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 1.
 Download the file AraGSM.tgz into the area in which you have been  using for your other practicals.		  1. Download the file AraGSM.tgz into the area in which you have been     using for your other practicals.
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 1.
 This is a compressed archive file and  you will need to extract the files before they can be used:		  1. This is a compressed archive file and  you will need to extract the files before they can be used:
  .
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 1.
 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.

 1.
 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.
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 1. 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.

 1. 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.
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 1.
 cd into Analysis/Knockouts		  1. cd into Analysis/Knockouts
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 Start [[http://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]]  and the load the model as before.  Start [[http://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]]        and the load the model as before.
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 Import the {{{KnockOut}}}  module.  Import the {{{KnockOut}}}      module.
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 This defines a single function also  called {{{KnockOut}}}{{{Effects}}}  that returns a dictionary recording the impact of remove each  reaction from the model (relative change in objective value)  This defines a single function also    called {{{KnockOut}}}{{{Effects}}}      that returns a dictionary recording the impact of remove each   reaction from the model (relative change in objective value)
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 1. lp = BuildLP.BiomassLP(m)
 1. lp = BuildLP.BiomassLP(m)
 1. lp.Solve()
           wild_type_solution = lp.GetPrimSol()

  . Observe the flux values of the Calvin Cycle enzymes
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 lp.Solve()  Load the'' KnockOutEffects'' from the KnockOut module and provide the reaction to knockout in the argument
     eg. mutant_solution = KnockOutEffects.KnockOut(m, 'SEDOHEPTULOSE-BISPHOSPHATASE-RXN_Plas', lp)
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 wild_type_solution = lp.GetPrimSol()
         Observe the flux values of the Calvin Cycle enzymes
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 Load the'' KnockOutEffects'' from the KnockOut module.  Investigate the differences in wild_type_solution and mutant_solution and interpret the results.
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 1.
 from Util import Set


 1.
 new_active_reactions = Set.Complement(mutant_solution, wild_type_solution)


 1.
 Similarly , Find the reactions that were inactive as


 1.
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  {{{$ cd S.Typhim/Analysis/ATPScan}}}   {{{$ cd A.thaliana/Analysis/LightScan}}}
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  {{{ >>> m = ScrumPy.Model("../../Model/MetaSal.spy") }}}   {{{ >>> m = ScrumPy.Model("../../Model/AraTopLevel.spy") }}}
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 1. Now import the module called ATPScan  1.
 Now import the module called LightScan
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  {{{ >>> import ATPScan }}}   {{{ >>> import LightScan }}}
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 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

Practical 8

Analysing a genome scale metabolic model of A. 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 AraGSM.tgz into the area in which you have been using for your other practicals.
  2. This is a compressed archive file and you will need to extract the files before they can be used:

    •  $ tar -zxf AraGSM.tgz 

  3. 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.
  4. 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 our the Calvin cycle enzymes from GSM of A. thaliana

  1. cd into Analysis/Knockouts

  2. Start ScrumPy and the load the model as before.

  3. Import the KnockOut module.

  4. This defines a single function also called KnockOutEffects that returns a dictionary recording the impact of remove each reaction from the model (relative change in objective value)

  5. lp = BuildLP.BiomassLP(m)
  6. lp.Solve()
    • Observe the flux values of the Calvin Cycle enzymes

  7. Load the KnockOutEffects from the KnockOut module and provide the reaction to knockout in the argument

  8. Investigate the differences in wild_type_solution and mutant_solution and interpret the results.
  9. from Util import Set
  10. new_active_reactions = Set.Complement(mutant_solution, wild_type_solution)
  11. Similarly , Find the reactions that were inactive as

Part B : Analysing the response to varying input of photon flux

  1. Change directory to the relevant area:

    • $ cd A.thaliana/Analysis/LightScan

  2. Start ScrumPy and load the model:

    •  >>> m = ScrumPy.Model("../../Model/AraTopLevel.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.)
  3. Examine the files that are now presented - how much can you recognise from previous work in this course?

  4. Now import the module called LightScan

    •  >>> import LightScan 

None: Meetings/Nepal2016/P4 (last edited 2016-06-30 09:58:48 by mark)