caBench-to-Bedside (caB2B) An easy to use tool for searching across the caGrid Mukesh Sharma Washington University School of Medicine

caB2B Overview Brief Description caB2B is an open-source, secure query tool that permits translational research scientists to search and combine data from virtually any caGrid data service. The caB2B suite is composed of three core components: the Web application, the Client Application and the Administrative Module. Web Application provides both keyword-based and templated queries that allow users to easily search for microarray, biospecimen, imaging data, and nanoparticle data. Client Application provides metadata-based query interface that enables users to search virtually any caGrid data service like caTissue Core/Suite, caArray, caFE, gridPIR, and GeneConnect. The Administrative Module provides a graphical user interface for customizing a particular instance of caB2B. The goal of the tool is to aid translational scientists in combining data from tools like a caBIG ® biospecimen repository service, caTissue Core/Suite, with data from a microarray data repository like caArray and visualize the results. Intended Audiences: Basic and translational researcher

Searching data across caGrid by domains, like biospecimen (caTissue Core), microarray (caArray), imaging data (National Biomedical Imaging Archive, NBIA), and nanoparticle data (caNano Lab). Keyword searches within a selected domain. Parameterized queries based on the most common community-defined use cases. Selecting and saving caGrid service instances to query. Hosting institution information is returned with the results. Exporting the results as.CSV files, the exported file contains the parameters used to execute the query. Optional login. Users may access public data without signing in. Login is required to access secure data (e.g. biospecimen data sets). Executing queries across multiple instances of an application available at different hosting research centers. Getting results from active instances while errors from inactive instances will be reported to users. caB2B Web Application v3.1

Executing a single form based query across multiple applications, i.e., a single query can be used to fetch data from caTissue Core and caTissue Suite. Submitting queries for offline execution. The query status can be checked later and the results can be downloaded once the query is complete. Query dashboard which shows all the queries submitted for offline execution. It shows the query status, result count, hosting institute information, query parameters etc. Exporting multiple files for a keyword query results as a single zip file. Enhancement in the result display for the form based and keyword queries. Reduced the time it takes to display the results additionally, the results are displayed as soon as it is retrieved.

caB2B Client Application v3.1 Metadata-based query enabling searches on any available data service (e.g. caTissue Core, caArray, caBIO). Semantically aware query interface that seamlessly creates distributed queries (i.e. across two or more applications such as caFE and GeneConnect) Saving and filtering data acquired as a result of a query with enhanced spreadsheet component. Grouping of query results by service instances. User based access control for experiments and saved queries. caGrid based authentication and anonymous login for users without grid account. Saving queries using the multi-model categories

Web-based administrative module. Ability to load models from caDSR into Metadata Repository. Dynamic discovery of services using Index Service. Ability to create multi-model categories. Administrator can create categories that span across multiple models. User interface to create categories and curate paths. User interface to define inter-model joins to facilitate interoperability between fully specified and underspecified models. Defining model groups. Administrator may assign user friendly names to caBIG ® application models reflecting the domain represented by the application. caB2B Administrative Module v3.1

Tool Installation & Usage Overview Installation Requirements Client JRE version > 1.6.0_03 Windows, Linux, Mac Recommended Memory 512MB caB2B Server JDK 1.6.0_03 JBoss GA MySQL Ant 1.7.x Recommended Memory 2GB Required Skill sets basic ANT knowledge basic database knowledge

Releases, Schedule & Contacts Current Release caB2B 3.1 Release date 30 September 2009 Previous Release caB2B 3.0 Release date 09 September 2009 Home page Contact Information

Acknowledgments Washington University Rakesh Nagarajan Mukesh Sharma Mark Watson NCI-CBIIT Ian Fore Juli Klemm Avinash Shanbhag Anand Basu Sapient Stephen Goldstein Capability Plus Solutions Chris Piepenbring Persistent Systems Srikanth Adiga Chandrakant Talele Chetan Patil Chetan Pundhir Deepak Shingan Gaurav Mehta Madhumita Shrikhande Pallavi Mistry Pooja Arora Rajesh Vyas 9