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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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 * 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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== Course Timetable and Resources Index ==
Contents below are subject to modification, especially the links.
 == 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) || || ||		 ||'''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/Nepal2018/ScrumPyInstall|Installation]] of !ScrumPy. ||All ||
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||'''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 || || ||		 ||'''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 ||
|| || ||<<BR>> ||<<BR>> || ||
||'''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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||'''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>>''' || || ||		 ||'''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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||'''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 || || ||
|| || || || || ||

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.

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

None: Meetings/Nepal2018/Timetable (last edited 2018-07-03 06:51:02 by mark)