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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

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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

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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

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Tea/coffee
L2. Computational representation of metabolic networks	Slides	MP
P1. Computers: checking internet connectivity, software installation.	Installation of ScrumPy.	All

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		Close
Wednesday	AM

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		Close
Wednesday	AM

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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

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Thursday

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Thursday

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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

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Friday

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Friday

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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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|| ||14:00 ||L1.  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L1.pdf|Slides]] ||DF ||




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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 '' ||
|| || ||Welcome and introduction to the course.    Outline of the week ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L0.pdf|Slides]] ||DF ||
|| ||14:00 ||L1.  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L1.pdf|Slides]] ||DF ||


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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 ||
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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 ||