Overview

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

[read more : Introduction] 

Screenshot

Implementation and Usage

STREAM is implemented in Java and is provided as an platform independent .jar file.

STREAM currently uses the thermodynamic model introduced by Reinitz et al.[1], but the framework is flexible and can be used in conjunction with other models implemented in Java. STREAM offers several optimization methods including gradient descent and simulated annealing for adjusting the internal parameters of the model to best fit the user's input data.

STREAM can be executed using a graphical user interface (GUI) as well as via the command-line. The GUI offers the same functionality (e.g., multistart options of the optimization or automatic cross-validation evaluation) as the command-line tool, but in an intuitive and dialogue-based fashion. Both the command-line and the GUI version can save the current result and settings of the program into a file, which makes saving and modifying previous experiments simple.

[read more : Documentation] 

Download 

More information as well as the program itself can be obtained from here.

Citing STREAM

Bauer, D.C. and Bailey, T.L, STREAM - Static Thermodynamic REgulAtory Model for transcriptional. Bioinformatics, 2008, 24, 2544-2545. PubMed Abstract

Research papers using STREAM

Bauer, D. C. & Bailey, T. L. Optimizing static thermodynamic models of transcriptional regulation. Bioinformatics, 2009, 25, 1640-1646, PubMed Abstract (Supplemental Material)

Bauer, D. C. & Bailey, T. L. Studying the functional conservation of cis-regulatory modules and their transcriptional output. BMC Bioinformatics, 2008, 9, 220 PubMed Abstract

Contact

Denis C. Bauer

Timothy L. Bailey

Awards

(1) John Reinitz, Shuling Hou, and David H. Sharp. Transcriptional Control in Drosophila. Complexus, 1:54–64, 2003.