Differences between revisions 3 and 4

Innotargets: Introduction to Metabolic Modelling

Barcelona 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: Response to varying ATP demand in a metabolic model of Salmonella typhimurium	Slides	MP
	10:30	Break
		P4 Central metabolism of S. epidermidis	Prac4	YS/DS

	13:00	Lunch
		Lecture 6: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
		P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	All

Friday
AM	09:00	Lecture 7: construction and validation	Slides	DS
		Finish practicals/General discussion/Something else	Prac6	(Optional if time allows)
	13:00	Lunch
		Go home!

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- * Dr Anu Raghunathan
 * Dr Dipali Singh
 * Pareena Verma
+ * Dr Anu Raghunathan (AR: NCL, Pune)
 * Dr Dipali Singh (DS: Quadram Institute, Norwich)
 * Pareena Verma  (PV: Oxford Brookes University)
 Line 10:
- * 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)
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+Line 11:
- * Dr. Rodriguez-Caso (University of Malaga)
+ * TBD
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+Line 15:
-||30/05/23 Tuesday || || || || ||
||AM ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
|| ||13:00 ||Lunch || || ||
+||Day 1 - Tues(17/09) || || || || ||
||AM ||09:00 ||Arrival, Admin & Registration etc || || ||
|| ||12:00 ||Lunch || || ||
-Line 24:
+Line 19:
-||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? || ||M, AR ||
|| ||13:30||Lecture 1:  Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||TBD ||
|| ||15:00 ||Tea/coffee || || ||
|| ||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 ||
-Line 30:
+Line 25:
-|| ||1800 ||Close || || ||
+|| || ||Close || || ||
-Line 32:
+Line 27:
-||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]] ||TBD ||
|| ||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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+Line 34:
-||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]]||TBD ||
|| ||15:00||tea/coffe|| || ||
|| ||15:30||P4: LP - maybe?|| || ||
|| ||16:00||FBA - Title to be added by Anu|| ||AR||
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+Line 40:
-||Thursday || || || || ||
||AM ||09:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||OE ||
+||Day 3 Thurs (19/09) || || || || ||
||AM ||09:00 || || || ||