Differences between revisions 62 and 64 (spanning 2 versions)

Metabolic Modelling: Tools, Techniques, and Applications in Research

Nepal 2024

Tutors

Dr Mark Poolman (MP: Oxford Brookes University - online)
Dr Dipali Singh (DS: Quadram Institute, Norwich)
Pareena Verma (PV: Oxford Brookes University - online)
Dr Trunil Desai (TD: Oxford Brookes University)

Guest Speaker

Dr Anu Raghunathan (AR: National Chemical Laboratory, Pune - online)

Course Timetable and Resources

Day	Time	Activity	Links	Tutor
Day 1 - Mon(23/09)
PM	09:30	Arrival, Admin & Registration etc
	10:00	Welcome and introduction to the course		DS
		From genome to pathway using Pathway Tools	Demo	DS
		Lecture 1: Introduction to metabolic modelling.	Slides	TD/MP
		P1. Computers: checking internet connectivity, software installation.	Prac1	All
AM	12:00	Lunch
		P1: Continue
	14:00	Lecture 2: Python and computational representation of metabolic networks.	Slides	TD/MP
		Lecture 3: Why do metabolic modelling?		MP
	15:00	Tea/Coffee Break
	15:30	P2: Python and https://mudshark.brookes.ac.uk/ScrumPy/Doc/Tutorial/ScrumPyIntro	Prac2	All
	17:00	Close
Day 2 - Tues(24/09)
AM	10:00	Lecture 4: Linear programming, Flux Balance Analysis and Applications	Guest Lecture	AR
PM	12:00	Lunch
	13:00	P4: Linear programming and Flux Balance Analysis	Prac4
	15:00	Tea/Coffee Break
	15:30	P4: Continue
	16:00	Lecture 5: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
		Close
Day 3 Wed (25/09)
	10:00	P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	All
PM	12:00	Lunch
	13:00	Lecture 6: Antimicrobial target identification by GSMM	Slides	PV/MP
AM	14:00	P6: Antimicrobial target identification by GSMM	Prac6 Materials	All
	15:00	Tea/Coffee Break
	15:30	Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied.
		Close
Day 4 - Thurs (26/09)
AM	10:00	Participants to present the outcome of the group discussion
PM	12:00	Lunch
	13:00	P6: Continue		All
	15:00	Finish Practicals/General Discussion		All
		Go Home!

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- * Dr Mark Poolman (MP: Oxford Brookes University)
+ * Dr Mark Poolman (MP: Oxford Brookes University - online)
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- * Pareena Verma  (PV: Oxford Brookes University)
+ * Pareena Verma  (PV: Oxford Brookes University - online)
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- * Dr Anu Raghunathan (AR: National Chemistry Laboratory, Pune)
+ * Dr Anu Raghunathan (AR: National Chemical Laboratory, Pune - online)
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-|| ||10:00 ||Welcome and introduction to the course - why do modelling? || ||DS/MP ||
+|| ||10:00 ||Welcome and introduction to the course || ||DS ||
|| || ||From genome to pathway using Pathway Tools ||Demo ||DS ||
-Line 18:
+Line 19:
-|| || ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L2.pdf|Slides]] ||TD/MP ||
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-|| ||13:00 ||P1: Continue || || ||
|| ||14:00 ||P2: Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac2|Prac2]] ||All ||
+|| || ||P1: Continue || || ||
|| ||14:00 ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L2.pdf|Slides]] ||TD/MP ||
|| || ||Lecture 3: Why do metabolic modelling? || ||MP ||
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+Line 25:
-|| ||15:30 ||P2: Continue || || ||
|| || ||Close || || ||
+|| ||15:30 ||P2: Python and [[https://mudshark.brookes.ac.uk/ScrumPy/Doc/Tutorial/ScrumPyIntro]] ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac2|Prac2]] ||All ||
|| ||17:00 ||Close || || ||
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+Line 28:
-||AM ||10:00 ||Lecture 3: Genome to Pathway using Pathway Tools ||Demo ||DS ||
|| ||11:00 ||Lecture 4: Linear programming, Flux Balance Analysis and Applications ||Guest Lecture ||AR ||
+||AM ||10:00 ||Lecture 4: Linear programming, Flux Balance Analysis and Applications ||Guest Lecture ||AR ||