Difference between revisions of "Construct composite modules on tracks (analysis)"

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** '''Elite size''' – Number of elite organisms (i.e. best organisms to survive unconditionally)
 
** '''Elite size''' – Number of elite organisms (i.e. best organisms to survive unconditionally)
 
** '''Mutation rate''' – This controls how often mutation occurs and how significant they are (0..1)
 
** '''Mutation rate''' – This controls how often mutation occurs and how significant they are (0..1)
* '''Parameters''' (expert) – Parameters
+
* '''Score calculation parameters''' (expert) – Parameters which control score calculation
 
** '''Penalty rate''' – Which penalty value will be assigned
 
** '''Penalty rate''' – Which penalty value will be assigned
 
** '''Site models in focus''' – At least one of these models must present in the resulting composite model to have non-zero score
 
** '''Site models in focus''' – At least one of these models must present in the resulting composite model to have non-zero score

Revision as of 12:31, 12 April 2013

Predict composite module using site search on tracks result

Parameters:

  • Experiment track – Path to experiment ('yes') track
  • Control track – Path to control ('no') track
  • Genetic algorithm parameters (expert) – Genetic algorithm parameters
    • Number of iterations – Number of iterations
    • Population size – Population size
    • Non-change limit – Number of iterations to stop after if best score is not improved
    • Elite size – Number of elite organisms (i.e. best organisms to survive unconditionally)
    • Mutation rate – This controls how often mutation occurs and how significant they are (0..1)
  • Score calculation parameters (expert) – Parameters which control score calculation
    • Penalty rate – Which penalty value will be assigned
    • Site models in focus – At least one of these models must present in the resulting composite model to have non-zero score
  • Model parameters – Model parameters
    • Min modules – Minimal number of modules
    • Max modules – Maximal number of modules
    • Gaussian model (expert) – Gaussian model
      • Min models – Minimal number of site models in module
      • Max models – Maximal number of site models in module
      • Min sites to account – Minimal number of sites to account
      • Max sites to account – Maximal number of sites to account
      • Min module width – Minimal width (sigma) of the module
      • Max module width – Maximal width (sigma) of the module
  • Output path – Path to store result
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