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⇤ ← Revision 2 as of 2016-06-09 23:11:43 →
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Comment: Additional info, tutors and funding
← Revision 3 as of 2016-06-09 23:59:44 → ⇥
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Editor: david
Comment: Provisional timetable
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The workshop is organised by Tribhuvan University and the Society for Biological Applications Nepal (SBAN).   		  . The workshop is organised by Tribhuvan University and the Society for Biological Applications Nepal (SBAN).
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The course is presented by:
  . The course is presented by:
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  * Kailash Adhikari, and 
  * Dipali Singh  
   all of Oxford Brookes University, Oxford, UK.		   * Kailash Adhikari, and
  * Dipali Singh
   . all of Oxford Brookes University, Oxford, UK.
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  To apply for the workshop, complete the registration form an the [[http://sbanepal.com/events/|SBAN website]]. If the workshop is over-subscribed, successful applicants will be selected and notified.		  .
 To apply for the workshop, complete the registration form an the [[http://sbanepal.com/events/|SBAN website]]. If the workshop is over-subscribed, successful applicants will be selected and notified.
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 .
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 . To help plan your attendance, the provisional workshop timetable is given below. The precise content and order of topics may be changed - even during the workshop itself!
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 To help plan your attendance, the provisional workshop timetable is given below. The precise content and order of topics may be changed - even during the workshop itself! ||<tablewidth="870px"width="64px" style="border:none;padding:0cm">'''Day''' ||<width="50px" style="border:none;padding:0cm">'''Time''' ||<width="57px" style="border:none;padding:0cm">'''Room''' ||<width="483px" style="border:none;padding:0cm">'''Activity''' ||<width="92px" style="border:none;padding:0cm">'''Resources''' ||<width="125px" style="border:none;padding:0cm">'''Who''' ||
||<width="64px" style="border:none;padding:0cm;text-align:center" |4>Mon 27th, AM ||<width="50px" style="border:none;padding:0cm">10:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Arrival and registration ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm">SBAN ||
||<width="50px" style="border:none;padding:0cm">11:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Welcome talks ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm">MP + TU ||
||<width="50px" style="border:none;padding:0cm">11:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Introductory theory ||<width="92px" style="border:none;padding:0cm">[[http://mudsharkstatic.brookes.ac.uk/Pune2016/L1/Slides.pdf|Slides]] ||<width="125px" style="border:none;padding:0cm">MP ||
||<width="50px" style="border:none;padding:0cm">12:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Lunch ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm">All ||
||<width="64px" height="44px" style="border:none;padding:0cm;text-align:center" |3>Mon 27th, PM ||<width="50px" style="border:none;padding:0cm">14:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Python, object-orientation and models. ||<width="92px" style="border:none;padding:0cm">[[http://mudsharkstatic.brookes.ac.uk/Pune2016/L2/Slides.pdf|Slides]] ||<width="125px" style="border:none;padding:0cm">MP ||
||<width="50px" style="border:none;padding:0cm">15:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Practical 0:''' Checking !ScrumPy Installation and familiarisation with the Python language. ||<width="92px" style="border:none;padding:0cm">[[http://mudshark.brookes.ac.uk/Meetings/Pune2016/P0|Instructions]] ||<width="125px" style="border:none;padding:0cm">All ||
||<width="50px" style="border:none;padding:0cm">17:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Close ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm"> ||
||<width="64px" style="border:none;padding:0cm;text-align:center" |3>Tue 28th, AM ||<width="50px" style="border:none;padding:0cm">09:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Structural analysis of small models. (+ break) ||<width="92px" style="border:none;padding:0cm">[[http://mudsharkstatic.brookes.ac.uk/Pune2016/L3/Slides.pdf|Slides]] ||<width="125px" style="border:none;padding:0cm">DF ||
||<width="50px" style="border:none;padding:0cm">11:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk: '''Introduction to plant metabolism and its modelling ||<width="92px" style="border:none;padding:0cm">Slides ||<width="125px" style="border:none;padding:0cm">DS, KA and MP ||
||<width="50px" style="border:none;padding:0cm">12:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Lunch ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm"> ||
||<width="64px" style="border:none;padding:0cm;text-align:center" |2>Tue 28th, PM ||<width="50px" style="border:none;padding:0cm">14:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Practical 1''': Structural analysis of small models ||<width="92px" style="border:none;padding:0cm">[[http://mudshark.brookes.ac.uk/Meetings/Pune2016/P1|Instructions]] ||<width="125px" style="border:none;padding:0cm">All ||
||<width="50px" style="border:none;padding:0cm">17:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Close ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm"> ||
||<width="64px" style="border:none;padding:0cm;text-align:center" |4>Wed 29th, AM ||<width="50px" style="border:none;padding:0cm">09:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Sources of data for metabolic models ||<width="92px" style="border:none;padding:0cm">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L2.pdf|Slides]] ||<width="125px" style="border:none;padding:0cm">DF ||
||<width="50px" style="border:none;padding:0cm">10:15 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Construction of Genome-Scale Models ||<width="92px" style="border:none;padding:0cm">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L7.pdf|Slides]] ||<width="125px" style="border:none;padding:0cm">MP ||
||<width="50px" style="border:none;padding:0cm">11:15 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Linear Programming and Flux Balance Analysis ||<width="92px" style="border:none;padding:0cm">[[http://mudsharkstatic.brookes.ac.uk/Pune2016/L5/Slides.pdf|Slides]] ||<width="125px" style="border:none;padding:0cm">MP ||
||<width="50px" style="border:none;padding:0cm">12:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Lunch ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm"> ||
||<width="64px" style="border:none;padding:0cm;text-align:center" |3>Wed 29th, PM ||<width="50px" style="border:none;padding:0cm">14:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Practical 2''''''a:''' Construction of a working !ScrumPy model from databases ||<width="92px" style="border:none;padding:0cm">[[http://mudshark.brookes.ac.uk/Meetings/C1netWork1/Prac5|Instructions]] ||<width="125px" style="border:none;padding:0cm">All ||
||<width="50px" style="border:none;padding:0cm">15:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Practical 2''''''a:''' Flux Balance Analysis of a simple model ||<width="92px" style="border:none;padding:0cm">[[http://mudshark.brookes.ac.uk/Meetings/C1netWork1/Prac6|Instructions]] ||<width="125px" style="border:none;padding:0cm">All ||
||<width="50px" style="border:none;padding:0cm">17:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Close''' ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm"> ||
||<width="64px" style="border:none;padding:0cm;text-align:center" |4>Thur 30^th^, AM ||<width="50px" style="border:none;padding:0cm">09:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Biotechnological Applications of Metabolic Network Analysis ||<width="92px" style="border:none;padding:0cm">[[http://mudsharkstatic.brookes.ac.uk/Pune2016/L6/Slides.pdf|Slides]] ||<width="125px" style="border:none;padding:0cm">DF ||
||<width="50px" style="border:none;padding:0cm">10:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Genome scale modelling of Arabidopsis ||<width="92px" style="border:none;padding:0cm">tbp ||<width="125px" style="border:none;padding:0cm">KA ||
||<width="50px" style="border:none;padding:0cm">11:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Talk:''' Genome scale modelling of a diatom for oil production ||<width="92px" style="border:none;padding:0cm">tbp ||<width="125px" style="border:none;padding:0cm">DS ||
||<width="50px" style="border:none;padding:0cm">12:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Lunch ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm"> ||
||<width="64px" style="border:none;padding:0cm;text-align:center" |3>Thur 30^th^, PM ||<width="50px" style="border:none;padding:0cm">14:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Practical 3: '''GSM of Arabidopsis – metabolic phenotypes of mutants – metabolic responses to light intensity ||<width="92px" style="border:none;padding:0cm">tbp ||<width="125px" style="border:none;padding:0cm">All ||
||<width="50px" style="border:none;padding:0cm">16:30 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">Concluding remarks and presentation of certificates ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm">All ||
||<width="50px" style="border:none;padding:0cm">17:00 ||<width="57px" style="border:none;padding:0cm"> ||<width="483px" style="border:none;padding:0cm">'''Close of the Workshop''' ||<width="92px" style="border:none;padding:0cm"> ||<width="125px" style="border:none;padding:0cm"> ||

Workshop: Metabolic Modelling and its Applications

27 - 30 June 2016

Tribhuvan University, Kirtipur, Kathmandu, Nepal

  • The workshop is organised by Tribhuvan University and the Society for Biological Applications Nepal (SBAN).

    A brief introduction to the workshop is available on the website for the SBAN.

Tutors

  • The course is presented by:
    • Dr Mark Poolman
    • Prof David Fell
    • Kailash Adhikari, and
    • Dipali Singh
      • all of Oxford Brookes University, Oxford, UK.

      Examples presented in the workshop will include results from their research, which has been funded by the EU via the AccliPhot project and the BBSRC (UK).

Application

  • To apply for the workshop, complete the registration form an the SBAN website. If the workshop is over-subscribed, successful applicants will be selected and notified.

Instructions for workshop attendees

  • You are required to bring a laptop to the workshop. The metabolic modelling package used in the course, !ScrumPy, will be made available to you. The two options for installing ScrumPy on your computer are to directly install the package on a suitable Linux operating system, or to run a virtual machine under other operating system. Instructions are here. (TO BE UPDATED)

Timetable

  • To help plan your attendance, the provisional workshop timetable is given below. The precise content and order of topics may be changed - even during the workshop itself!

Day

Time

Room

Activity

Resources

Who

Mon 27th, AM

10:30

Arrival and registration

SBAN

11:00

Welcome talks

MP + TU

11:30

Talk: Introductory theory

Slides

MP

12:30

Lunch

All

Mon 27th, PM

14:00

Talk: Python, object-orientation and models.

Slides

MP

15:00

Practical 0: Checking ScrumPy Installation and familiarisation with the Python language.

Instructions

All

17:30

Close

Tue 28th, AM

09:30

Talk: Structural analysis of small models. (+ break)

Slides

DF

11:00

Talk: Introduction to plant metabolism and its modelling

Slides

DS, KA and MP

12:30

Lunch

Tue 28th, PM

14:00

Practical 1: Structural analysis of small models

Instructions

All

17:00

Close

Wed 29th, AM

09:30

Talk: Sources of data for metabolic models

Slides

DF

10:15

Talk: Construction of Genome-Scale Models

Slides

MP

11:15

Talk: Linear Programming and Flux Balance Analysis

Slides

MP

12:30

Lunch

Wed 29th, PM

14:00

Practical 2a: Construction of a working ScrumPy model from databases

Instructions

All

15:30

Practical 2a: Flux Balance Analysis of a simple model

Instructions

All

17:00

Close

Thur 30th, AM

09:30

Talk: Biotechnological Applications of Metabolic Network Analysis

Slides

DF

10:30

Talk: Genome scale modelling of Arabidopsis

tbp

KA

11:30

Talk: Genome scale modelling of a diatom for oil production

tbp

DS

12:30

Lunch

Thur 30th, PM

14:00

Practical 3: GSM of Arabidopsis – metabolic phenotypes of mutants – metabolic responses to light intensity

tbp

All

16:30

Concluding remarks and presentation of certificates

All

17:00

Close of the Workshop

None: Meetings/Nepal2016 (last edited 2016-09-16 13:21:02 by mark)