iBioSim/learn

iBioSim Learn

The learn project includes parameter estimation and a regulatory network learning method from time-series data based on the GeneNet procedure.

How to use it:

After building the executable jar, you need to invoke the following command:

 java -jar target/iBioSim-learn-3.0.0-SNAPSHOT-jar-with-dependencies.jar [options] input directory

where

Required	Description
input	arbitrary SBML file
directory	location of the time-series data

Options	Description
-e	perform parameter estimation. Default is GeneNet.
-l [list]	a flag to specify which parameters need to be estimated, where the value is a comma separated list of parameter ids (e.g., "p1,p2,p3")
-ta [num]	Sets the activation threshold. Default 1.15
-tr [num]	Sets the repression threshold. Default 0.75
-ti [num]	Sets how high a score must be to be considered a parent. Default 0.5
-tm [num]	Sets how close IVs must be in score to be considered for combination. Default 0.01
-tn [num]	Sets minimum number of parents to allow through in SelectInitialParents. Default 2
-tj [num]	Sets the max parents of merged influence vectors, Default 2
-tt [num]	Sets how fast the bound is relaxed for ta and tr, Default 0.025
-d [num]	Sets the debug or output level. Default 0
-wr [num]	Sets how much larger a number must be to be considered as a rise. Default 1
-ws [num]	Sets how far the TSD points are when compared. Default 1
-nb [num]	Sets how many bins are used in the evaluation. Default 4
--lvl	Writes out the suggested levels for every specie
--readLevels	Reads the levels from level.lvl file for every specie
--cpp_harshenBoundsOnTie	Determines if harsher bounds are used when parents tie in CPP.
--cpp_cmp_output_donotInvertSortOrder	Sets the inverted sort order in the 3 places back to normal
--cpp_seedParents	Determines if parents should be ranked by score, not tsd order in CPP.
--cmp_score_mustNotWinMajority	Determines if score should be used when following conditions are not met a > r+n
--score_donotTossSingleRatioParents	Determines if single ratio parents should be kept
--output_donotTossChangedInfluenceSingleParents	Determines if parents that change influence should not be tossed
-binNumbers	Equal spacing per bin
-noSUCC	to not use successors in calculating probabilities
-PRED	use preicessors in calculating probabilities
-basicFBP	to use the basic FindBaseProb function