Differences between revisions 5 and 28 (spanning 23 versions)

This web page under is under construction.

Metabolic Modelling: Tools, Techniques, and Applications in Research

India 2024

Tutors

Dr Mark Poolman (MP: Oxford Brookes University)
Dr Anu Raghunathan (AR: NCL, Pune)
Dr Dipali Singh (DS: Quadram Institute, Norwich)
Pareena Verma (PV: Oxford Brookes University)
Dr Trunil Desai (TD: Oxford Brookes University)

Guest Speaker

Course Timetable and Resources

Day	Time	Activity	Links	Tutor
Day 1 - Tues(17/09)
AM	09:00	Arrival, Admin & Registration etc
	12:00	Lunch

PM	13:00	Welcome and introduction to the course - why do modelling?		MP, AR
	13:30	Lecture 1: Introduction to metabolic modelling.	Slides	PV/TD
	15:00	Tea/coffee
	15:30	Lecture 2: Python and computational representation of metabolic networks.	Slides	TD
	16:30	P1. Computers: checking internet connectivity, software installation.	Prac1	All
		P2. Python and ScrumPy	Prac2	All
		Close

Day 2 - Wed (18/09)
AM	09:00	Lecture 3: Null space, elementary modes and conserved cycles	Slides	MP
	10:00	P3. Null space, subsets and elementary modes	Prac3	All
	11:00	tea/coffee
	11:30	P3 continues		All
		Lunch

PM	13:00	Guest lecture		Sudip
	14:00	Lecture 4. Linear programming and Flux Balance Analysis	Slides	MP
	15:00	tea/coffe
	15:30	P4: Linear programming and Flux Balance Analysis	Prac4
	16:00	FBA - Title to be added by Anu		AR

Day 3 Thurs (19/09)
AM	09:00	Lecture 5: Construction and Validation of GSMs	Slides	DS
	10:00	Lecture 6: Application of GSMM in cancer biology/CoVID model?		AR
	11:00	Lecture 7: Antimicrobial target identification by GSMM - INNOTARGETS	Slides	MP/PV
	12:00	P5: Antimicrobial target identification by GSMM - INNOTARGETS	Prac5 Materials	All

		Lunch

	14:00	Lecture 8: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
	15:00	P6: Determination of minimal media requirements for Campylobacter jejuni	Prac6	All

Day 4 - Fri (20/09)
AM	09:00	Finish Practicals/General Discussion		All
		Go Home!

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-= Innotargets: Introduction to Metabolic Modelling =
== India 2023 ==
+= This web page under is under construction. =
= Metabolic Modelling: Tools, Techniques, and Applications in Research =
== India 2024 ==
-Line 14:
+Line 15:
-||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' ||
+||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Tutor''' ||
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-||PM ||13:00 ||Welcome and introduction to the course - why do modelling? || ||M, AR ||
|| ||13:30 ||Lecture 1:  Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||TBD ||
+||PM ||13:00 ||Welcome and introduction to the course - why do modelling? || ||MP, AR ||
|| ||13:30 ||Lecture 1:  Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L1.pdf|Slides]] ||PV/TD ||
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-|| ||15:30 ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L2.pdf|Slides]] ||TBD ||
|| ||16:30 ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona2023/ScrumPyInstall|Prac1]] ||All ||
|| || ||P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
+|| ||15:30 ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L2.pdf|Slides]] ||TD ||
|| ||16:30 ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/ScrumPyInstall|Prac1]] ||All ||
|| || ||P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac2|Prac2]] ||All ||
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-||AM ||09:00 ||Lecture 3: Null space, elementary modes and conserved cycles ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||TBD ||
|| ||10:00 ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona/Prac3|Prac3]] ||All ||
+||AM ||09:00 ||Lecture 3: Null space, elementary modes and conserved cycles ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||MP ||
|| ||10:00 ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac3|Prac3]] ||All ||
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-||PM ||13:00 ||Guest lecture || ||Sudip? ||
|| ||14:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||TBD ||
+||PM ||13:00 ||Guest lecture || ||Sudip ||
|| ||14:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L4.pdf|Slides]] ||MP ||
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-|| ||15:30 ||P4: LP - maybe? || || ||
+|| ||15:30 ||P4: Linear programming and Flux Balance Analysis ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac4|Prac4]] || ||
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-||AM ||09:00 ||Lecture 5: Construction and Validation of GSMs||Slides||DS||
|| ||10:00||Lecture 6: Application of GSMM in cancer biology/CoVID model? || ||AR ||
|| ||11:00 ||Lecture 7: INNOTARGETS - AMR || ||PV||
|| ||12:00||P5: INNOTARGETS practical || ||All ||
+||AM ||09:00 ||Lecture 5: Construction and Validation of GSMs ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L5.pdf|Slides]] ||DS ||
|| ||10:00 ||Lecture 6: Application of GSMM in cancer biology/CoVID model? || ||AR ||
|| ||11:00 ||Lecture 7: Antimicrobial target identification by GSMM - INNOTARGETS ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L7.pdf|Slides]] ||MP/PV ||
|| ||12:00 ||P5: Antimicrobial target identification by GSMM - INNOTARGETS ||[[http://mudsharkstatic.brookes.ac.uk/India2024/P5_instructions.pdf|Prac5]]  [[http://mudsharkstatic.brookes.ac.uk/India2024/P5_tar.tar|Materials]] ||All ||
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-|| ||14:00||Lecture 8: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L6.pdf|Slides]] ||DS ||
|| ||15:00||P6: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac6]] ||All ||
+|| ||14:00 ||Lecture 8: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L8.pdf|Slides]] ||DS ||
|| ||15:00 ||P6: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac6]] ||All ||
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-||Day 4 - Friday(20/09) || || || || ||
+||Day 4 - Fri (20/09) || || || || ||
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-|| || || || || ||
|| || || || || ||