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.

Instructions for BIRN users on how to install the Globus client software are here:
https://xwiki.nbirn.org:8443/bin/view/BIRNCC+Software/Command%2Dline+Tools+Documentation

Federated Informatics Research Environment (FIRE) 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. It’s built based on functional and structural neuroimaging, but if you have other data types, you don’t have to start from scratch figuring everything out. These tools are built to generalize to other formats and study designs.

See the FIRE Primer for more information on the suite of tools, both current and coming.

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. It makes grid portals easy to use, but maintains the security and delegation capabilities of GSI. GAMA consists of two components, a backend security service that provides secure management of credentials, and a front-end set of portlets that provide tight integration into web/grid portals.

The BIRN CC operates this tool for the BIRN community; however, BIRN does not package it for community download. This tool is available publicly here: http://code.google.com/p/gamav2/

For questions about the use of GAMA in BIRN, contact Rachana Ananthakrishnan (ranantha at mcs.anl.gov).

MyProxy is an online credential repository and can function as an Online CA. You can store X.509 proxy credentials in the MyProxy repository, protected by a passphrase, for later retrieval over the network. This eliminates the need for manually copying private key and certificate files between machines. In the Online CA mode, MyProxy can issue X.509 certificates to authenticated users and supports custom authentication using PAM module.  MyProxy can also be used for authentication to grid portals and credential renewal with job managers.

The BIRN CC operates this tool for the BIRN community; however, BIRN does not package it for community download. This tool is available publicly here: http://grid.ncsa.uiuc.edu/myproxy/about/

For information about how this tool is used within BIRN, go to https://wiki.birncommunity.org/display/BIRNDOC/Credential+Management

GridFTP is a high-performance, secure, reliable data transfer protocol optimized for high-bandwidth wide-area networks. The GridFTP protocol is based on FTP, the highly-popular Internet file transfer protocol. It includes a set of protocol features and extensions defined already in IETF RFCs as well as a few additional features to meet requirements from current data grid projects.

For information specific to using GridFTP in BIRN, see https://wiki.birncommunity.org/display/BIRNDOC/GridFTP+Guides.

You can also download it as part of the Globus Toolkit here.

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.

Organizing and locating information, both clinical metadata and imaging information, in a distributed data environment can be challenging. Because each site in the collaboratory maintains its own linked data storage, it is very important to develop standards for how and where the images are stored, metadata descriptions of what the images are, and how to find them.

To address these requirements the BIRN has implemented standardized data storage hierarchies on GridFTP servers. The data storage hierarchy was designed to be amenable to automated processing scripts and robust enough to account for differences in storage requirements across BIRN consortia. Not only is the physical organization of files maintained, but so are XML-based descriptors of what the files mean, which aids in data analysis.

The goals of the data upload scripts are:

• getting imaging information into the standardized data storage hierarchies,
• creating XML-based metadata about the data acquisition,
• converting scanner-specific, proprietary data formats into standard “useable” formats, and
• linking data locations within the distributed file system into a site’s human imaging database (HID)

Once the data has been “uploaded” using these scripts, any site in the collaboratory can locate the datasets by querying their local site’s HID database for particular imaging parameters, protocol specifications, or clinical metadata and downloading the images for further analyses. Using this decentralized approach, the BIRN has put the sites in control of their data while still maintaining shareability and access to the information.

Status: New upload scripts working with the HID and GridFTP are scheduled to be available by the end of 2010. The previous versions which worked with the SRB are available here for archival purposes.

The Capability Registry capability enables the BIRN community to discover using a central authoritative repository what capabilities the BIRN community provides. This capability repository includes capability definition information published by capability owners, and capability deployment information published by capability operators.  Users will general use the capability registry thru web sites and other software systems that access the capability registry’s software interfaces.

The BIRN operates this tool for the BIRN community; however, BIRN does not package it for community download.

To access this tool: http://info.nbirn.org/

The BIRN_ID generator can be used to assign a unique ID to subjects in any type of experiment. Subjects in experiments, whether human or animal, are often assigned random numbers as identifiers. When data are being shared and compiled across studies, these numbers must be unique. The BIRN_ID Generator can be used to assign a unique identifying 12-digit number for a subject.

The BIRN_ID Generator package generates unique HIPAA-compliant IDs, a BIRN_ID, from scratch or from already-assigned local IDs.  It is a Java application that runs on any platform.  It uses a cryptographically-strong pseudo-random number generating algorithm, SHA1PRNG, provided by Sun, and a one-way MD5 hash.

The BIRN_ID Generator also can find a BIRN_ID for a given local ID when the link table and local ID are provided.  The one-way hash ensures that the user cannot use a BIRN_ID alone to find a local ID and identify a subject.

The birn-id generator can be checked out with this command:

svn co https://www.nitrc.org/svn/hid/utilities/trunk/utilities/birn-id_gen

BIRN_ID GENERATOR README

Prerequisites

Java JDK (or JRE) 1.3.1 or higher needs to be installed on your system

Installation

• Put the BIRN_ID Generator package in a selected installation directory
• Create a new environment variable, BIRNIDGEN_HOME, pointing to the installation directory

Usage

• To generate BIRNIDs:$BIRNIDGEN_HOME/bin/birnid_gen.sh -create -p <prefix> -l <linkTableFilename> [-cf <clinicalIdsFilename> | -c <clinicalId>]where <linkTableFilename> is a text file to store MD5 one-way hashes of clinicalIDs, <clinicalIdsFilename> is a file that contains a list of clinicalIDs (each line is a clinicalID) and <clinicalId> is a single clinicalID.

• To find the BIRNID from a clinicalID:$BIRNIDGEN_HOME/bin/birnid_gen.sh -find -c <clinicalId> -l <linkTableFilename>where <clinicalId> is a single clinicalID and <linkTableFilename> is a text file to store MD5 one-way hashes of clinicalIDs.

Background Information on the Random Number Generation

SHA1PRNG: The name of the pseudo-random number generation (PRNG) algorithm supplied by the SUN provider. This implementation follows the IEEE P1363 standard, Appendix G.7: “Expansion of source bits”, and uses SHA-1 as the foundation of the PRNG. It computes the SHA-1 hash over a true-random seed value concatenated with a 64-bit counter which is incremented by 1 for each operation. From the 160-bit SHA-1 output, only 64 bits are used.

SHA-1 is the Secure Hash Algorithm, as defined in Secure Hash Standard, NIST FIPS 180-1.

SHA1PRNG is a cryptographically strong pseudo-random number generator (PRNG). A cryptographically strong pseudo-random number minimally complies with the statistical random number generator tests specified in FIPS 140-2, Security Requirements for Cryptographic Modules, section 4.9.1. Additionally, SecureRandom must produce non-deterministic output and therefore it is required that the seed material be unpredictable and that output of SecureRandom be cryptographically strong sequences as described in RFC 1750: Randomness Recommendations for Security.

MRI Studio (https://www.mristudio.org/ ) 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 package supports a number of different image data types from Philips PAR and REC files to DICOM.  MRI Studio can be obtained from the S. Mori group website here. The package is supported through several mailing lists (https://lists.mristudio.org/mailman/listinfo).

To access this tool: https://www.mristudio.org/

The Center for Imaging Science (CIS) at Johns Hopkins University (JHU) has been successful in providing Shape Analysis tools to the BIRN community. These tools are able to compare complex-shaped brain structures and detect differences over the entire surface of the structure. Large-scale shape-analysis processing has been established through the use of Large Deformation Diffeomorphic Metric Mapping (LDDMM, http://cis.jhu.edu/software/lddmm-volume/index.html) and the use of the TeraGrid.

The Large Deformation Diffeomorphic Metric Mapping (LDDMM) tool aims to quantify metric distances on anatomical structures in medical images. This allows for the direct comparison and quantization of morphometric changes due to, for example, disease or aging. As part of these efforts, the Center for Imaging Science at Johns Hopkins University developed techniques to not only compare images, but also to visualize the changes and differences.