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GeNOSA - Integrated Platform for Gene Regulatory Networks
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GeNOSA: Inferring and Experimentally Supporting Quantitative Gene Regulatory Networks in Prokaryotes

Home | Download | Datasets | Contact || Release 1.0, Last update: Jul 31 2015 


Description

This package included several tools to perform reconstruction of gene regulatory networks from microarray data and connectivity information.

Downloads

GeNOSA package

Usage of parameters

Optimal NCA for GRNs v1.2.13
Usage: OptNCA [options] 
options:
-h: Display this help.

[Input data parameters]
-P: Pass symbols.
-a: Maximum value of each gene. (Default: 10)
-b: Minimum value of each gene. (Default: -10)
-c: Input file of control strenth.  (Default: CS.txt)
-C: Compare to input file of control strenth.  (Default: CS0.txt)
-e: Input file of expression profiles. (Default: E.txt)
-t: Input file of transcription factors activities. (Default: TFA.txt)
-T: Compare to input file of transcription factors activities. (Default: TFA0.txt)
-F: Fitness function for optimization. (Default: 0)
    0 : Least Square Error
    1 : Root Mean Square Error
    2 : Model Error

[Perturbation parameters]
-s: The standard deviation of perturbation copies. (Default: 0.5)
-m: Perturbation handler. (Default: 0)
    0 : None
    1 : Read
    2 : Export
-n: The number of perturbation copies. (Default: 20, Maximum: 50)
-N: Using pre-defined perurbation set. (Default: E%02d.txt)
-x: Optimization stretegy.  (Default: 1)
    1 : optimize TFA only
    2 : optimize TFA and CS (no constraints)
    3 : optimize TFA and CS (with loose constraints)
    4 : optimzie TFA and CS (with tight constraints)
-v: Message verbose level from simple to verbose: 0->9 (Default: 0)

[Post-processing parameters]
-M: Post process for analysis. (Default: 0)
    0 : None
    1 : LSE
    2 : CS difference
    3 : TFA standard deviation
    4 : Overall mean from data
-I: Input pattern. (Default: IN%02d.txt)

[OSA parameters]
-i: OSA initial temperature. (Default: 1000)
-r: OSA cooling rate. (Default: 0.999)
-u: OSA radius. (Default: 0.05)
-S: Steps to run. (Default: 1000)

Datasets

Synthetic datasets

Experimental datasets

Related publications

Contact Information

EMail: Yi-Hsiung Chen and Hsinn-Ying Ho