Our laboratory has developed a number of software tools, including:

MetaR: blending user interfaces and scripting to help biologist analyze data.

NYoSh Analysis Workbench: A data analysis workbench built on top of MPS. Takes advantage of composable languages to create a platform intermediate between command line flexibility and user-friendly custom interfaces. Includes MetaR and BDVal for MPS.

GobyWeb: a web front-end that leverages Goby and simplifies next-generation sequencing data analysis. Supports data sharing and parallel computations on grids of computers.

goby logo

Goby: high-performance next-gen data management framework.
bdval-logoBDVal: Program for biomarker model development and validation in high-throughput datasets.

GPCR-OKB: The G Protein-Coupled Receptor Oligomerization Knowledge Base.

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TEPSS: Tissue Expression Profile Similarity Searches. Find transcripts that have similar tissue expression profiles to a group of transcripts of interest.

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Twease: Biomedical search engine (Twease/Medline searching abstracts from the Medline database and Twease/OTMI searching an OTMI text corpus).

SigPathLogo

SigPath: an information system designed to support quantitative studies on the signaling pathways and networks of the cell. Retired. The link and application have been discontinued.

TissueInfo: information management and  mining of EST data for cancer biomarker discovery.

RbDe: The Residue-based Diagram Editor is a web user interface that supports the construction of 2D diagrams of proteins.

RbDgLogo

RbDg: The Residue-based Diagram Generator is a batch version of RbDe. RbDg is used by many bioinformatics databases to create snake-like and other diagrams.