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= !!! Page under construction - Ignore it!!! =
= Workshop on Metabolic Modelling =
== Introduction to Structural Modelling ==
__'''Note: **Items** in the timetable in represent new material.'''__		 = 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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== Course Timetable and Resources Index ==
Contents below are subject to modification, especially the links.		 == Course Timetable and Resources ==
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||'''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 ||		 ||'''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 ||
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||'''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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||'''Friday''' || || || || ||
||29/06/18 || ||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 ||



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|| || ||P2. Python and !ScrumPy (continued) ||[[Meetings/C1netWork4/Prac2|Prac2]] instructions ||DF, MP, TDC,NM ||



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||'''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 || || ||




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|| || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||ALL ||




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|| || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/C1netWork4/Prac4|Prac 4 instructions]] ||ALL ||




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|| || ||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 ||




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




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||******* ||****** ||I think we should scrap P5 - we don't do any LP/FBA practicals until the last day ||****** ||******* ||
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|| ||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/Nepal2018/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/Nepal2018/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 || ||L8. a, ''Acetobacterium woodii''. b.''** Need soething else (was Nicole) **'' ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop4/L8_NM.pdf|Noah's slides]]; ||NM, **??** ||
|| || || || || ||		 ||'''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, **??** ||
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|| || ||L8 Modelling photosynthesis in eukaryotes (title TBC) ||**Need link to slides**||KA ||



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|| || ||L8 Modelling photosynthesis in eukaryotes (title TBC) ||**Need link to slides** ||KA ||
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||'''Monday''' || ||Breakfast || || ||
||02/07/18 || ||P7 continued || ||All ||
|| || || || || ||
|| || || || ||All ||
|| || || || ||DF& MP ||
||'''Tuesday''' || || || || ||
||03/07/18 || || || || ||

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

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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

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Monday

AM

L5. Linear Programming and Flux Balance Analysis

Slides

NM

L6. Sources of data for metabolic models

Slides

DF

Break

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P4. Structural analysis of the Calvin Cycle.

Prac 4 instructions

ALL

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P4. Structural analysis of the Calvin Cycle.

Prac 4 instructions

ALL

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Lunch

PM

L7. Building genome-scale metabolic networks

Slides

MP

P5. Building a ScrumPy model from databases

Prac 5 instructions

All

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*******

******

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

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*******

******

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

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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)