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Workshop on Metabolic Modelling

Nottingham 2022

Tutors

Mark Poolman (MP: Oxford Brookes University)
David Fell (DF: Oxford Brookes University)
Yanica Said (YS: Oxford Brookes University)
Oliver Ebenhöh (OE: Heinrich-Heine-Universität, Dusseldorf)
Dipali Singh (DS: Quadram Institute, Norwhich)
Nicole Pearcy (NP: University of Nottingham)

Reading List

A reading list for topics covered in the course is provided here.

Course Timetable and Resources

Day

Time

Activity

Links

Lecturer

Tuesday	AM
03/04/22	09:00	Arrival, Admin & Registration
	PM
	13:00	Lunch
'	???	Introductions. Each participant introduces themself in 2-3 sentences: name, place of study/work; what they do.	?? Do this or similar ??	Everyone
		Welcome and introduction to the course. Outline of the week	Slides	DF
	14:00	L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks.	Slides	DF
		Tea/coffee
		L2. Computational representation of metabolic networks	Slides	MP
		P1. Computers: checking internet connectivity, software installation.	Installation of ScrumPy.	All
		Close
Wednesday	AM
	09:30	L3. Null space and elementary modes	Slides	NM
		Demo for Prac 2.		TBC
		P2. Python and ScrumPy (Part 1)	Prac2	All
	11:00	Break
		P2. Python and ScrumPy (Part 2)	Prac2	All
	13:00	Lunch
	PM	L3b. Examples of Elementary Modes Analysis	Slides	DF
		L4. Biotechnological applications of metabolic network analysis	Slides	DF
		Demo for Prac 3		TBC
		P3. Models, kernels, subsets and elementary modes	Prac 3	All
		Break
		P3. Models, kernels, subsets and elementary modes (continued)		All
	16:45	Close
Thursday
	09:30	Demo for Prac4		MP
		P4. Structural analysis of the Calvin Cycle.	Prac 4 ***instructions	ALL
	11:00	Break
		L5. Linear Programming and Flux Balance Analysis	Slides	NM
		L6. Sources of data for metabolic models	Slides	DF
	13:00	Lunch
	PM	L7. The unique metabolism of Acetobacterium woodii	Slides ScrumPy_demo	NM
		P5. Flux Balance Analysis of alkane biosynthesis in E coli.	Prac 5	All
	16:45	close
Friday	AM
	09:30	L8. a: Summary of Null-space and linear programming approaches b: Practical applications of LP	Slides; Slides	MP, DF
		P5 Flux Balance Analysis of alkane biosynthesis in E coli.	Prac 5
	11:00	Break
		Practical 5 continues
	13:00	Lunch
	14:00	L9 Modelling photosynthesis in eukaryotes.	Slides	KA
		L10 Beyond structural modelling		EA
		Closing and Presentation of Certificates
	16:45	Depart

None: Meetings/Nottingham2022/Timetable (last edited 2024-11-20 15:33:18 by mark)

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||''''||???||''Introductions.  Each participant introduces themself in 2-3 sentences: name, place of study/work; what they do. '' ||''?? Do this or similar ??<<BR>>''||''Everyone '' ||
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|| ||13:00 ||Lunch || || ||
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-|| ||'''PM''' ||L3b.  Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3b.pdf|Slides]] ||DF ||
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-|| ||'''PM''' ||L7.  The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] [[Meetings/Nepal2018/ScrumPy_demo|ScrumPy_demo]] ||NM ||
+|| ||PM  ''' ''' ||L7.  The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] [[Meetings/Nepal2018/ScrumPy_demo|ScrumPy_demo]] ||NM ||
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|| ||09:30 ||L8. '''a''': Summary of Null-space and linear programming approaches   '''b''': Practical applications of LP ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||MP, DF ||
+||Friday  ''' ''' ||AM  ''' ''' || || || ||
|| ||09:30 ||L8. a: Summary of Null-space and linear programming approaches   b''': Practical applications of LP ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||MP, DF ||
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