Differences between revisions 2 and 14 (spanning 12 versions)

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.

Tutors

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

Course Timetable and Resources

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

Friday	AM	L3. Null space and elementary modes	Slides	NM
		P2. Python and ScrumPy	Prac2 instructions	All
		Break
		P2. Python and ScrumPy (continued)	Prac2 instructions	All
		Lunch
	PM	L4. Biotechnological applications of metabolic network analysis	Slides	DF
		P3. Models, kernels, subsets and elementary modes	Prac 3 instructions	All
		Break
		P3. Models, kernels, subsets and elementary modes (continued)		All


Monday	AM	P4. Structural analysis of the Calvin Cycle.	Prac 4 instructions	ALL
		Break
		L5. Linear Programming and Flux Balance Analysis	Slides	NM
		L6. Sources of data for metabolic models	Slides	DF
		Lunch
	PM	L7. Building genome-scale metabolic networks	Slides	MP
		P5. Flux Balance Analysis of fatty acid biosynthesis in E coli.	Prac 5 instructions	All

Tuesday		L8. a: The unique metabolism of Acetobacterium woodii. b: Beyond Structural Modelling.	Noah's slides;	NM, EA
		P6. Analysing a genome scale model	Instructions	All
		Break
		L8 Modelling photosynthesis in eukaryotes (title TBC)	Need link to slides	KA
		Lunch		All
		P6 ctd.		All
		Closing remarks
		Certificates

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-= !!! Page under construction - Ignore it!!! =
= Workshop  on Metabolic Modelling =
== Introduction to Structural Modelling ==
+= 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.
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- * Ela Al-Saidi (ES: Oxford Brookes University)
+ * Ela Al-Saidi (EA: Oxford Brookes University)
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-== Course Timetable and Resources Index ==
Contents below are subject to modification, especially the links.
+== Course Timetable and Resources ==
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-||'''Thursdaay''' || ||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''' ||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 ||
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-|| || ||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 ||
+|| || ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L2.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software                  installation. ||[[Meetings/C1netWork4/ScrumPyInstall|Installation]]                   of !ScrumPy. ||All ||
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+||'''Friday''' ||'''AM''' ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L3.pdf|Slides]] ||NM ||
|| || ||P2. Python and !ScrumPy ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||All ||
|| || ||Break || || ||
|| || ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||All ||
|| || ||Lunch || || ||
|| ||'''PM''' ||L4. Biotechnological applications of metabolic network analysis ||[[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 ||
|| || ||Break || || ||
|| || ||P3. Models, kernels, subsets and elementary modes (continued) || ||All ||
|| || ||
||
|| ||
||'''Monday''' ||'''AM''' ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||ALL ||
|| || ||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/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/C1netWork4/Prac6|Prac 5 instructions]] ||All ||
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+||'''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 ||
|| || ||P6. Analysing a genome scale model ||[[Meetings/C1NetWork4/Prac7|Instructions]] ||All ||
|| || ||Break || || ||
|| || ||L8 Modelling photosynthesis in eukaryotes (title TBC) ||**Need link to slides** ||KA ||
|| || ||Lunch || ||All ||
|| || ||P6 ctd. || ||All ||
|| || ||Closing remarks || || ||
|| || ||Certificates || || ||
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-||'''Friday''' || || || || ||
||29/06/18 || ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L3.pdf|Slides]] ||MP ||
|| || ||P2. Python and !ScrumPy ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM ||
|| || ||Coffee/Tea || || ||
|| || ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM ||
|| || || || || ||
|| || ||L4. Biotechnological applications of metabolic network analysis L4a.  Elementary modes analysis of novel product synthesis. ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4.pdf|Slides]] [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L4_NP_EMA.pdf|Slides]] ||DF, NP ||
|| || ||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]] ||MP ||
|| || ||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. ''Cupriavidus necator'' ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's                         slides]]; [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NP_GS.pdf|Nicole's                         slides]] ||NM, NP ||
|| || || || || ||
|| ||11:00 ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E                      coli''. ||[[Meetings/C1netWork4/Prac6|Prac 6 instructions]] ||All ||
|| || || || || ||
|| || ||L8 c.  ''Clostridium autoethanogenum''.  L9. Modelling metabolism of Non-Aureus Staphylococci ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_RN.pdf|Rupert's                         slides]]; [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L9_Maite.pdf|Maite's slides]] ||RN, TDC ||
|| || ||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 || || || || ||