Differences between revisions 1 and 38 (spanning 37 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 talks.

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 Meetings/Nepal2018/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.		KA
		L10 Beyond structural modelling		EA
		Closing and Presentation of Certificates
	16:45	Depart

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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 talks.
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- * Rupert Norman (RN: University of Nottingham)
 * Nicole Pearcy (NP: University of Nottingham)
 * Teresa Diaz Calvo (TDC: University of East Anglia)
+ * Ela Al-Saidi (ES: Oxford Brookes University)
 * Kailash Adhikari (KA)
-Line 12:
+Line 11:
-== 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]].
-Line 15:
+Line 14:
+== Course Timetable and Resources ==
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-||'''Monday''' ||12:00 ||Registration opens at The Park Hotel || || ||
||15/1/18 ||12:30 ||Lunch || || ||
|| ||13:30 ||Opening and introductions || ||DF ||
|| ||14:00 ||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 ||
|| ||15:30 ||Tea/coffee || || ||
|| ||16:00 ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L2.pdf|Slides]] ||MP ||
|| ||17:00 ||P1. Computers: checking internet connectivity, software                  installation. ||[[Meetings/C1netWork4/ScrumPyInstall|Installation]]                   of !ScrumPy. ||DF, MP, TDC,NM ||
|| ||18:00 ||Close and room registration (cont) || || ||
|| ||19:00 ||Dinner (resident delegates only) || || ||
|| || || || || ||
||'''Tuesday''' ||08:00 ||Breakfast (resident delegates only) || || ||
||16/1/18 ||09:00 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L3.pdf|Slides]] ||MP ||
|| ||10:00 ||P2. Python and !ScrumPy ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM ||
|| ||10:30 ||Coffee/Tea || || ||
|| ||10:45 ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM ||
|| ||12:30 ||Lunch || || ||
|| ||13:30 ||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 ||
|| ||14:30 ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/C1netWork4/Prac3|Prac 3 instructions]] ||All ||
|| ||15:30 ||Tea/Coffee || || ||
|| ||15:45 ||P3. Models, kernels, subsets and elementary modes (continued) || ||All ||
|| ||17:30 ||Close || || ||
|| ||19:00 ||Dinner || || ||
|| || || || || ||
||'''Wednesday''' ||08:00 ||Breakfast || || ||
||17/1/18 ||09:00 ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L5.pdf|Slides]] ||MP ||
|| ||10:00 ||L6.  Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L6.pdf|Slides]] ||DF ||
|| ||10:30 ||Coffee/Tea || || ||
|| ||11:00 ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||DF, MP, TDC,NM ||
|| ||12:30 ||Lunch || || ||
|| ||13:30 ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L7.pdf|Slides]] ||MP ||
|| ||14:30 ||P5. Building a !ScrumPy model from databases ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork4/Prac5|Prac 5 instructions]] ||All ||
|| ||15:30 ||Tea/Coffee || || ||
|| ||15:30 ||'''Free time (Hotel sports facilities/ Nottingham Castle?)   ''' || || ||
|| ||19:00 ||'''Workshop dinner (All participants)<<BR>>''' || || ||
|| || || || || ||
||'''Thursday''' ||08:00 ||Breakfast || || ||
||18/1/18 ||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 ||
|| ||10:30 ||Coffee/Tea || || ||
|| ||11:00 ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E                      coli''. ||[[Meetings/C1netWork4/Prac6|Prac 6 instructions]] ||All ||
|| ||12:30 ||Lunch || || ||
|| ||13:30 ||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 ||
|| ||14:30 ||P6 continued || ||All ||
|| ||15:30 ||Tea/Coffee || || ||
|| ||16:00 ||P7. Analysing a genome scale model ||[[Meetings/C1NetWork4/Prac7|Instructions]] ||All ||
|| ||17:30 ||Close || || ||
|| ||19:00 ||Dinner || || ||
|| || || || || ||
||'''Friday''' ||08:00 ||Breakfast || || ||
||19/1/18 ||09:00 ||P7 continued || ||All ||
|| ||10:30 ||Coffee/Tea || || ||
|| ||11:00 ||Discussion of results and prospective applications of modelling                  in attendees' projects || ||All ||
|| ||12:00 ||Any questions? Closing remarks || ||DF& MP ||
|| ||12:30 ||(Sandwich?) lunch and departure || || ||
|| || || || || ||
+||'''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 ||
|| || ||Tea/coffee || || ||
|| || ||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]] ||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. || ||KA ||
|| || ||L10 Beyond structural modelling || ||EA ||
|| || ||Closing and Presentation of Certificates || || ||
|| ||16:45 ||Depart || || ||