Inferelator_2013.3.RC2.tar.gz was used to generate results for the paper "Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks."
Other versions are newer and include the option to estimate transcription factor activities using prior known interactions. The Modified Elastic Net method has not been tested in those versions.
Inferelator_2015.08.05.tar.gz was used to generate results for the paper "An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network."
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You can follow Inferelator development on GitHub: github.com/ChristophH/Inferelator