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FastSL

Fast-SL is an efficient algorithm to identify synthetic lethal gene/reaction sets in genome-scale metabolic models.

Requirements

To perform synthetic lethality analysis using Fast-SL the following tools are needed:

  1. COBRA Toolbox
  2. A linear programming (LP) solver such as Gurobi, GLPK etc.
  3. CPLEX v12.0 or higher for the parallel version of Fast-SL. For the serial version of Fast-SL, any COBRA-supported solver can be used. CPLEX is available free for academics from IBM

Citing Fast-SL

If you use Fast-SL in your work, please cite

Aditya Pratapa, Shankar Balachandran and Karthik Raman (2015) "Fast-SL: An efficient algorithm to identify synthetic lethal sets in metabolic networks" Bioinformatics 31:3299–3305 doi:10.1093/bioinformatics/btv352

Description of Available files

Models/

'Eco_iAF1260.mat' :: SBML model of Escherichia coli - iAF1260 used for analysis

'eliList_eco_iAF1260.mat' :: List of reactions eliminated for lethality analysis- Exchange, ATPM etc

'Mtu_iNJ661.mat' :: SBML model of Mycobacterium Tuberculosis used for analysis

'eliList_mtu_iNJ661.mat' :: List of reactions eliminated for lethality analysis

'STM_v1.0.mat' :: SBML model of Salmonella Typhimurium used for analysis

'eliList_sty_STM_v1.0.mat' :: List of reactions eliminated for lethality analysis

Sample Results/

Reaction and Gene lethals for the models used

Documentation (MATLAB)

>>help fastSL

fastSL(model,cutoff,order,eliList,atpm) 

  

  INPUT

  model (the following fields are required - others can be supplied)       

    S            Stoichiometric matrix

    b            Right hand side = dx/dt

    c            Objective coefficients

    lb           Lower bounds

    ub           Upper bounds

    rxns         Reaction Names

  OPTIONAL

  cutoff         cutoff percentage value for lethality.Default is 0.01.

  order          Order of SLs required.Default order is 2. Max value 3.

  eliList        List of reactions to be ignored for lethality

  analysis:Exchange Reactions, ATPM etc.

  atpm           ATPM Reaction Id in model.rxns if other than 'ATPM'

  OUTPUT

  A 'modelname_Rxn_Lethals.mat' file containing all the lethal reaction sets of the order specified



>>example_fastSL

>>example_fastSLgenes

Acknowledgements