{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T10:50:07Z","timestamp":1742381407375,"version":"3.33.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3256,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: For testing and sensitivity analysis purposes, it is beneficial to have known transcription networks of sufficient size and variability during development of microarray data and network deconvolution algorithms. Description of such networks in a simple language translatable to Systems Biology Markup Language would allow generation of model data for the networks.<\/jats:p><jats:p>Results: Described herein is software (RANGE: RAndom Network GEnerator) to generate large random transcription networks in the NEMO (NEtwork MOtif) language. NEMO is recognized by a grammar for transcription network motifs using lex and yacc to output Systems Biology Markup Language models for either specified or randomized gene input functions. These models of known networks may be input to a biochemical simulator, allowing the generation of synthetic microarray data.<\/jats:p><jats:p>Availability: \u00a0http:\/\/range.sourceforge.net<\/jats:p><jats:p>Contact: \u00a0jlong@alaska.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm529","type":"journal-article","created":{"date-parts":[[2007,11,4]],"date-time":"2007-11-04T00:24:17Z","timestamp":1194135857000},"page":"132-134","source":"Crossref","is-referenced-by-count":8,"title":["Synthetic microarray data generation with RANGE and NEMO"],"prefix":"10.1093","volume":"24","author":[{"given":"James","family":"Long","sequence":"first","affiliation":[{"name":"1 Biotechnology Computing Research Group, University of Alaska Fairbanks, PO Box 757000 and 2Department of Computer Science, University of Alaska Fairbanks, PO Box 756670, Fairbanks, AK 99775, USA"}]},{"given":"Mitchell","family":"Roth","sequence":"additional","affiliation":[{"name":"1 Biotechnology Computing Research Group, University of Alaska Fairbanks, PO Box 757000 and 2Department of Computer Science, University of Alaska Fairbanks, PO Box 756670, Fairbanks, AK 99775, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,11,3]]},"reference":[{"key":"2023020209444382200_B1","doi-asserted-by":"crossref","DOI":"10.1201\/9781420011432","volume-title":"An Introduction to Systems Biology: Design Principles of Biological Circuits.","author":"Alon","year":"2006","edition":"1st"},{"key":"2023020209444382200_B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pbio.0050008","article-title":"Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles","volume":"5","author":"Faith","year":"2007","journal-title":"PLoS Biol"},{"key":"2023020209444382200_B3","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"COPASI \u2013 a COmplex PAthway SImulator","volume":"22","author":"Hoops","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020209444382200_B4","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1093\/bioinformatics\/bti1049","article-title":"Mining coherent dense subgraphs across massive biological networks for functional discovery","volume":"21","author":"Hu","year":"2005","journal-title":"Bioinformatics (ISMB 2005)"},{"key":"2023020209444382200_B5","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020209444382200_B6","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1080\/10618600.1996.10474713","article-title":"R: a language for data analysis and graphics","volume":"5","author":"Ihaka","year":"1996","journal-title":"J. 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