Differences between revisions 9 and 10

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
Tue 28th, PM	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 30^th, 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 30^th, 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

-  ⇤ ← Revision 9 as of 2016-06-16 14:25:23 → 
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+   ← Revision 10 as of 2016-06-16 14:39:27 → ⇥
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-Deletions are marked like this.
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-= Practical ... =
== Analysing a genome scale metabolic model of Arabidopsis thaliana ==
In this practical we (you !) will be replicating some the analysis that was discussed in the previous lecture.  In order to do this you will need to download the files associated with the model:

 1.
 Download the file (TBA) into the area in whch you have been using for your other practicals.
+= 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).
 .
 .
 {{http://mudsharkstatic.brookes.ac.uk/Graphics/Tribhuvan University.png|University logo|align="top",height="200",width="192"}} {{http://mudsharkstatic.brookes.ac.uk/Graphics/SBAN.png|SBAN logo|align="top",height="150",width="295"}}
-Line 9:
+Line 10:
-. This is a compressed archive file and you will need to extract the files before they can be used:
 {{{ $ tar -zxf P7.tgz }}}
+ .
 A brief introduction to the workshop is available on the website for the [[http://sbanepal.com/events/|SBAN]].
-Line 13:
+Line 14:
-. This  will generate a directory, A.thaliana, containing two sub-directories:  Model and Analysis. Model contains the model definition files and an  additional python module (in Model/Tools). Analysis contains the python  modules you will need for this practical.
+==== Tutors ====
 . The course is presented by:
  * Dr Mark Poolman
  * Prof David Fell
  * Kailash Adhikari, and
  * Dipali Singh
   . all of Oxford Brookes University, Oxford, UK.
-Line 15:
+Line 22:
-. For the  sake of the practical we have made a few simplifications and the model  and results will not be identical to those in the lecture. the aim of  the practical is to illustrate the techniques used.

== Part A: Investigating the effect of knocking out the Calvin cycle enzymes ==
 1. cd into Analysis/Knockouts
 1.
 Start ScrumPy and the load the model as before.
+  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).
-Line 23:
+Line 25:
-.
 Import the {{{KnockOutImpacts}}} module.


 1.
 This defines a single function also called  {{{KnockOutImpacts}}} that returns a dictionary recording the impact of remove each reaction from the model (relative change in objective value) eg:
-Line 31:
+Line 26:
-  {{{ >>> res = KnockOutImpacts.KnockOutImpacts(m)}}}
+  {{http://mudsharkstatic.brookes.ac.uk/Graphics/brookes.jpg|brookes logo|align="bottom",height="100",width="243"}}      {{http://mudsharkstatic.brookes.ac.uk/Graphics/accliphot-logo.png|accliphot logo|align="bottom",height="90",width="352"}}    {{http://mudsharkstatic.brookes.ac.uk/Graphics/bbsrc_new.png|bbsrc logo|height="80",width="319"}}
-Line 35:
+Line 30:
-. Use this to
  . a)   Identify the lethal knockouts. b) Identify the non lethal knockouts   that have the greatest impact. c) From b investigate the impact of dual   knockouts, e.g.:
   .
   {{{ >>> lp.SetFixedFlux({Reac1:0,Reac2:0}) }}} {{{ >>> lp.Solve() }}} etc. Remember to clear the constraint before proceeding:

   {{{ >>> lp.ClearFluxConstraint([Reac1,Reac2]) }}}
+==== Application ====
 .
 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.
-Line 43:
+Line 35:
-   .
   (Generate lp by: {{{>>> lp = KnockOutImpacts.BuildLP.BuildLP(m) }}} )
+==== Instructions for workshop attendees ====
 .
 You are required to bring a laptop to the workshop.  The metabolic modelling package used in the course, [[http://mudshark.brookes.ac.uk/ScrumPy|!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 [[Meetings/Pune2016/ScrumPyVM|here]]. (TO BE UPDATED)
-Line 47:
+Line 40:
+==== 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!
-Line 48:
+Line 43:
-== Part B:  Analysing the response to varying input of light. ==
 1. Change directory to the relevant area:
  .
  {{{$ cd S.Typhim/Analysis/ATPScan}}}



 1.
 Start ScrumPy and load the model:

  .
  {{{ >>> m = ScrumPy.Model("../../Model/MetaSal.spy") }}}


  . (If you wish to avoid a bit of typing, leave the model name blank and use the file selector to find the model file instead.)


 1. Examine the files that are now presented - how much can you recognise from previous work in this course?

 1. Now import the module called ATPScan
  .
  {{{ >>> import ATPScan }}}



 1.
 The module contains a function, also called {{{ATPScan}}}  that will generate a data set (as shown in previous lectures)  containing the lp solutions over a range of imposed ATP demand values,  e.g.:


 1.
 {{{ >>> results = ATPScan.ATPScan(m, 0, 10, 50) }}}


 1. Will generate a dataset containing 50 solutions for the model with the imposed ATPase flux varying between 0 and 10 flux units.

 1. The ATPScan module also contains three functions to aid in the analysis of results:
  .
  {{{ GetChangers(results, tol=1e-6) }}} A list of reactions whose flux value changes by more than tol (default = 1e-6).

  {{{ GetSwitchers(results)          }}} A list of reactions that carry no flux at some point.

  {{{ GetRanges(results, tol=1e-6)   }}} A dictionary mapping reactions to the amount of change in flux over the range of ATP demand.


  * For example, to plot the reactions that at some point carry no flux:
   .
   {{{ results.AddToPlot(ATPScan.GetSwitchers(results)) }}}



  * Use these functions to identify which fluxes show the greatest response to changes in ATP demand
+||<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">                        ||