Dream3

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It is a package we developed for the DREAM3 in silico gene regulatory network reconstruction competition ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008121 Yip et al., PLoS ONE 5(1):e8121, 2010]). To run the program, [http://http://www.oracle.com/technetwork/java/javase/downloads/index.html Java] and [http://ant.apache.org/ Apache Ant] need to be installed. Then unzip all the files into a directory, and use a command window to type "ant runall3" at the directory to run the program. In order to keep the package size small, we have only included the DREAM3 size-10 networks. The size-50 and size-100 networks can be downloaded from the [http://wiki.c2b2.columbia.edu/dream/index.php/D3c4 DREAM3 web site].
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This is a [http://archive.gersteinlab.org/proj/dream3/dream3.zip package] we developed for the DREAM3 in silico gene regulatory network reconstruction competition ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008121 Yip et al., PLoS ONE 5(1):e8121, 2010]). To run the program, [http://http://www.oracle.com/technetwork/java/javase/downloads/index.html Java] and [http://ant.apache.org/ Apache Ant] need to be installed. Then unzip all the files into a directory, and use a command window to type "ant runall3" at the directory to run the program. In order to keep the package size small, we have only included the DREAM3 size-10 networks. The size-50 and size-100 networks can be downloaded from the [http://wiki.c2b2.columbia.edu/dream/index.php/D3c4 DREAM3 web site].
The program was developed mainly for DREAM3, and was not written in a very generic way. To run it on other datasets or to use to for some other tasks, the source code needs to be modified.
The program was developed mainly for DREAM3, and was not written in a very generic way. To run it on other datasets or to use to for some other tasks, the source code needs to be modified.

Latest revision as of 12:44, 21 November 2011

This is a package we developed for the DREAM3 in silico gene regulatory network reconstruction competition (Yip et al., PLoS ONE 5(1):e8121, 2010). To run the program, Java and Apache Ant need to be installed. Then unzip all the files into a directory, and use a command window to type "ant runall3" at the directory to run the program. In order to keep the package size small, we have only included the DREAM3 size-10 networks. The size-50 and size-100 networks can be downloaded from the DREAM3 web site.

The program was developed mainly for DREAM3, and was not written in a very generic way. To run it on other datasets or to use to for some other tasks, the source code needs to be modified.

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