# 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 || r > a + 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|