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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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| * Dr Mark Poolman (MP: Oxford Brookes University) * Dr Anu Raghunathan (AR: NCL, Pune) |
* 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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| TBD | * Dr Anu Raghunathan (AR: National Chemical Laboratory, Pune - online) |
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| ||<(v height="17px">'''Day'''||<(v>'''Time'''||<(v>'''Activity'''||<(v>'''Links'''||<(v>'''Tutor'''|| ||<(v height="17px">Day 1 – Monday||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>|| ||<(v height="17px">AM||<)v>09:30:00||<(v>Arrival, Admin etc ||<(v><<BR>>||<(v><<BR>>|| ||<( height="17px"> ||<)>10:00:00||<(>Welcome and introduction to the course - why do modelling?||<(> ||<(>MP|| ||<( height="17px"> ||<)>10:30:00||<(v>Lecture 1: Introduction to metabolic modelling. ||<(> ||<(>TBD|| ||<( height="17px"> ||<(> ||<(v>Lecture 2: Python and computational representation of metabolic networks.||<(> ||<(>TBD|| ||<( height="17px"> ||<(> ||<(v>P1. Computers: checking internet connectivity, software installation.||<(> ||<(>All|| ||<(v height="17px"><<BR>>||<)v>12:00:00||<(v>Lunch ||<(v><<BR>>||<(v><<BR>>|| ||<(v height="17px">PM||<)v>13:00:00||<(v>P1. Contd.||<(v><<BR>>||<(v>All|| ||<(v height="17px"><<BR>>||<)v>13:30:00||<(>P2. Python and ScrumPy||<(v><<BR>>||<(v>All|| ||<(v height="17px"><<BR>>||<)v>17:00:00||<(v>Close||<(v><<BR>>||<(v><<BR>>|| ||<( height="17px"> ||<(> ||<(> ||<(> ||<(> || ||<(v height="17px">Day 2 – Tuesday||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>|| ||<(v height="17px">AM||<)v>10:00:00||<(v>Lecture 3: Null space, elementary modes and conserved cycles||<(v><<BR>>||<(v>TBD|| ||<(v height="17px"><<BR>>||<(v><<BR>>||<(v>P3. Null space, subsets and elementary modes||<(v><<BR>>||<(v>All|| ||<(v height="17px"><<BR>>||<)v>12:00:00||<(v>Lunch||<(v><<BR>>||<(v><<BR>>|| ||<(v height="17px">PM||<)v>13:00:00||<(v>Lecture 4: Linear programming and Flux Balance Analysis||<(v><<BR>>||<(v>TBD|| ||<(v height="17px"><<BR>>||<(v><<BR>>||<(v>P4. LP – Central metabolism of Staphylococcus epidermidis||<(v><<BR>>||<(v>All|| ||<(v height="17px"><<BR>>||<)v>17:00:00||<(v>Close||<(v><<BR>>||<(v><<BR>>|| ||<( height="17px"> ||<(> ||<(> ||<(> ||<(> || ||<(v height="17px">Day 3 – Wednesday||<(> ||<(> ||<(> ||<(> || ||<(v height="17px">AM||<)v>10:00:00||<(v>Lecture 5: Construction, Validation and Applications of GSMs||<(v><<BR>>||<(v>DS|| ||<(v height="17px"><<BR>>||<)v>11:00:00||<(v>Lecture 6: Antimicrobial resistance mechanism in E.coli||<(v><<BR>>||<(v>PV|| ||<(v height="17px"><<BR>>||<(v><<BR>>||<(v>Lunch||<(v><<BR>>||<(v><<BR>>|| ||<( height="17px">PM||<)v>13:00:00||<(v>P5: LP – Antimicrobial resistance ||<(v><<BR>>||<(v>All|| ||<(v height="17px"><<BR>>||<)v>15:00:00||<(v>Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied.||<(v><<BR>>||<(v>All|| ||<(v height="17px"><<BR>>||<)v>17:00:00||<(v>Close||<(v><<BR>>||<(v><<BR>>|| ||<(v height="17px"><<BR>>||<(> ||<(> ||<(> ||<(> || ||<( height="17px"> ||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>|| ||<(v height="17px">Day 4 – Thursday||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>|| ||<(v height="17px">AM||<)v>10:00:00||<(v>Participants to present the outcome of the group discussion||<(v><<BR>>||<(v>All|| ||<(v height="17px"><<BR>>||<(v><<BR>>||<(v>Lunch||<(v><<BR>>||<(v><<BR>>|| ||<(v height="17px">PM||<)v>13:00:00||<(v>Lecture 7: Determination of minimal media requirements for Campylobacter jejuni||<(v><<BR>>||<(v>DS|| ||<(v height="17px"><<BR>>||<)v>14:00:00||<(v>P6: Determination of minimal media requirements for Campylobacter jejuni||<(v><<BR>>||<(v>All|| ||<(v height="17px"><<BR>>||<)v>17:00:00||<(v>Close||<(v><<BR>>||<(v><<BR>>|| |
== 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. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L1.pdf|Slides]] ||TD/MP || || || ||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 || || ||15:00 ||Tea/Coffee Break || || || || ||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 || || || ||Day 2 - Tues(24/09) || || || || || ||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'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] || || || ||15:00 ||Tea/Coffee Break || || || || ||15:30 ||P4: Continue || || || || ||17:00 ||Close || || || ||Day 3 Wed (25/09) || || || || || ||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 || ||PM ||12:00 ||Lunch || || || || ||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 || || ||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) || || || || || ||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! || || || |
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 |
|
|
|
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) |
|
|
|
|
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 |
|
|
|
15:00 |
Tea/Coffee Break |
|
|
|
15:30 |
P4: Continue |
|
|
|
17:00 |
Close |
|
|
Day 3 Wed (25/09) |
|
|
|
|
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) |
|
|
|
|
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! |
|
|