Differences between revisions 3 and 40 (spanning 37 versions)

Workshop on Metabolic Modelling

Tutors

David Fell (DF: Oxford Brookes University)
Mark Poolman (MP: Oxford Brookes University)
Noah Mesfin (NM: Oxford Brookes University)
Ela Al-Saidi (ES: Oxford Brookes University)
Kailash Adhikari (KA)

Reading List

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

Course Timetable and Resources

Day	Time	Activity	Links	Lecturer
Thursday	AM
28/06/18	09:00	Admin & Registration
	10:00	Opening Ceremony
	10:30	Introductions. Each participant introduces themself in 2-3 sentences: name, place of study/work; what they do.		Everyone
	11:00	Tea
	11:30	Welcome and introduction to the course	Slides	DF
	13:00	Lunch
	PM
	14:00	L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week	Slides	DF
		Tea/coffee
		L2. Computational representation of metabolic networks	Slides	MP
		P1. Computers: checking internet connectivity, software installation.	Installation of ScrumPy.	All
	!6:45	Close
Friday	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
Monday
	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
Tuesday	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

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-== Introduction to Structural Modelling ==
__'''Note: **Items** in the timetable in represent new material.'''__
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-== Course Timetable and Resources Index ==
Contents below are subject to modification, especially the links.
+== Reading List ==
 . A reading list for topics covered in the course is provided [[Meetings/Nepal2018/Reading|here]].

== Course Timetable and Resources ==
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-||'''Thursday''' || ||Admin & Registration || || ||
||28/06/18 || ||Lunch || || ||
|| || ||Opening and introductions || ||DF ||
|| || ||L1.  Introduction to metabolic modelling.  Mathematical                     representation of metabolic networks.  Outline of the week ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L1.pdf|Slides]] ||DF ||
+||'''Thursday''' ||'''AM''' || || || ||
||28/06/18 ||09:00 ||Admin & Registration || || ||
|| ||10:00 ||Opening Ceremony || || ||
|| ||10:30 ||Introductions.  Each participant introduces themself in 2-3 sentences: name, place of study/work; what they do. || ||Everyone ||
|| ||11:00 ||Tea || || ||
|| ||11:30 ||Welcome and introduction to the course ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L0.pdf|Slides]] ||DF ||
|| ||13:00 ||Lunch || || ||
|| ||'''PM''' || || || ||
|| ||14:00 ||L1.  Introduction to metabolic modelling.  Mathematical                     representation of metabolic networks.  Outline of the week ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L1.pdf|Slides]] ||DF ||
-Line 21:
+Line 24:
-|| || ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L2.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software                  installation. ||[[Meetings/C1netWork4/ScrumPyInstall|Installation]]                   of !ScrumPy. ||DF, MP, TDC,NM ||
|| || || || || ||
|| || || || || ||
|| || || || || ||
||'''Friday''' || || || || ||
||29/06/18 || ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L3.pdf|Slides]] ||NM ||
|| || ||P2. Python and !ScrumPy ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM ||
|| || || || || ||
|| || ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM ||
|| || || || || ||
|| || ||L4. Biotechnological applications of metabolic network analysis L4a.**L4 B need something else (was Nicole)** ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4.pdf|Slides]] ||DF, ** ?? ** ||
|| || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/C1netWork4/Prac3|Prac 3 instructions]] ||All ||
|| || || || || ||
|| ||15:45 ||P3. Models, kernels, subsets and elementary modes (continued) || ||All ||
|| || ||Close || || ||
|| || || || || ||
|| || || || || ||
||'''Saturday''' || || || || ||
||30/06/18 || ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L5.pdf|Slides]] ||NM ||
|| || ||L6.  Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L6.pdf|Slides]] ||DF ||
|| || ||Coffee/Tea || || ||
|| || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||DF, MP, TDC,NM ||
|| || || || || ||
|| || ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L7.pdf|Slides]] ||MP ||
|| || ||P5. Building a !ScrumPy model from databases ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork4/Prac5|Prac 5 instructions]] ||All ||
|| || || || || ||
|| || || || || ||
|| || || || || ||
|| || || || || ||
||'''Sunday''' || || || || ||
||01/07/18 ||09:00 ||L8. a, ''Acetobacterium woodii''.  b.''** Need soething else (was Nicole) **'' ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's                         slides]]; ||NM, **??** ||
|| || || || || ||
|| ||11:00 ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E                      coli''. ||[[Meetings/C1netWork4/Prac6|Prac 6 instructions]] ||All ||
|| || || || || ||
|| || ||L8 ** what to do here? Was Rupert and Maite's talks (Ask Kailash)** || ||**?KA?** ||
|| || ||P6 continued || ||All ||
|| || ||Tea/Coffee || || ||
|| || ||P7. Analysing a genome scale model ||[[Meetings/C1NetWork4/Prac7|Instructions]] ||All ||
|| || ||Close || || ||
|| || ||Dinner || || ||
|| || || || || ||
||'''Monday''' || ||Breakfast || || ||
||02/07/18 || ||P7 continued || ||All ||
|| || || || || ||
|| || || || ||All ||
|| || || || ||DF& MP ||
||'''Tuesday''' || || || || ||
||03/07/18 || || || || ||
+|| || ||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 ||
|| ||!6:45 ||Close || || ||
||'''Friday''' ||'''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 ||
|| ||11:00 ||Break || || ||
|| || ||P2. Python and !ScrumPy  (Part 2) ||[[Meetings/Nepal2018/Prac2|Prac2]] ||All ||
|| ||13:00 ||Lunch || || ||
|| ||'''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 ||
|| || ||Demo for Prac 3 || ||TBC ||
|| || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nepal2018/Prac3|Prac 3]] ||All ||
|| || ||Break || || ||
|| || ||P3. Models, kernels, subsets and elementary modes (continued) || ||All ||
|| ||16:45 ||Close || || ||
||'''Monday''' || || || || ||
|| ||09:30 ||Demo for Prac4 || ||MP ||
|| || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/Nepal2018/Prac4|Prac 4]] ***instructions ||ALL ||
|| ||11:00 ||Break || || ||
|| || ||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 ||
|| ||13:00 ||Lunch || || ||
|| ||'''PM''' ||L7.  The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] [[Meetings/Nepal2018/ScrumPy_demo|ScrumPy_demo]] ||NM ||
|| || ||P5. Flux Balance Analysis of alkane biosynthesis in ''E                      coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] ||All ||
|| ||16:45 ||close || || ||
||'''Tuesday''' ||'''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 ||
|| || ||P5  Flux Balance Analysis of alkane biosynthesis in ''E                      coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] || ||
|| ||11:00 ||Break || || ||
|| || ||Practical 5 continues || || ||
|| ||13:00 ||Lunch || || ||
|| ||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 || || ||