Self

Practical 2

Note

This practical requires a small update to ScrumPy.

  1. Download this file

  2. Unpack it: tar zxf patch.tgz

  3. cd into the newly created directory: cd patch

  4. Become root.
  5. Execute the "patchit" script: ./patchit

That's it !

Analysing a genome scale model of Salmonella

In this practical we (you !) will be replicating some the analysis that was described in the previous lecture . In order to do this you will need to download the files associated with the model:

  1. Download the file P2.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 P2.tgz 

  3. This will generate a directory, S.Typhim, 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: Analysing the response to varying ATP demand.

Part B: Impact of single and double reaction knockouts

  1. cd into Analysis/Knockouts
  2. Start ScrumPy and the load the model as before.

  3. Import the KnockOutImpacts module.

  4. 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:

    •  >>> res = KnockOutImpacts.KnockOutImpacts(m)

  5. 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.ClearFluxConstraints([Reac1,Reac2]) 

      • (Generate lp by: >>> lp = KnockOutImpacts.BuildLP.BuildLP(m)  )

None: Meetings/Pune2016/P2 (last edited 2016-03-16 10:10:03 by hassan)