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Workshop on Metabolic Modelling

Introduction to Structural Modelling

Note: **Items** in the timetable in represent new material.

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)

Course Timetable and Resources Index

Contents below are subject to modification, especially the links.

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



Friday
29/06/18		L3. Null space and elementary modes	Slides	NM
		P2. Python and ScrumPy	Prac2 instructions	DF, MP, TDC,NM

		P2. Python and ScrumPy (continued)	Prac2 instructions	DF, MP, TDC,NM

		L4. Biotechnological applications of metabolic network analysis L4a.L4 B need something else (was Nicole)	Slides	DF, ??
		P3. Models, kernels, subsets and elementary modes	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	Slides	NM
		L6. Sources of data for metabolic models	Slides	DF
		Coffee/Tea
		P4. Structural analysis of the Calvin Cycle.	Prac 4 instructions	DF, MP, TDC,NM

		L7. Building genome-scale metabolic networks	Slides	MP
		P5. Building a ScrumPy model from databases	Prac 5 instructions	All




Sunday
01/07/18	09:00	L8. a, Acetobacterium woodii. b. Need soething else (was Nicole)	Noah's slides;	NM, ??

	11:00	P6. Flux Balance Analysis of fatty acid biosynthesis in E coli.	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	Instructions	All
		Close
		Dinner

Monday		Breakfast
02/07/18		P7 continued		All

				All
				DF& MP
Tuesday
03/07/18

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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)
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+||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' ||
||'''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 ||
|| || ||Tea/coffee || || ||
|| || ||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 || || || || ||
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-||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' ||
||'''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 || || ||
|| || || || || ||