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Innotargets: Introduction to Metabolic Modelling

Barcelona 2023

Tutors

Dr Mark Poolman (MP: Oxford Brookes University)
Dr Anu Raghunathan
Dr Dipali Singh
Pareena Verma
Dr Trunil Desai (TD: Oxford Brookes University)
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)

Guest Speaker

Dr. Rodriguez-Caso (University of Malaga)

Course Timetable and Resources

Day	Time	Activity	Links	Lecturer
30/05/23 Tuesday
AM	09:00	Arrival, Admin & Registration Hotel check-in etc
	13:00	Lunch

PM	14:00	Welcome and introduction to the course - why do modelling?		MP
		Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks.	Slides	YS
	15:30	Tea/coffee
		Lecture 2: Python and computational representation of metabolic networks.	Slides	MP
		P1. Computers: checking internet connectivity, software installation.	Prac1	All
		P2. Python and ScrumPy	Prac2	All
	1800	Close

Wednesday
AM	09:00	Lecture 3: Null space, elementary modes and conserved cycles	Slides	OE
		P3. Null space, subsets and elementary modes	Prac3	All
	10:30	tea/coffee
		P3 continues
	13:00	Lunch

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

Thursday
AM	09:00	Lecture 4. Linear programming and Flux Balance Analysis	Slides	OE
		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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+= Innotargets: Introduction to Metabolic Modelling =
== Barcelona 2023 ==
== Tutors ==
 * Dr Mark Poolman (MP: Oxford Brookes University)
 * Dr Anu Raghunathan
 * Dr Dipali Singh
 * Pareena Verma
 * Dr Trunil Desai (TD: Oxford Brookes University)

 * 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)

== Guest Speaker ==
 * Dr. Rodriguez-Caso (University of Malaga)

== Course Timetable and Resources ==
||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' ||
||30/05/23 Tuesday || || || || ||
||AM ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
|| ||13:00 ||Lunch || || ||
|| || || || || ||
||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 ||
|| || ||P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
|| ||1800 ||Close || || ||
|| || || || || ||
||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 || || ||
|| || || || || ||
||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 ||
|| || || || || ||
||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 ||
|| || || || || ||
|| ||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 ||
|| || || || || ||
||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! || || ||