. Null space, subsets and elementary modes ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">12:00:00 ||<style=""text-align:left;vertical-align:bottom"">Lunch ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">PM ||<style=""text-align:right;vertical-align:bottom"">13:00:00 ||<style=""text-align:left;vertical-align:bottom"">Lecture 4: Linear programming and Flux Balance Analysis ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">TBD || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">P4. LP – Central metabolism of Staphylococcus epidermidis ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">17:00:00 ||<style=""text-align:left;vertical-align:bottom"">Close ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot" ;&quot""> ||<style=""text-align:left""> ||<style=""text-align:left""> ||<style=""text-align:left""> ||<style=""text-align:left""> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">Day 3 – Wednesday ||<style=""text-align:left""> ||<style=""text-align:left""> ||<style=""text-align:left""> ||<style=""text-align:left""> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">AM ||<style=""text-align:right;vertical-align:bottom"">10:00:00 ||<style=""text-align:left;vertical-align:bottom"">Lecture 5: Construction, Validation and Applications of GSMs ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">DS || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">11:00:00 ||<style=""text-align:left;vertical-align:bottom"">Lecture 6: Antimicrobial target identification by GSMM - INNOTARGETS ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">PV || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">Lunch ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot" ;&quot"">PM ||<style=""text-align:right;vertical-align:bottom"">13:00:00 ||<style=""text-align:left;vertical-align:bottom"">P5: Antimicrobial target identification by GSMM - INNOTARGETS ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">15:00:00 ||<style=""text-align:left;vertical-align:bottom"">Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied. ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">17:00:00 ||<style=""text-align:left;vertical-align:bottom"">Close ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:left""> ||<style=""text-align:left""> ||<style=""text-align:left""> ||<style=""text-align:left""> || ||<height=""" style=""text-align:left; 17px& quot" ;&quot""> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">Day 4 – Thursday ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">AM ||<style=""text-align:right;vertical-align:bottom"">10:00:00 ||<style=""text-align:left;vertical-align:bottom"">Participants to present the outcome of the group discussion ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">Lunch ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot"">PM ||<style=""text-align:right;vertical-align:bottom"">13:00:00 ||<style=""text-align:left;vertical-align:bottom"">Lecture 7: Determination of minimal media requirements for Campylobacter jejuni ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">DS || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">14:00:00 ||<style=""text-align:left;vertical-align:bottom"">P6: Determination of minimal media requirements for Campylobacter jejuni ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom"">All || ||<height=""" style=""text-align:left; 17px& quot; ;vertical-align:bottom" ;&quot""><<BR>> ||<style=""text-align:right;vertical-align:bottom"">17:00:00 ||<style=""text-align:left;vertical-align:bottom"">Close ||<style=""text-align:left;vertical-align:bottom""><<BR>> ||<style=""text-align:left;vertical-align:bottom""><<BR>> || |
* Dr Anu Raghunathan (AR: National Chemistry Laboratory, Pune) |
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| == Course Timetable and Resources == ||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Tutor''' || ||Day 1 - Mon(23/09) || || || || || ||PM ||09:30 ||Arrival, Admin & Registration etc || || || || ||10:00 ||Welcome and introduction to the course - why do modelling? || ||DS/MP || || || ||Lecture 1: Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L1.pdf|Slides]] ||PV/TD || || || ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L2.pdf|Slides]] ||TD || || || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/ScrumPyInstall|Prac1]] ||All || ||AM ||12:00 ||Lunch || || || || ||13:00 ||P1 Continue || || || || ||14:00 ||P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac2|Prac2]] ||All || || ||15:00 ||Tea/Coffee Break || || || || ||15:30 ||P2 Continue || || || || || ||Close || || || ||Day 2 - Tues(24/09) || || || || || ||AM ||10:00 ||Lecture 3: Genome to Pathway using Pathway Tools ||Demo ||DS || || ||11:00 ||Lecture 4. Linear programming, Flux Balance Analysis and Applications || ||AR || ||PM ||12:00 ||Lunch || || || || ||13:00 ||P4: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] || || || ||15:00 ||Tea/Coffee Break || || || || ||15:30 ||P4. Continue || || || || ||16:00 ||Lecture 5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L8.pdf|Slides]] ||DS || || || ||Close || || || ||Day 3 Wed (25/09) || || || || || || ||10:00 ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All || ||PM ||12:00 ||Lunch || || || || ||13:00 ||Lecture 6: Antimicrobial target identification by GSMM ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L7.pdf|Slides]] ||PV/MP || ||AM ||14:00 ||P6: Antimicrobial target identification by GSMM ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/P5_instructions.pdf|Prac6]] [[http://mudsharkstatic.brookes.ac.uk/Nepal2024/P5_tar.tar|Materials]] ||All || || ||15:00 ||Tea/Coffee Break || || || || ||15:30 ||Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied. || || || || || ||Close || || || ||Day 4 - Thurs (26/09) || || || || || ||AM ||10:00 ||Participants to present the outcome of the group discussion || || || ||PM ||12:00 ||Lunch || || || || ||13:00 ||P6. Continue || || || || ||15:00 ||Finish Practicals/General Discussion || ||All || || || ||Go Home! || || || |
Metabolic Modelling: Tools, Techniques, and Applications in Research
Nepal 2024
Tutors
- Dr Mark Poolman (MP: Oxford Brookes University)
- Dr Dipali Singh (DS: Quadram Institute, Norwich)
- Pareena Verma (PV: Oxford Brookes University)
- Dr Trunil Desai (TD: Oxford Brookes University)
Guest Speaker
- Dr Anu Raghunathan (AR: National Chemistry Laboratory, Pune)
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Tutor |
Day 1 - Mon(23/09) |
|
|
|
|
PM |
09:30 |
Arrival, Admin & Registration etc |
|
|
|
10:00 |
Welcome and introduction to the course - why do modelling? |
|
DS/MP |
|
|
Lecture 1: Introduction to metabolic modelling. |
PV/TD |
|
|
|
Lecture 2: Python and computational representation of metabolic networks. |
TD |
|
|
|
P1. Computers: checking internet connectivity, software installation. |
All |
|
AM |
12:00 |
Lunch |
|
|
|
13:00 |
P1 Continue |
|
|
|
14:00 |
P2. Python and ScrumPy |
All |
|
|
15:00 |
Tea/Coffee Break |
|
|
|
15:30 |
P2 Continue |
|
|
|
|
Close |
|
|
Day 2 - Tues(24/09) |
|
|
|
|
AM |
10:00 |
Lecture 3: Genome to Pathway using Pathway Tools |
Demo |
DS |
|
11:00 |
Lecture 4. Linear programming, Flux Balance Analysis and Applications |
|
AR |
PM |
12:00 |
Lunch |
|
|
|
13:00 |
P4: Linear programming and Flux Balance Analysis |
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|
|
15:00 |
Tea/Coffee Break |
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|
15:30 |
P4. Continue |
|
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|
16:00 |
Lecture 5: Determination of minimal media requirements for Campylobacter jejuni |
DS |
|
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|
Close |
|
|
Day 3 Wed (25/09) |
|
|
|
|
|
10:00 |
P5: Determination of minimal media requirements for Campylobacter jejuni |
All |
|
PM |
12:00 |
Lunch |
|
|
|
13:00 |
Lecture 6: Antimicrobial target identification by GSMM |
PV/MP |
|
AM |
14:00 |
P6: Antimicrobial target identification by GSMM |
All |
|
|
15:00 |
Tea/Coffee Break |
|
|
|
15:30 |
Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied. |
|
|
|
|
Close |
|
|
Day 4 - Thurs (26/09) |
|
|
|
|
AM |
10:00 |
Participants to present the outcome of the group discussion |
|
|
PM |
12:00 |
Lunch |
|
|
|
13:00 |
P6. Continue |
|
|
|
15:00 |
Finish Practicals/General Discussion |
|
All |
|
|
Go Home! |
|
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