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.
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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.
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
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