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Leandro Watanabe d51db27bc7 Update README.md		2017-12-13 16:04:33 -07:00
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src	Initial commit for instructions on how to use analysis and learn.	2017-12-12 18:05:57 -07:00
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pom.xml	Added scripts to build executable jar for learn and javadocs.	2017-07-09 17:17:37 -06:00
README.md	Update README.md	2017-12-13 16:04:33 -07:00

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 [-e] [-l ...] input directory

where

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

Optional	Description
`-e`	perform parameter estimation. Default is GeneNet.
`-l ...`	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")