Sharing Data

All members of the SDCSB are firmly committed to the NIH policy on sharing of research data (NOT-OD-03-032). Central to this policy is the timely sharing of data produced in the course of Center research. A major function of the San Diego Center for Systems Biology is to build a resource of large data sets relevant to fundamental biological processes and model systems, which we foresee will be widely used and re-used in the course of systems biology research by the biomedical research community. Such content includes, or is expected to soon include, large datasets related to genomic DNA, epigenetic profiles, chromatin structure, mRNA levels and splicing, protein levels and post-translational modifications, and networks of protein-DNA, protein-protein, genetic and drug-target interactions.

Sharing Maps and Models

Separate from data, an important feature of our Center is the timely release of the network maps, data-driven ontologies and predictive models generated in the course of research. These will be derived as important primary products through analysis of the raw data. For example, one of the major outcomes of our Systems Approach will be the creation of one or more data-driven ontologies, comparable to the manually-curated Gene Ontology (GO). These ontologies will be released in multiple formats, including a version browsable in Cytoscape using Cytoscape format (CYS) and a version that conforms to the Open Biological and Biomedical Ontologies (OBO) format. OBO files can be loaded into most ontology browsers, including OBO-Edit and QuickGO and many others.

Sharing Software

All member of the SDCSB are committed to open source software and open data access. All of the software we develop will be made available under the open source GNU Library General Public License (LGPL), and all other computational resources developed through this project will also be made available under the LGPL. All software will be disseminated through publicly accessible online avenues in the form of public web servers, FTP sites, source code version management servers (i.e., a Subversion code repository) and publications. Other content, such as training material, will be made available under a Creative Commons license that allows redistribution without restrictions.