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Under Construction - Ignore !

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, 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	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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- * Oliver Ebenhöh (OE:  Heinrich-Heine-Universität, Dusseldorf)
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-||Tuesday ||AM     ''' ''' || || || ||
+||Tuesday ||AM       ''' ''' || || || ||
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-|| || ||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 ||
+|| || ||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 ||
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-|| || ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L2.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software                  installation. ||[[Meetings/Nepal2018/ScrumPyInstall|Installation]]                   of !ScrumPy. ||All ||
+|| || ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software                  installation. ||[[Meetings/Nottingham2022/ScrumPyInstall|Installation]]                   of !ScrumPy. ||All ||
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-||Wednesday    ''' ''' ||AM    ''' ''' || || || ||
|| ||09:30 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3.pdf|Slides]] ||NM ||
|| || ||Demo for Prac 2. || ||TBC ||
|| || ||P2. Python and !ScrumPy (Part 1) ||[[Meetings/Nepal2018/Prac2|Prac2]] ||All ||
+||Wednesday      ''' ''' ||AM      ''' ''' || || || ||
|| ||09:30 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||NP ||
|| || ||Demo for Prac 2. || ||MP ||
|| || ||P2. Python and !ScrumPy (Part 1) ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
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-|| || ||P2. Python and !ScrumPy  (Part 2) ||[[Meetings/Nepal2018/Prac2|Prac2]] ||All ||
+|| || ||P2. Python and !ScrumPy  (Part 2) ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
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-|| ||PM   ''' ''' ||L3b.  Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3b.pdf|Slides]] ||DF ||
|| || ||L4. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4.pdf|Slides]] ||DF ||
+|| ||PM     ''' ''' ||L3b.  Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF ||
|| || ||L4. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||DF ||
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-|| || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nepal2018/Prac3|Prac 3]] ||All ||
+|| || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac 3]] ||All ||
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-||Thursday   ''' ''' || || || || ||
+||Thursday     ''' ''' || || || || ||
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-|| || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/Nepal2018/Prac4|Prac 4]] ***instructions ||ALL ||
+|| || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/Nottingham2022/Prac4|Prac 4]] ***instructions ||ALL ||
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-|| || ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L5.pdf|Slides]] ||NM ||
|| || ||L6.  Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L6.pdf|Slides]] ||DF ||
+|| || ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||NM ||
|| || ||L6.  Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.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/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/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/Nottingham2022/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||MP, DF ||
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-|| ||14:00 ||L9 Modelling photosynthesis in eukaryotes. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L9.pdf|Slides]] ||KA ||
|| || ||L10 Beyond structural modelling || ||EA ||
|| || ||Closing and Presentation of Certificates || || ||
|| ||16:45 ||Depart || || ||
+|| || ||Conclusions|| || ||
|| || || || || ||
|| || || || || ||
|| || || || || ||