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This web page under is under construction.

Innotargets: Introduction to Metabolic Modelling

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: 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: Antimicrobial target identification by GSMM - INNOTARGETS		MP/PV
	12:00	P5: Antimicrobial target identification by GSMM - INNOTARGETS		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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+= This web page under is under construction. =
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-== Barcelona 2023 ==
+== India 2024 ==
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+Line 5:
- * Mark Poolman (MP: Oxford Brookes University)
 * Oliver Ebenhoeh (OE: Heinrich Heine University, Dusseldorf)
 * Yanica Said     (YS:  Oxford Brookes University)
 * Dipali Singh     (DS: Quadram Institute, Norwich)
+ * 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)
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- * Dr. Rodriguez-Caso (University of Malaga)
+ * TBD
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-||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' ||
||30/05/23 Tuesday || || || || ||
||AM ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
|| ||13:00 ||Lunch || || ||
+||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Tutor''' ||
||Day 1 - Tues(17/09) || || || || ||
||AM ||09:00 ||Arrival, Admin & Registration etc || || ||
|| ||12:00 ||Lunch || || ||
 Line 20:
-||PM ||14:00 ||Welcome and introduction to the course - why do modelling? || ||MP ||
|| || ||Lecture 1:  Introduction to metabolic modelling.   Mathematical  representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||YS ||
|| ||15:30 ||Tea/coffee || || ||
|| || ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L2.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona2023/ScrumPyInstall|Prac1]] ||All ||
+||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/Barcelona2023/L1.pdf|Slides]] ||PV/TD ||
|| ||15:00 ||Tea/coffee || || ||
|| ||15:30 ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L2.pdf|Slides]] ||TD ||
|| ||16:30 ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona2023/ScrumPyInstall|Prac1]] ||All ||
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-|| ||1800 ||Close || || ||
+|| || ||Close || || ||
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-||Wednesday || || || || ||
||AM ||09:00 ||Lecture 3: Null space, elementary modes and conserved cycles ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||OE ||
|| || ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona/Prac3|Prac3]] ||All ||
|| ||10:30 ||tea/coffee || || ||
|| || ||P3 continues || || ||
|| ||13:00 ||Lunch || || ||
+||Day 2 - Wed (18/09) || || || || ||
||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/Barcelona/Prac3|Prac3]] ||All ||
|| ||11:00 ||tea/coffee || || ||
|| ||11:30 ||P3 continues || ||All ||
|| || ||Lunch || || ||
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-||PM ||14:00 ||Guest lecture - Synthetic Biology: Uncovering principles of biological design applying math and experiments. || ||Dr. Rodriguez-Caso ||
|| ||15:00 ||Depart social activity || ||All ||
+||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]] ||MP ||
|| ||15:00 ||tea/coffe || || ||
|| ||15:30 ||P4: LP - maybe? || || ||
|| ||16:00 ||FBA - Title to be added by Anu || ||AR ||
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+Line 41:
-||Thursday || || || || ||
||AM ||09:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||OE ||
|| || ||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 ||
+||Day 3 Thurs (19/09) || || || || ||
||AM ||09:00 ||Lecture 5: Construction and Validation of GSMs ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.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 || ||MP/PV ||
|| ||12:00 ||P5: Antimicrobial target identification by GSMM - INNOTARGETS || ||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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+Line 49:
-||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 - Fri (20/09) || || || || ||
||AM ||09:00 ||Finish Practicals/General Discussion || ||All ||
|| || ||Go Home! || || ||