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