BIRN Glossary

The following terms are useful in understanding many of the basic concepts discussed in this Web site.To ensure consistency and to enable the reader to easily explore related concepts, many of the definitions here were abstracted from their original entries in the Webopedia at Internet.com. The meanings of other terms were extracted from the relevant web pages of their host organizations. All such terms are displayed as hyperlinks in the 'Term' column.

Term	Usage
3D Slicer	A tool produced by Harvard's Brigham and Women's Hospital for surgical planning and guidance that integrates image registration, segmentation, visualization, quantization, and real-time tracking.
AHM	All Hands Meeting is the annual event where BIRN participants gather to share results and plan future research.
API	Application Programming Interface is a set of routines, protocols, and tools that serve as building blocks for interconnecting software applications.
BDR	To further promote a collaborative research environment, the BIRN has undertaken the development of the public BIRN Data Repository (BDR). This sustainable archive accepts data generated by the biomedical research community and makes these data freely available for sharing and exchange, towards fulfillment of NIH guidelines. Not only does the BDR enable the sharing of existing data, the BIRN also envisions the BDR as a mechanism to facilitate active collaborations that will lead to sharing.
BIRN	The Biomedical Informatics Research Network is a test bed for development of hardware, software, and protocols to effectively share and mine data in a site-independent manner for both basic and clinical research. It currently comprises 3 brian imaging research test beds: Mouse, Human Morphometry and Function.
BIRNLex	BIRNLex was created as a controlled terminology for annotation of BIRN data sources. These sources currently include image databases, containing data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer?s disease and schizophrenia, and multiscale imaging of mouse models of human neurological disease using MRI, light and electron microscopic imaging. The BIRNLex provides terms, utilized by BIRN scientists in the context of their research, covering neuroanatomy, molecular species, behavioral and cognitive processes, subject information, experimental practice and design, and associated elements of primary data provenance required for large-scale data integration across disparate experimental studies.
BIRN-CC	The BIRN Coordinating Center supports the BIRN scientific test beds by designing, developing, deploying and maintaining the hardware, federated databases, and scientific applications comprising their distributed cyberinfrastructure.
BIRN rack	A pre-configured set of rack-mounted servers and network equipment that can be rapidly and consistently deployed as a grid point-of-presence for BIRN sites.
BIRN on a Disc	This virtualized version of the BIRN software environment would allow any interested user to download an image of a portion of the BIRN environment and run this environment on their own computer (i.e. via virtualization software such as VMware) without the need to dedicate extra hardware and systems administrator time to see and work with the BIRN infrastructure.
BONFIRE	This data structure is used by the BIRN to integrate bridge terms and relations across disparate ontologies.
BVDG	BIRN Virtual Data Grid is a software “fabric” for seamlessly federating data repositories across the geographically distributed BIRN sites
Cal-IT2	Cal-IT2 focuses its work in the context of telecommunications and information technology as related to the evolving Internet at UCSD.
CCDB	The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging.
Cluster	A computer is a group of loosely coupled computers that work together closely so that in many respects they can be viewed as though they are a single computer.
Condor	A specialized workload management system (developed by Livny et al, University of Wisconsin) supporting high throughput computing on large collections of distributed computing resources. (Condor-G is the Globus-enabled version.)
CVS	Concurrent Version System is an open-source, network-transparent program that allows developers to keep track of different development versions of source code.
Cyberinfrastructure	The term "cyberinfrastructure" describes the new research environments that support advanced data acquisition, data storage, data management, data integration, data mining, data visualization and other computing and information processing services over the Internet. In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.
Data Integration	BIRN employs a 'mediator architecture' to link multiple databases together, each with a unique schema, into an accessible format or data federation. The mediator architecture is flexible, scalable, and powerful. It allows individual researchers to manage their own data in databases tailored to meet their specific needs. Those searching the BIRN system, however, will see the collection of federated databases as if it were a single database.
DES	Data Encryption Standard is a popular symmetric-key encryption method developed in 1975 and standardized by ANSI in 1981 as ANSI X.3.92. Its 56-bit key is considered inadequate and is often applied three times sequentially to generate the equivalent of a 168-bit key - known as 'triple DES' or 3DES.
DICOM	The Digital Imaging and Communications in Medicine (DICOM) standard was created by the National Electrical Manufacturers Association (NEMA) to aid the distribution and viewing of medical images, such as CT scans, MRIs, and ultrasound.
DNS	Domain Name System (or Service or Server) - An Internet service that translates domain names into IP addresses. For example, the domain name www.example.com might translate to 198.105.232.4.
Federation or Federated data system	1. A mechanism for presenting heterogeneous data held at widely distributed sites to appear as a unified and persistent data archive. 2. a group of multiple SRB Servers which coordinate with each other to service client's requests.
FIPS	FBIRN Image Processing Scripts (Based on FSL). FIPS is a package for the comprehensive management of large-scale multi-site fMRI projects, including data storage, retrieval, calibration, analysis, multi-modal integration, and quality control. It provides a flexible, modular set of scripts so that the user can set up their own standardized analysis and run it quickly on many datasets. By default it incorporates the latest FBIRN recommended processing stream.
Function (FIRST) BIRN	The Functional Imaging Research of Schizophrenia Test Bed is studying regional brain dysfunctions related to the progression and treatment of schizophrenia. (Also referred to as Function BIRN)
FMRI	Functional Magnetic Resonance Imaging is the process of using MRI scanners to obtain information about the activity occurring inside the brain by measuring the metabolic consumption of oxygen as expressed by small variations in magnetic flux.
FreeSurfer	A set of semi-automated tools (developed by Fischl et al, Massachusetts General Hospital) for reconstruction of the brain's cortical surface and overlay of functional data onto the reconstructed surface.
FSL	FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.
GAMA	Grid Account Management Architecture. GAMA is a complete GSI credential management and integration solution tailored for use in emerging cyberinfrastructure through web portals or web service-based clients. In a nutshell, GAMA makes grid security as easy to use as any comercial web site while maintaining 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.
Ganglia	A scalable distributed monitoring system for high-performance computing systems such as clusters and Grids.
GCRC	The General Clinical Research Centers are a national network of approximately 78 centers usually located in units within hospitals of academic medical centers. Their primary mission is to provide a reseach infrastucture for clinical investigators who receive their primary support from NIH components as well as other Federal agencies.
GGF	Global Grid Forum is a community promoting and supporting the development, deployment, and implementation of Grid technologies and applications via the creation and documentation of "best practices" - technical specifications, user experiences, and implementation guidelines. Also referred to as the Open Grid Forum.
Globus	The Globus Project is developing fundamental technologies needed to build computational grids and publishing many of them in the Globus Toolkit while working to standardize them with the GGF.
GSI	Grid Security Infrastructure provides secure authentication and communication over an open network through a series of services built on top of X.509 certificates.
Grid	A collection of widely-distributed computers that are loosely coupled as a computing network, as opposed to a tightly-coupled group of computers that are co-located (i.e., a traditional cluster). Grid computing requires the use of software that can divide and farm out pieces of a program to as many as several thousand computers.
GridSphere	The GridSphere portal framework provides an open-source portlet based Web portal. GridSphere enables developers to quickly develop and package third-party portlet web applications that can be run and administered within the GridSphere portlet container.
HID	Human Clinical and Imaging Database. This extensible database management system has been developed and implemented to address the problems associated with managing the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories, and throughout clinical imaging communities at large.
HIPAA	The Health Insurance Portability and Accountability Act of 1996 includes a provision that covered entities must implement standards to protect and guard against the misuse of individually identifiable health information.
Home collection	The default collection where you start when initially logging in or initializing a session.
Help Desk	BIRN provides a Help Desk that is available 7 x 24 where users can report problems or request new services. The Help Desk phone number is 1-866-924-BIRN.
HTML	HyperText Markup Language is the authoring language used to create documents on the World Wide Web. HTML defines the structure and layout of a Web document by using a variety of tags and attributes.
HTTP	HyperText Transport Protocol is the underlying stateless protocol used by the World Wide Web. HTTP defines how messages are formatted and transmitted, and what actions Web servers and browsers should take in response to various commands.
Internet2	Internet2 is a consortium being led by over 200 universities working in partnership with industry and government to develop and deploy advanced network applications and technologies, accelerating the creation of tomorrow's Internet.
Iperf	A tool to measure maximum network bandwidth, to allow the tuning of various parameters and protocol characteristics, and to report bandwidth, delay jitter, and datagram loss.
IPv6	Internet Protocol version 6 replaces IPv4 and increases the Internet address space from 32 to 64 bits. It also adds many improvements to IPv4 in areas such as security, routing, and network autoconfiguration.
IRB	An Institutional Review Board is a specially constituted review body established or designated by an entity to protect the welfare of human subjects recruited to participate in biomedical or behavioral research
iRODS	iRODS™ is a new data grid software system being developed by the SDSC Storage Resource Broker team and collaborators. The management policies (sets of assertions that these communities make about their collections) are being characterized in terms of rules and state information. At the iRODS core, a Rule Engine interprets rules to decide how the system is to respond to various requests and conditions. iRODS is open source under a BSD-type license.
IT	Information Technology is a broad subject concerned with all aspects of managing and processing information, but especially with computer hardware and software.
Java	An object-oriented language similar to C++, but simplified to eliminate language features that caused common programming errors. Java code can run on most computers because Java interpreters and runtime environments, known as Java Virtual Machines (JVMs), exist for most operating systems.
Java Web Start	A technology for simplifying deployment of Java applications by enabling them to be launched with a single click from a Web browser.
JDBC	Java Database Connectivity is an API that enables Java programs to execute SQL statements. The JDBC 2.0 API enables access to virtually any data source, from relational databases to spreadsheets and other flat files.
JViewer	A general-purpose 3D viewer developed by NCMIR that can read and display Microbrightfield's Neurolucida V3 ASCII, XVotrace, and Synu.
Kerberos	A network authentication protocol that is designed to provide strong authentication for client/server applications by using secret-key cryptography. (KX.509 is a mechanism for allowing Kerberos to interoperate with X.509.)
KNOW-ME	Knowledge Map Explorer is a graph-viewing tool that traverses an ontology using a very limited form of recursive queries to request data associated with a specified node or a sub-graph.
LDAP	Lightweight Directory Access Protocol is a set of protocols for accessing information directories (organizations, individuals, devices, etc.). It is the simplified version of the original X.500 standard for implementing directories published by ISO (International Standards Organization).
LDDMM	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) and the use of the TeraGrid.
LONI Pipeline	An application provided by the UCLA Laboratory for Neuro Imaging offering a simple graphical environment for constructing complex scientific analyses of data. It provides a visually intuitive interface to data analysis, while allowing diverse programs to interact seamlessly.
MBAT	The Mouse BIRN Atlasing Toolkit is a JAVA application designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types.
MCAT	Metadata Catalog is a database that operates as an 'index' for the Storage Resource Broker (SRB) by maintaining attribute information (name, location, permissions, etc.) for all files stored in that system.
MCU	The Polycom Multi-point Control Unit enables up to 12 sites to simultaneously connect in a single videoconference.
Metadata	The classic definition is 'data about data.' More precisely, metadata comprises the details of how and when and by whom a particular set of data was collected, and how the data is formatted. (Metadata, when capitalized, is the name of a U.S. corporation and a registered trademark in the United States.)
Morphometry BIRN	BIRN’s Morphometry Test Bed focuses on pooling and analyzing data across neuroimaging sites for potential relationships between anatomical differences and specific memory dysfunctions, such as depression, mild Alzheimer’s disease, and mild cognitive impairment.By acquiring and pooling patient data across sites, scientists are analyzing data from a large group of subjects, in order to investigate what structural brain differences correlate to symptoms of memory dysfunction or depression. This line of research has already uncovered new diagnostic differences and is expected to lead to potential therapies.
Mouse BIRN	The Mouse BIRN Test Bed is helping scientists study neurodegenerative diseases by marshaling multi-modal data from the mouse, as an animal model, to investigate neurological disorders. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder.
MRI	Magnetic resonance imaging (MRI) is primarily used in medical imaging to visualize the structure and function of the body. It provides detailed images of the body in any plane. MR has much greater soft tissue contrast than computed tomography (CT) making it especially useful in neurological, musculoskeletal, cardiovascular, and oncological imaging. Unlike CT it uses no ionizing radiation, but uses a powerful magnetic field to align the magnetization of hydrogen atoms in the body. Radio waves are used to systematically alter the alignment of this magnetization, causing the hydrogen atoms to produce a rotating magnetic field detectable by the scanner. This signal can be manipulated by additional magnetic fields to build up enough information to reconstruct an image of the body.
MyProxy	A credential repository for storing security credentials so that users or services can retrieve a proxy credential whenever and wherever one is needed, without worrying about managing private key and certificate files.
NAS	A Network-Attached Storage device is a server dedicated to file sharing. High-capacity disks are typically directly attached to the server and mounted on the network as a series of volumes. (see SAN)
NCMIR	National Center for Microscopy Research
NCRR	National Center for Research Resources
NDAR	The National Database for Autism Research (NDAR) is a collaborative bioinformatics system being created by the National Institutes of Health (NIH) to support research in autism spectrum disorder (ASD) and help accelerate scientific discovery.
NIDA	National Institute for Drug Abuse
NIF	Neuroscience Information Framework is an effort sponsored by the NIH Neuroscience Blueprint effort and administered by NIDA. This effort aims to catalog electronic and non-electronic neuroscience research resources, and make them searchable by content and usage. A further goal is to enable more uniform access to those resources that are online. This site is intended to assist with developing this catalog by allowing registered users to enter in information on neuroscience resources. These entries are then checked and formalized by curators who are part of the NIF project.
NIH	National Institutes of Health
NMI	The NSF Middleware Initiative is focused on providing the software infrastructure to effectively share instruments, laboratories and data, as well as to enable collaboration among research colleagues.
NOC	Network Operations Center is an automated, fault-tolerant facility for monitoring and managing groups of servers and their interconnecting networks.
NPACI	National Partnership for Advanced Computational Infrastructure
NSF	National Science Foundation
NWS	Network Weather Service is a distributed system that periodically monitors and dynamically forecasts the performance various network and computational resources can deliver over a given time interval.
OASIS	Organization for the Advancement of Structured Information Standards is a not-for-profit, global consortium that drives the development, convergence and adoption of e-business standards.
OGSA	Open Grid Services Architecture is a proposed evolution of the current Globus Toolkit towards a grid system architecture based on an integration of grid and web services concepts and technologies.
OWL	The OWL Web Ontology Language is designed for use by applications that need to process the content of information instead of just presenting information to humans. OWL facilitates greater machine interpretability of Web content than that supported by XML, RDF, and RDF Schema (RDF-S) by providing additional vocabulary along with a formal semantics.
P41	NCRR Biotechnology Resource Grants
PDA	A Personal Digital Assistant is a handheld device that combines computing, telephony, and wireless networking features. They range from as simple as an electronic address book to as complex as a diagnostic tool for database, network and other IT alerts.
Pipeline	A computing pipeline is a set of data processing elements connected in series, so that the output of one element is the input of the next one. The elements of a pipeline are often executed in parallel or in time-sliced fashion; in that case, some amount of buffer storage is often inserted between elements.
PKI	Public Key Infrastructure is a system of digital certificates, Certificate Authorities, and other entities that authenticate the validity of each party involved in a distributed transaction. PKI provides the underpinnings of encryption and many other security mechanisms.
Portal	A web portal is a site that provides a single function via a web page or site. Web portals often function as a point of access to information on the World Wide Web. Portals present information from diverse sources in an unified way.
Portlets	Portlets are pluggable user interface components that are managed and displayed in a web portal. Portlets produce fragments of markup code that are aggregated into a portal page. Typically, following the desktop metaphor, a portal page is displayed as a collection of non-overlapping portlet windows, where each portlet window displays a portlet. Hence a portlet (or collection of portlets) resembles a web-based application that is hosted in a portal.
Provenance	When referring to data, provenance indicates its origin and the record of any transformations, changes in custody or other events of interest.
QoS	Quality of Service is a networking term that specifies a guaranteed throughput level. Often used to imply application availability as well as bandwidth and other qualities (see SLA).
RAID	Redundant Array of Inexpensive Disks is a means of aggregating storage in a fault-tolerant configuration. Common modes include striping (RAID 0), mirroring (RAID 1), and parity striping (RAID 5).
RDBMS	Relational Database Management System is a generic term for the software that manages data as a set of tables that are connected by certain key attributes. Most commercial databases use this design.
Register directory	Like register file, with the addition that the user can associate and query metadata for the directory, its subdirectories, and underlying files, as for any SRB object. The registered directory appears in a list of shadow objects in MySRB.
Registry	The BIRN will maintain a "Federation Registry" which contains a list of sources registered with the mediator. These sources will include both knowledge bases and databases present at the various sites. In some cases the registration process may be automated, in others it may require interaction between the BIRN-CC and the participating site.
RMON	Remote MONitoring is a network management protocol that reports on media access control layer statistics. RMON2 includes nine more classes of information for devices capable of running these agents.
Rocks	A toolkit produced by NPACI designed for integrating, deploying and installing software on remote clusters of computers.
RPC	Remote Procedure Call is a type of protocol that allows a program on one computer to execute a program on a server computer. A client program sends a message to a server with appropriate arguments and the server returns a message containing the results of the program executed.
RPM	Red Hat Package Manager is a powerful command line driven system capable of installing, uninstalling, verifying, querying, and updating computer software packages.
SAML	Security Assertion Markup Language is an XML-based framework for exchanging security information expressed in the form of assertions about subjects, where a subject is an entity (either human or computer) that has an identity in some security domain.
SAN	A Storage Area Network is a high-speed network of shared storage devices. It offers a dynamically configurable, switched architecture for block-level management of the pooled storage. (see NAS)
SDSC	San Diego Supercomputer Center
SLA	Service Level Agreement is a contract between two parties that stipulates QoS levels and a required level of service between the provider and the consumer.
Smart-Atlas	A spatial markup and rendering tool that can create a spatial database from a standard brain atlas for data registration and querying and can be launched from the BIRN portal.
SNMP	Simple Network Management Protocol is set of protocols for managing complex networks using agents and Management Information Bases (MIBs).
SOAP	Simple Object Access Protocol is a standard XML-based protocol for exchanging information in a distributed environment and one of the four key standards that web services are built upon.
SQL	Structured Query Language is an ANSI standard query language for requesting information from a database.
SRB	Storage Resource Broker is a virtualized file management system supported by the San Diego Supercomputer Center for maintaining large collections of widely distributed files.
SSL	Secure Sockets Layer is a technology developed originally by Netscape to enable a browser to establish a secure connection with a web server. Server-side digital certificates are used to encrypt the session. SSL in conjunction with HTTP is often referred to as HTTPS.
SSO	Single Sign-On is an authentication process in a client/server relationship where the user, or client, can enter one name and password and have access to more than one application or resource across an enterprise.
TeraGrid	Using high-performance network connections, the TeraGrid integrates high-performance computers, data resources and tools, and high-end experimental facilities around the country. Currently, TeraGrid resources include more than 750 teraflops of computing capability and more than 30 petabytes of online and archival data storage, with rapid access and retrieval over high-performance networks. Researchers can also access more than 100 discipline-specific databases. With this combination of resources, the TeraGrid is the world's largest, most comprehensive distributed cyberinfrastructure for open scientific research.
UMLS	Unified Medical Language System is a set of knowledge sources, thesauri, and lexical programs intended to aid biomedical researchers in linking information across disparate sources and systems.
Unfolding	In the sense of views that expose data sources and relations, unfolding is the process by which a complex expression is progressively expanded until it reaches its most simple terms.
Views	A particular way of looking at a database that filters the records to make only certain fields visible. They are generally expressed as SQL statements that can be processed by applications or other databases.
UPS	An Uninterruptible Power Supply is power conditioning and storage device that protects servers from spikes and sags in line voltage, as well as providing them with enough reserve power to shut down gracefully in the event of a power outage.
VLAN	Virtual Local Area Network - A software configuration that enables a network of computers to behave as if they are connected to the same wire even though they may actually be physically located on different segments of the local area network.
Voxel	A volume pixel is the smallest distinguishable part of a 3D image.
VPN	Virtual Private Network is a mechanism for using certificates and encryption to create secure channels of communication across an otherwise public network like the Internet.
WAN	A Wide Area Network spans a relatively large geographical area using public and private carriers, such as the telephone system, leased lines, and satellites.
Web Services	A standardized way of integrating Web-based applications using the XML, SOAP, WSDL and UDDI open standards over the Internet. Web services allow different applications from different sources to communicate with each other without time-consuming custom coding.
WSDL	Web Services Description Language is an XML-formatted language used to describe a Web Service's capabilities as collections of communication endpoints with the bindings and protocols needed to exchange messages.
X.509	The most widely used standard for defining digital certificates and an essential technology in deploying PKI systems. (KX.509 is a mechanism for allowing X.509 to interoperate with Kerberos.)
XACML	eXtensible Access Control Markup Language defines a core schema and corresponding namespace for the expression of authorization policies in XML.
XML	eXtensible Markup Language is a pared-down version of the Standardized General Markup Language and is designed especially for Web documents. It allows designers to create their own customized attribute tags, enabling the definition, transmission, validation, and interpretation of data between different applications and organizations.
XNAT	The eXtensible Neuroimaging Archive Toolkit (XNAT) provides a web-based data management for diverse data sets. XML is used within XNAT
Wrapper	Code that acts as an interface between a calling application and the wrapped code. This is often done for compatibility (e.g., the wrapped code is in a different programming language or uses different calling conventions) and usually the wrapped code can only be accessed via its wrapper.