Differences between revisions 1 and 9 (spanning 8 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 (ES: 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.	DF, MP, TDC,NM
Friday	AM	L3. Null space and elementary modes	Slides	NM
		P2. Python and ScrumPy	Prac2 instructions	DF, MP, TDC,NM
		Break
		P2. Python and ScrumPy (continued)	Prac2 instructions	DF, MP, TDC,NM
		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	L5. Linear Programming and Flux Balance Analysis	Slides	NM
		L6. Sources of data for metabolic models	Slides	DF
		Break
		P4. Structural analysis of the Calvin Cycle.	Prac 4 instructions	DF, MP, TDC,NM
		Lunch
	PM	L7. Building genome-scale metabolic networks	Slides	MP
		P5. Building a ScrumPy model from databases	Prac 5 instructions	All
Tuesday		L8. a, Acetobacterium woodii. b. Need soething else (was Nicole)	Noah's slides;	NM, ??
		P6. Flux Balance Analysis of fatty acid biosynthesis in E coli.	Prac 6 instructions	All

		L8 Modelling photosynthesis in eukaryotes (title TBC)	Need link to slides	KA
		P6 continued		All
		Tea/Coffee
		P7. Analysing a genome scale model	Instructions	All
		Close
		Dinner

-  ⇤ ← Revision 1 as of 2018-06-12 12:51:22 → 
  Size: 5203
  Editor: mark
  Comment:
+   ← Revision 9 as of 2018-06-15 14:19:41 → ⇥
  Size: 3602
  Editor: mark
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= !!! 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.
 Line 8:
- * 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.
+== Course Timetable and Resources ==
-Line 16:
+Line 13:
-||'''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) || || ||
+||'''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 ||
|| || ||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/C1netWork4/ScrumPyInstall|Installation]]                   of !ScrumPy. ||DF, MP, TDC,NM ||
||'''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 ||DF, MP, TDC,NM ||
|| || ||Break || || ||
|| || ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM ||
|| || ||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''' ||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 ||
|| || ||Break || || ||
|| || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||DF, MP, TDC,NM ||
|| || ||Lunch || || ||
|| ||'''PM''' ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L7.pdf|Slides]] ||MP ||
|| || ||P5. Building a !ScrumPy model from databases ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork4/Prac5|Prac 5 instructions]] ||All ||
||'''Tuesday''' || ||L8. a, ''Acetobacterium woodii''.  b.''** Need soething else (was Nicole) **'' ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's                         slides]]; ||NM, **??** ||
|| || ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E                      coli''. ||[[Meetings/C1netWork4/Prac6|Prac 6 instructions]] ||All ||
-Line 26:
+Line 40:
-||'''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 || || ||
+|| || ||L8 Modelling photosynthesis in eukaryotes (title TBC) ||**Need link to slides** ||KA ||
|| || ||P6 continued || ||All ||
|| || ||Tea/Coffee || || ||
|| || ||P7. Analysing a genome scale model ||[[Meetings/C1NetWork4/Prac7|Instructions]] ||All ||
|| || ||Close || || ||
|| || ||Dinner || || ||
-Line 39:
+Line 47:
-||'''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 || || ||
|| || || || || ||