RAndom Network GEnerator

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RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.

Download Now! range_nemo-1.4.tar.gz (4.0 MB) OR View all files

http://range.sourceforge.net

Release Date:

2008-01-22

Topics:

Bio-Informatics, Code Generators, XML, Modeling, Simulations, Molecular Science

Licenses:

BSD License, GNU General Public License (GPL)

Intended Audience:

Science/Research

User Interface:

Command-line

Programming Language:

C, Yacc

Registered:

2007-06-20

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RANGE_NEMO ver 1.4 released

RANGE produces random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Can be used to generate synthetic microarray data with a biochemical simulator, or NEMO alone can be used to SBML-ize your network with specified or random input functions. ver 1.4 adds a compiler flag to produce an XGMML file so that the network may be visualized in cytoscape.

posted by jlong777 664 days ago
File released: /range_nemo/range_nemo-1.4/range_nemo-1.4.tar.gz

posted 664 days ago
range_nemo range_nemo-1.4 file released: range_nemo-1.4.tar.gz

2007/8/6 first code release 2007/8/6 uncommented #define NON_LINEAR 2007/8/17 fixed bug in Hill function for multi_out, added noise generator in R 2007/8/21 fixed bug in user defined input functions 2007/8/21 fixed precedence for user defined input functions 2007/9/10 several minor enhancements 2007/9/14 changed exp dist in range to power law, and bug fixes 2007/9/19 increased DOR percentage from 50% to 75% in range 2007/10/5 RANGE: rewritten, scale-free claim is dropped for now NEMO: added debugging flag 2007/10/12 RANGE: rewritten, scale-free "fat-tail" implemented, added flag to set random seed NEMO: added flag to set random seed 2007/10/13 RANGE: minor bug fix. Added libsbml-2.3.5 to this release, 3.0.0 has trouble finding its own include files. 2007/10/22 RANGE: minor bug fix. Improved error reporting in nemo2sbml, and added a flag to output kinetic law info, deprecated -d by making -p output the same info. 2007/10/24 RANGE: minor bug fix. removed -d flag in nemo2sbml 2007/12/17 NEMO: changed nemo.y semantic stack 2008/1/22 RANGE: included range.c from ver 0.8 that makes different networks NEMO: added a "-x" flag to nemo2sbml that produces an XGMML (eXtensible Graph Markup and Modeling Language) file for the network, allowing it to be viewed in cytoscape

posted 664 days ago

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