Open Source S/R Software Development Software

GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. Contact: bmhoan@gmail.com or walter.vincent.fr@gmail.com

The Dataverse Network is a Java EE5 app that enables researchers to share data on-line. It provides data citation standards, facilitates preservation, distribution and replication of data, and includes statistical analysis. More at: http://thedata.org

InPUT offers a descriptive and programming language independent format and IoC (Inversion of Control) container for the configuration and design of computer experiments. Code and more info can be found on github: http://github.com/feldob/InPUT

A simple tool to help you create an R interface for your Java project. Simply annotate the constructors and methods you want to make available and JAnnotateR will produce a working package, complete with documentation generated from javadocs.

Web application providing analysis of biomedical relationships. Built using the Grails web application framework (http://grails.org/) with MySQL (http://www.mysql.com/) as a back-end datastore and utilizing R (http://www.r-project.org/) for statistical analysis. Developed by the Dana Farber Cancer Institute (http://compbio.dfci.harvard.edu/) and Entagen (http://www.entagen.com).

For software developers in domains involving statistical analysis, the "R + Java = Inf" project analyses and enhances the interoperability between the R and Java programming languages. The deliverables are source code, documentation and benchmarks.

TOPS provides the benchtop scientist with a free toolset to analyze, filter and visualize data from functional genomic gene-gene and gene-drug interaction screens with a flexible interface to accommodate various different technologies and analysis algorithms in addition to those already provided here.

The Vyper Dynamic Server framework is a pure-java library for use in the creation of backend / server platforms. VDS is specifically tailored for financial applications, and suited for many high-throughput, asynchronous and distributed environments.

Java-based scientific graphics with support for Java, Groovy, MATLAB, Python, the R statistical environment, Scala and SciLab.