Differences between revisions 18 and 40 (spanning 22 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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-= Workshop  on Metabolic Modelling - Provisional Timetable =
This timetable is not yet finalised. Both timings and content are liable to change, but the material here represents what will be covered in the talk.
+= Workshop  on Metabolic Modelling =
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+== Reading List ==
 . A reading list for topics covered in the course is provided [[Meetings/Nepal2018/Reading|here]].
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-||'''Thursday''' ||'''AM''' ||Admin & Registration || || ||
||28/06/18 || ||Opening Ceremony || || ||
|| || ||Welcome and introduction to the course || ||DF ||
|| || ||Lunch || || ||
|| ||'''PM''' ||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 ||
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-|| || || || || ||
||'''Friday''' ||'''AM''' ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3.pdf|Slides]] ||NM ||
+|| ||!6:45 ||Close || || ||
||'''Friday''' ||'''AM''' || || || ||
|| ||09:30 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3.pdf|Slides]] ||NM ||
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-|| || ||P2. Python and !ScrumPy (Part 1) ||[[Meetings/Nepal2018/Prac2|Prac2]] ***instructions ||All ||
|| || ||Break || || ||
|| || ||P2. Python and !ScrumPy  (Part 2) ||[[Meetings/Nepal2018/Prac2|Prac2]] ***instructions ||All ||
|| || ||Lunch || || ||
|| ||'''PM''' ||L4. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4.pdf|Slides]] ||DF ||
+|| || ||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 ||
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-|| || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nepal2018/Prac3|Prac 3]] ***instructions ||All ||
+|| || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nepal2018/Prac3|Prac 3]] ||All ||
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-|| || ||<<BR>> ||<<BR>> || ||
||'''Monday''' ||'''AM''' ||Demo for Prac4 (??) || || ||
+|| ||16:45 ||Close || || ||
||'''Monday''' || || || || ||
|| ||09:30 ||Demo for Prac4 || ||MP ||
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-|| || ||Break || || ||
+|| ||11:00 ||Break || || ||
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-|| || ||L6.  Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L6.pdf|Slides]] ||DF ||
|| || ||Lunch || || ||
|| ||'''PM''' ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] ||MP ||
|| || ||P5. Flux Balance Analysis of fatty acid biosynthesis in ''E                      coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] ***instructions ||All ||
|| || || || || ||
||'''Tuesday''' || ||L8. '''a''': The unique metabolism of ''Acetobacterium woodii''.  '''b''': Beyond Structural Modelling. ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's                         slides]]; ||NM, EA ||
|| || ||Intro to P6|| ||MP||
|| || ||P6. Analysing a genome scale model ||[[Meetings/Nepal2018/Prac6|Prac 6]] ***instructions ||All ||
|| || ||Break || || ||
|| || ||L8 Modelling photosynthesis in eukaryotes (title TBC) ||**Need link to slides** ||KA ||
|| || ||Lunch || ||All ||
|| || ||P6 ctd. || ||All ||
|| || ||Closing remarks || || ||
|| || ||Certificates || || ||
|| || || || || ||
+|| || ||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 || || ||