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Innotargets: Introduction to Metabolic Modelling

India 2023

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	Lecturer
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?		M, AR
	13:30	Lecture 1: Introduction to metabolic modelling.	Slides	TBD
	15:00	Tea/coffee
	15:30	Lecture 2: Python and computational representation of metabolic networks.	Slides	TBD
	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	TBD
	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	TBD
	15:00	tea/coffe
	15:30	P4: LP - maybe?
	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: INNOTARGETS - AMR		PV
	12:00	P5: INNOTARGETS practical		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 - Friday(20/09)
AM	09:00	Finish Practicals/General Discussion		All
		Go Home!

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-== Barcelona 2023 ==
+== India 2023 ==
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-|| ||13:30||Lecture 1:  Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||TBD ||
+|| ||13:30 ||Lecture 1:  Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||TBD ||
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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 ||
+|| ||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 ||
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-|| ||10:00||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona/Prac3|Prac3]] ||All ||
+|| ||10:00 ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona/Prac3|Prac3]] ||All ||
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-|| ||11:30||P3 continues || ||All||
+|| ||11:30 ||P3 continues || ||All ||
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-|| ||14:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]]||TBD ||
|| ||15:00||tea/coffe|| || ||
|| ||15:30||P4: LP - maybe?|| || ||
|| ||16:00||FBA - Title to be added by Anu|| ||AR||
+|| ||14:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||TBD ||
|| ||15:00 ||tea/coffe || || ||
|| ||15:30 ||P4: LP - maybe? || || ||
|| ||16:00 ||FBA - Title to be added by Anu || ||AR ||
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-||AM ||09:00 || || || ||
|| || ||Lecture 5: Response to varying ATP demand in a metabolic model of '' Salmonella typhimurium'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L5.pdf|Slides]] ||MP ||
|| ||10:30 ||Break || || ||
|| || ||P4 Central metabolism of ''S. epidermidis'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] ||YS/DS ||
+||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 ||
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-|| ||13:00 ||Lunch || || ||
|| || ||Lecture 6: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L6.pdf|Slides]] ||DS ||
|| || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All ||
+|| || ||Lunch || || ||
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-||Friday || || || || ||
||AM ||09:00 ||Lecture 7: construction and validation ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.pdf|Slides]] ||DS ||
|| || ||Finish practicals/General discussion/Something else ||[[https://mudshark.brookes.ac.uk/Meetings/C1NetWork1/Prac7|Prac6]] ||(Optional if time allows) ||
|| ||13:00 ||Lunch || || ||
|| || ||Go home! || || ||
+|| ||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 ||
|| || || || || ||
||Day 4 - Friday(20/09) || || || || ||
||AM ||09:00 ||Finish Practicals/General Discussion || ||All ||
|| || ||Go Home! || || ||
|| || || || || ||
|| || || || || ||