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| * Dr Mark Poolman (MP: Oxford Brookes University) | * Dr Mark Poolman (MP: Oxford Brookes University - online) |
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| * Pareena Verma (PV: Oxford Brookes University) | * Pareena Verma (PV: Oxford Brookes University - online) |
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| * Dr Anu Raghunathan (AR: National Chemistry Laboratory, Pune) | * Dr Anu Raghunathan (AR: National Chemical Laboratory, Pune - online) |
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| ||PM ||09:30 ||Arrival, Admin & Registration etc || || || || ||10:00 ||Welcome and introduction to the course - why do modelling? || ||DS/MP || |
||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 || |
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| || || ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L2.pdf|Slides]] ||TD/MP || || || ||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 || |
|| || ||P1: Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Nepal2024/ScrumPyInstall|Prac1]] ||All || ||PM ||12:00 ||Lunch || || || || || ||P1: Continue || || || || ||14:00 ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L2.pdf|Slides]] ||TD/MP || || || ||Lecture 3: Why do metabolic modelling? || ||MP || |
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| || ||15:30 ||P2: Continue || || || || || ||Close || || || |
|| ||15:30 ||P2: Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/Nepal2024/Prac2|Prac2]] [[https://mudshark.brookes.ac.uk/Meetings/Nepal2024/Prac3|Prac3]] ||All || || ||17:00 ||Close || || || |
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| ||AM ||10:00 ||Lecture 3: Genome to Pathway using Pathway Tools ||Demo ||DS || || ||11:00 ||Lecture 4: Linear programming, Flux Balance Analysis and Applications ||Guest Lecture ||AR || |
||AM ||10:00 ||Lecture 4: Linear programming, Flux Balance Analysis and Applications ||Guest Lecture ||AR || |
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| || ||13:00 ||P4: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] || || | || ||13:00 ||P4: Biofilm formation in opportunistic human pathogen ''Staphylococcus epidermidis'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] || || |
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| || ||16:00 ||Lecture 5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L7.pdf|Slides]] ||DS || || || ||Close || || || |
|| ||17:00 ||Close || || || |
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| || ||10:00 ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All || | ||AM ||10:00 ||Lecture 5: Identification of nutrient requirements for growth of ''Campylobacter jejuni '' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L7.pdf|Slides]] ||DS || || ||11:00 ||P5: Identification of nutrient requirements for growth of ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All || |
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| || ||13:00 ||Lecture 6: Antimicrobial target identification by GSMM ||[[http://mudsharkstatic.brookes.ac.uk/India2024/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 || |
|| ||14:00 ||Lecture 6: Antimicrobial target identification by GSMM ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L6.pdf|Slides]] ||PV/MP || || || ||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 || |
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| || || ||Close || || || | || ||17:00 ||Close || || || |
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| ||AM ||10:00 ||Participants to present the outcome of the group discussion || || || ||PM ||12:00 ||Lunch || || || || ||13:00 ||P6: Continue || ||All || |
||AM ||10:00 ||P6: continue || ||All|| ||APM ||12:00 ||Lunch || || || || ||13:00 ||Participants to present the outcome of the group discussion || ||All || |
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) |
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AM |
09:30 |
Arrival, Admin & Registration etc |
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10:00 |
Welcome and introduction to the course |
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DS |
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From Genome Sequence to Pathway using Pathway Tools |
Demo |
DS |
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Lecture 1: Introduction to metabolic modelling. |
TD/MP |
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P1: Computers: checking internet connectivity, software installation. |
All |
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PM |
12:00 |
Lunch |
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P1: Continue |
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14:00 |
Lecture 2: Python and computational representation of metabolic networks. |
TD/MP |
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Lecture 3: Why do metabolic modelling? |
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MP |
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15:00 |
Tea/Coffee Break |
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15:30 |
P2: Python and ScrumPy |
All |
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17:00 |
Close |
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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 |
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13:00 |
P4: Biofilm formation in opportunistic human pathogen Staphylococcus epidermidis |
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15:00 |
Tea/Coffee Break |
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15:30 |
P4: Continue |
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17:00 |
Close |
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Day 3 Wed (25/09) |
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AM |
10:00 |
Lecture 5: Identification of nutrient requirements for growth of Campylobacter jejuni |
DS |
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11:00 |
P5: Identification of nutrient requirements for growth of Campylobacter jejuni |
All |
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PM |
12:00 |
Lunch |
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14:00 |
Lecture 6: Antimicrobial target identification by GSMM |
PV/MP |
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P6: Antimicrobial target identification by GSMM |
All |
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15:00 |
Tea/Coffee Break |
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15:30 |
Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied. |
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17:00 |
Close |
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Day 4 - Thurs (26/09) |
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AM |
10:00 |
P6: continue |
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All |
APM |
12:00 |
Lunch |
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13:00 |
Participants to present the outcome of the group discussion |
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All |
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15:00 |
Finish Practicals/General Discussion |
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All |
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Go Home! |
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