Bioinformatics Software Development Projects

Galaxy

Galaxy software: An application for doing large network graph analysis using dynamic transitive closure.

Galaxy is an application for conducting large-scale graph network analysis using a novel algorithm developed by Dan Dougherty of the Ohio State University Math Biosciences Institute. The parallel application conducts a dynamic transitive closure analysis of networks ranging in size of over 8000 nodes. The application was developed to find unique relationships between gene and drug interactions in Wolfgang Sadeeā€™s cancer research at the Ohio State University Medical Center. Galaxy is available in the Ohio Biosciences Library.

ExtractProp

ExtractProp: A portable application for extracting properties from computational biology applications.

ExtractProp is a Java-based application for selecting key fields of interest from many bioinformatics applications to aid building digital databases. The application is a spin-out of the NSF funded research efforts of Iris Meier and Annkatrin Rose of the Ohio State University Plant Biology department which resulted in the creation of the Arabicoil Arabidopsis Coiled-coil database (www.coiled-coil.org). The ExtractProp java application jar file and associated documentation is available upon request by contacting biosoftware@osc.edu.

Biosequence
Secure Sequence ID: An application to support secure exchange of biosequence information.

The Biosequence Exchange ID is a unique piece of technology developed to aid efficient and secure handling of biosequence data. Using a one-way hashing algorithm developed specifically for biosequence data, the Biosequence Exchange ID (or BXID) provides a novel way to catalog, index and share biosequence information for use in databases and sharing of biosequence data. The one-way hashing algorithms have been developed to minimize collisions while provide an efficient storage retrieval index. Routines encoding the BXID are available in the Ohio Biosciences Library. Java, C and Fortran source code implementations are available by contacting biosoftware@osc.edu. A free website is available for determining the BXID for any sequence of interest, as well as large scale file updates for files in FASTA format.