title: STREAM: Static Thermodynamic REgulAtory Model of transcription.
abstract: BACKGROUND
  Understanding the transcriptional regulation of a gene in detail is a crucial step towards uncovering and ultimately utilizing the regulatory grammar of the genome. Modeling transcriptional regulation using thermodynamic equations has become an increasingly important approach towards this goal. Here, we present stream, the first publicly available framework for modeling, visualizing and predicting the regulation of the transcription rate of a target gene. Given the concentrations of a set of transcription factors (TFs), the TF binding sites (TFBSs) in a regulatory DNA region, and the transcription rate of the target gene, stream will optimize its parameters to generate a model that best fits the input data. This trained model can then be used to (a) validate that the given set of TFs is able to regulate the target gene and (b) to predict the transcription rate under different conditions (e.g. different tissues, knockout/additional TFs or mutated/missing TFBSs).
  
  
  BACKGROUND
  The platform independent executable of stream, as well as a tutorial and the full documentation, are available at http://bioinformatics.org.au/stream/. stream requires Java version 5 or higher.
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld. 4072, Australia.
authors.forename: Denis C
authors.initials: DC
authors.lastname: Bauer
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Bailey
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D012984:Software; D013816:Thermodynamics; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors
references.citation: Bioinformatics. 2000 Jan;16(1):16-23
references.pmid: 10812473
references.citation: Genetics. 2004 Aug;167(4):1721-37
references.pmid: 15342511
references.citation: BMC Bioinformatics. 2008 Apr 29;9:220
references.pmid: 18442418
references.citation: Nat Genet. 2006 Oct;38(10):1159-65
references.pmid: 16980977
references.citation: Curr Biol. 2006 Jul 11;16(13):1358-65
references.pmid: 16750631
references.citation: Nature. 2008 Jan 31;451(7178):535-40
references.pmid: 18172436