The name of the Stream Java application is an abbreviation of the following long name: Static Thermodynamic REgulAtory Model of transcription.
In brief, Stream is a bioinformatics application for researchers, who want to model the transcriptional regulation of a specific gene and predict its transcriptional output in different situations.
Stream is the first publicly available framework for modeling, visualizing, and predicting the regulation of the transcription rate of a target gene.
Understanding 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.
Given the concentration of a set of transcription factors as well as the transcription factor binding sites in a regulatory DNA region and the concentration 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:
·validate that the given set of TFs is able to regulate the target gene and
·predict the transcription rate under different conditions (e.g. different tissues, knockout/additional TFs or mutated/missing TFBS).
Requirements:
· Java
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