The following BIRN capabilities provide important functions that can help biomedical research projects achieve their goals using cutting edge software developed in a bottom-up approach based on user requirements. They are all mature and have already been in production use for various BIRN users. To learn about capabilities that are under development, click here.
Data Grid
Data Grids play a vital role in large scale collaborative biomedical research projects. Sharing large file sets among geographically dispersed groups presents significant challenges. The BIRN Data Grid infrastructure can help groups seeking to deploy their own Data Grids. The infrastructure is based on two mature services from the widely used Globus Toolkit. The Globus GridFTP Server is a high performance extension to the ubiquitous File Transfer Protocol standard. It is optimized for heavy workloads and high performance networks. The Globus Replica Location Service (RLS) is a lightweight distributed file registry that allows users on a data grid to register and query for file locations with minimal overhead. BIRN has worked with the Globus project to ensure that these tools can satisfy the unique requirements of the biomedical research community. The BIRN packages also include additional utilities for tar-on-the-fly, remote directory listing, remote file statistics, remote file synchronization, and remote file checksum generation.
- Documentation
- Related Working Group: Data Management
- Contact: Data Management Working Group chair, Rob Schuler (schuler AT isi.edu).
Credential Management
BIRN data services require security credentials for users to store or access data. The BIRN-wide credential service, accessed via a client tool on the user’s home system, provides a simple way for users to get a credential whenever they choose to access BIRN services or data.
- Documentation
- Related Working Group: Security
- Contact: Security Working Group chair, Rachana Ananthakrishnan (ranantha at mcs.anl.gov)
Group Policy Management
This service will enable BIRN user teams to create new user groups and control their membership. User teams also will be able to assign access control privileges for other BIRN services, such as data access and storage.
- Documentation
- Related Working Group: Security
- Contact: Security Working Group chair, Rachana Ananthakrishnan (ranantha at mcs.anl.gov)
User Registration Service/Certificate Authority
Because BIRN data services are distributed across many institutions, we provide a centralized registration mechanism for new users. This web-based registration service allows a user to become eligible to sign up to access data used by BIRN teams. They also gain access to BIRN’s infrastructure, software tools, data-sharing strategies and advisory services. The process also establishes BIRN-wide security credentials for new users.
- Related Working Group: Security
- Contact: Security Working Group Chair, Rachana Ananthakrishnan (ranantha at mcs.anl.gov)
Query Mediator
The capability allows research teams to issue queries to a collection of databases hosted by independent organizations and to receive unified results from all of the databases in a standard format.
- Related Working Group: Information Integration
- Contact: Information Integration WG chair, Jose-Luis Ambite (ambite AT isi.edu)
Graphical Pipeline Workflow for Computational Genomics and Visual Informatics
This capability allows BIRN users to design, execute, modify, and share openly advanced computational protocols for diverse types of informatics, imaging and genomics applications.
- Related Working Groups:Workflow and Vertical Integration
- Contact: Genomics Working Group chair, Ivo Dinov
Neuroimaging Workflows Pipeline
This capability, also known as the LONI Pipeline, based in the LONI department of UCLA, is a free workflow application primarily aimed at neuroimaging researchers. With the LONI Pipeline users can quickly create workflows that take advantage of all the greatest neuroimaging tools available.
BioScholar
This capability supports scientists building a simple data repository for their laboratory by modeling their experimental designs in an online graphical modeling tool (without requiring any database knowledge). The system is available for download from http://www.bioscholar.org/ and is a simple one-click install. The approach is designed to be intuitive and understandable to scientists, rather than needing help from computational experts.
- Documentation
- Contact: Knowledge Engineering chair, Gully Burns (gully AT usc.edu)
Grant Analysis Support (nihmaps.org)
This web application (which is available at www.nihmaps.org) provides a “topic map” that enables all grant proposals funded by NIH in a particular year to be queried in several ways. The map shows the similarity of topics between grants, providing an intuitive, interactive clustered representation. Users may view grant patterns based on changing coloring schemes, overlays and other viewing options. Future developments will include creating subject-specific MEDLINE maps for specific scientific communities and comparing these maps with others derived from CRISP.
Related Working Group: Knowledge Engineering
To use this capability, go to www.nihmaps.org.
