BIRN – Biomedical Informatics Research Network

The Globus clients software provides MyProxy, GSI security, GridFTP, UberFTP, and RLS client software that enables users and applications to interact with BIRN operated MyProxy, GridFTP, and RLS servers.

FIRE (coming in 2010) is an integrated suite of tools to put your data on a gridFTP set of servers, link it to a database which is automatically federated, to be able to retrieve it from multiple sites, with the data wrapped in XCEDE (XML) wrappers.

Grid Account Management Architecture, GAMA, provides an end-to-end security infrastructure suitable for multi-institution collaborations with support for grid computing, cloud computing, and web portals.

MyProxy is an online credential repository. You can store X.509 proxy credentials in the MyProxy repository, protected by a passphrase, for later retrieval over the network.

GridFTP is a high-performance, secure, reliable data transfer protocol optimized for high-bandwidth wide-area networks.

The Upload scripts work in concert with the GridFTP servers, XCEDE, and the standardized data hierarchies to put data onto the GridFTP servers and link it to the appropriate database.

Status: In testing (forecast for October 2009)
The Capability Registry capability enables the BIRN community to discover using a central authoritative repository what capabilities the BIRN [...]

The BIRN_ID generator can be used to assign a unique ID to subjects in any type of experiment.

MRI Studio is a Windows-based software package, developed at Johns Hopkins University that includes support for 3D visualization, the processing of diffusion tensor data, and image registration.

The Large Deformation Diffeomorphic Metric Mapping (LDDMM) tool is an application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes.

The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data.

Provides an extensive metadata hierarchy for describing and documenting research and clinical studies.

REM registers N-D image pairs that may contain topological differences.

NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction.

Captures the results from activation maps using the XCEDE schema.

MBAT provides a workflow environment bringing together online resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace.

An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views.

The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.

Provides a visual programming interface that allows researchers to link many independently developed analysis programs into a processing “pipeline.”

The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files.

The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats.

Developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities.

The goal of this software is to provide a 3D correction of image distortions in MRI data due to non-linearity of the magnetic fields from the imaging gradient coils.

Used to verify and measure the scanner stability during a typical fMRI scanning sequence during routine quality assurance scans.

Set of semi-automated tools for reconstruction of the brain’s cortical surface and overlay of functional data onto the reconstructed surface.