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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/C1netWork4/ScrumPyInstall|Installation]] of !ScrumPy. ||DF, MP, TDC,NM ||
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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 ||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 ||
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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>>''' || || ||		 ||'''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]] ||ALL ||
|| || ||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 ||
||*******||******||I think we should scrap P5 - we don't do any LP/FBA practicals until the last day||******||*******||
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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 || || ||		 ||'''Tuesday''' || ||L8. a, ''Acetobacterium woodii''. b.''** Need soething else ?? Mark or Ela ?? (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 ||
|| || ||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 || || ||
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||'''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.

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

ALL

Lunch

PM

L7. Building genome-scale metabolic networks

Slides

MP

P5. Building a ScrumPy model from databases

Prac 5 instructions

All

*******

******

I think we should scrap P5 - we don't do any LP/FBA practicals until the last day

******

*******

Tuesday

L8. a, Acetobacterium woodii. b.** Need soething else ?? Mark or Ela ?? (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

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