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Overview

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)
Dipali Singh (DS: Quadram Institute, Norwich)
Nicole Pearcy (NP: University of Nottingham)

Guest Speaker

Prof. John Wain (JW: Quadram Institute, Norwich)

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
	12:00	Lunch
	13:00	Welcome and introduction to the course. Outline of the week.	'	MP et al
		Lecture 1: Title TBC		JW
		Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks.	Slides	DF
		Tea/coffee
		Lecture 3: Python and computational representation of metabolic networks.	Slides	MP
		P1. Computers: checking internet connectivity, software installation.	Installation of ScrumPy.	All
		Close
Wednesday	AM
	09:00	L3. Null space and elementary modes	Slides	NP
		Demo for Prac 2.		MP
		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
		Conclusions

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

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+= Overview =
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- * David Fell (DF: Oxford Brookes University)
 * Yanica Said (YS:  Oxford Brookes University)
 * Dipali Singh  (DS: Quadram Institute, Norwhich)
 * Nicole Pearcy (NP: University of Nottingham)
+ * David Fell        (DF: Oxford Brookes University)
 * Yanica Said     (YS:  Oxford Brookes University)
 * Dipali Singh     (DS: Quadram Institute, Norwich)
 * Nicole Pearcy  (NP: University of Nottingham)

== Guest Speaker ==
 * Prof. John Wain  (JW: Quadram Institute, Norwich)
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- . A reading list for topics covered in the course is provided [[Meetings/Nepal2018/Reading|here]].
+ . A reading list for topics covered in the course is provided [[Meetings/Nottingham2022/Reading|here]].
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-'''
||Tuesday ||AM       ''' ''' || || || ||
+||Tuesday ||AM           ''' ''' || || || ||
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-|| ||13:00 ||Lunch || || ||
||' ||??? ||''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/Nottingham2022/L0.pdf|Slides]] ||DF ||
|| ||14:00 ||L1.  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||DF ||
+|| ||12:00 ||Lunch || || ||
|| ||13:00 ||Welcome and introduction to the course.    Outline of the week. ||'''' ''' ||MP et al ||
|| || ||Lecture 1: Title TBC || ||JW ||
|| || ||Lecture 2:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||DF ||
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-|| || ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||MP ||
+|| || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||MP ||
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-||Wednesday      ''' ''' ||AM      ''' ''' || || || ||
|| ||09:30 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||NP ||
+||Wednesday           ''' ''' ||AM           ''' ''' || || || ||
|| ||09:00 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||NP ||
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-|| ||PM     ''' ''' ||L3b.  Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF ||
+|| ||PM          ''' ''' ||L3b.  Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF ||
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-||Thursday     ''' ''' || || || || ||
+||Thursday          ''' ''' || || || || ||
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-|| ||PM     ''' ''' ||L7.  The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM ||
+|| ||PM          ''' ''' ||L7.  The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM ||
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-||Friday     ''' ''' ||AM     ''' ''' || || || ||
|| ||09:30 ||L8. a: Summary of Null-space and linear programming approaches   b: Practical applications of LP   ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/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/Nottingham2022/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||MP, DF ||
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-|| || ||Conclusions|| || ||
+|| || ||Conclusions || || ||
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-'''
+''' '''