Metabolic Modelling: Tools, Techniques, and Applications in Research
Nepal 2024
Tutors
- Dr Mark Poolman (MP: Oxford Brookes University - online)
- Dr Dipali Singh (DS: Quadram Institute, Norwich)
- Pareena Verma (PV: Oxford Brookes University - online)
- Dr Trunil Desai (TD: Oxford Brookes University)
Guest Speaker
- Dr Anu Raghunathan (AR: National Chemical Laboratory, Pune - online)
Course Timetable and Resources
Day |
Time |
Activity |
Links |
Tutor |
Day 1 - Mon(23/09) |
|
|
|
|
AM |
09:30 |
Arrival, Admin & Registration etc |
|
|
|
10:00 |
Welcome and introduction to the course |
|
DS |
|
|
From Genome Sequence to Pathway using Pathway Tools |
Demo |
DS |
|
|
Lecture 1: Introduction to metabolic modelling. |
TD/MP |
|
|
|
P1: Computers: checking internet connectivity, software installation. |
All |
|
PM |
12:00 |
Lunch |
|
|
|
|
P1: Continue |
|
|
|
14:00 |
Lecture 2: Python and computational representation of metabolic networks. |
TD/MP |
|
|
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Lecture 3: Why do metabolic modelling? |
|
MP |
|
15:00 |
Tea/Coffee Break |
|
|
|
15:30 |
P2: Python and ScrumPy |
All |
|
|
17:00 |
Close |
|
|
Day 2 - Tues(24/09) |
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|
|
|
AM |
10:00 |
Lecture 4: Linear programming, Flux Balance Analysis and Applications |
Guest Lecture |
AR |
PM |
12:00 |
Lunch |
|
|
|
13:00 |
P4: Biofilm formation in opportunistic human pathogen Staphylococcus epidermidis |
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|
|
15:00 |
Tea/Coffee Break |
|
|
|
15:30 |
P4: Continue |
|
|
|
17:00 |
Close |
|
|
Day 3 Wed (25/09) |
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|
|
|
AM |
10:00 |
Lecture 5: Identification of nutrient requirements for growth of Campylobacter jejuni |
DS |
|
|
11:00 |
P5: Identification of nutrient requirements for growth of Campylobacter jejuni |
All |
|
PM |
12:00 |
Lunch |
|
|
|
14:00 |
Lecture 6: Antimicrobial target identification by GSMM |
PV/MP |
|
|
|
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. |
|
|
|
17:00 |
Close |
|
|
Day 4 - Thurs (26/09) |
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|
|
|
AM |
10:00 |
P6: continue |
|
All |
APM |
12:00 |
Lunch |
|
|
|
13:00 |
Participants to present the outcome of the group discussion |
|
All |
|
15:00 |
Finish Practicals/General Discussion |
|
All |
|
|
Go Home! |
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