FLYNET OVERVIEW
===============

This archive contains the source code, executable, and datasets used to generate and validate the integrative transcriptional regulatory network of Drosophila described in the paper:

Daniel Marbach*, Sushmita Roy*, Ferhat Ay, Patrick E. Meyer, Rogerio Candeias, Tamer Kahveci, Christopher A. Bristow, and Manolis Kellis (2012) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Submitted.

The paper is available at: http://compbio.mit.edu/flynet

The code allows (1) generating the integrative networks based on the input datasets, (2) performing the network validation based on enrichment with REDfly edges, and (3) computing the five types of functional enrichments that we considered.

The software is released open source under an MIT license (see below).


DOWNLOAD
========

The latest version of flynet can be checked out from the git repository:
http://code.google.com/p/flynet/source/checkout

Major releases are also posted as zip files on the downloads tab:
http://code.google.com/p/flynet/downloads/list


HOW TO RUN FLYNET
=================

Flynet is a command-line java application, we provide both the source code (see below) and a jar file. To display a list of available options, launch flynet with the option '-h':

	java -jar flynet.jar -h
	
For most analyses, you will have to increase the Java heap size using the option '-Xmx', otherwise an "out of memory" error will occur. For example:

	java -jar -Xmx4g flynet.jar <option>
	
Examples
--------

Generating recovery rate curves (Fig. 2B):
java -jar flynet.jar --dir resources/restricted_networks --recovery redflynet.tsv integrative_unsup.tsv integrative_sup.tsv chip.tsv motif.tsv chromtc.tsv chromcl.tsv microarray.tsv rnaseq.tsv


HOW TO COMPILE FLYNET
=====================

If you are new to Java, we recommend that you use Eclipse. You can download Eclipse from: www.eclipse.org. 

From the File menu, choose "New->Java Project". Select the option "Create project from existing source", choose the flynet directory, and click "Finish".


LICENSE
=======

We release this software open source under an MIT license (see below). If this software was useful for your scientific work, please cite our paper available at:
http://compbio.mit.edu/flynet

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
