Glossary
| Term | Definition | ||
Annotation |
a virtual "sticky note;" a way to add information or make comments about a data object without it actually becoming part of the object. Annotations are searchable. |
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California Institute for Telecommunications and Information Technology |
a research initiative developed at UCSD and UC Irvine that aims to extend the reach of the Internet throughout the physical world. This NCMIR affiliate conducts research to determine how the Internet can accelerate advances in environmental science, civil infrastructure, intelligent transportation, genomic medicine, new media arts, and educational practices. |
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a web accessible database created to house the types of high-resolution 3D light and electron microscopic reconstructions of cellular structures and protein distributions produced at NCMIR. |
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Center for Research in Biological Systems (CRBS) |
a UCSD-organized research unit that exists to provide human resources, high technology equipment, and administrative services to scientists researching cell structure and function relationships in central nervous system processes, cardiovascular networking, and muscular contraction through multiple scales and modalities. |
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Charge coupled device (CCD) |
captures photos on a grid array that can then be converted to digital images. CCDs can register as little as a single photon event. |
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process in which light transmitted through or reflected from the subject is passed through a series of lenses, to be detected directly by the eye or imaged on a photographic plate; also called optical light microscopy. |
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Collaborative project |
requires significant involvement of NCMIR staff who will expand an already active area of technological research and development to accommodate new research endeavors. |
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Computer-aided 3D image reconstruction |
techniques that use computers to process data. |
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Concurrent Version System (CVS) |
an open-source, network-transparent program that allows developers to keep track of different development versions of source code. |
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Confocal microscopy |
light microscopic technique in which out-of-focus light is removed from an image of a thick specimen through a pinhole aperture. This technique can produce high-resolution images and 3D reconstructions of fluorescently labeled structures and their architecture. |
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provides researchers with a service in the form of a technique, assay, or instrumentation at a lower cost or of higher quality than if a researcher performed the same process individually; offers specialized services not easily duplicated in an individual laboratory; also called service facility. NCMIR is not a core facility. |
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Cyberinfrastructure |
an NSF initiative encompassing distributed instruments, computers, data sources, analytical applications, and communication technologies that, when combined with personnel and integration components, provides a long-term platform to empower the modern scientific research endeavor. |
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Database |
one or more large, structured sets of persistent data associated with software to update, access, reassemble, and query the data. |
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Dendrite |
a slender, branched projection of a nerve cell, or neuron, that conducts the electrical stimulation received from other cells to the body, or soma, of the cell from which it projects. This stimulation arrives through synapses, which are near the tips of the dendrites and away from the soma. |
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small protuberances emanating from the dendrites of certain types of neurons that are the major site of excitatory synapses in the central nervous system; key in mediating synaptic plasticity. |
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Electron energy loss spectroscopy (EELS) |
method in which material is exposed to a beam of electrons with a known kinetic energy; the energy loss experienced is used to understand the nature of the specimen. Some of the electrons will lose energy in the collision process. Their kinetic energy is analyzed and a spectrum is constructed. The spectrum contains information on the vibrational states of the specimen. |
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Electron microscope |
an electron-optical instrument that utilizes a beam of electrons, rather than light, to image a specimen. Due to the smaller wavelength of electrons compared to photons, the resolution of electron microscopy can be several orders of magnitude greater than optical light microscopy. |
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Electron microscopy |
process that utilizes a beam of electrons, rather than light, to focus on cell surfaces of a very thin specimen to produce an enlarged image on a fluorescent screen or photographic plate. Resolution (the ability to distinguish adjacent objects as separate) is better, and magnification is 1,000 times that of an optical light microscope. |
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Electron tomography |
any technique that employs the electron microscope to collect projections of an object to reconstruct the entire object (Frank, Electron Tomography). Computational methods are used to calculate a 3D structure from many 2D images or projections recorded over a wide range of tilt angles. |
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F-actin |
filamentous proteins that are the main constituent of the cells and thin filaments of muscle fibers. |
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a membrane-permeant nonfluorescent biarsenical derivative of fluorescein; becomes fluorescent green upon binding to tetracysteine motifs. NCMIR introduced FlAsH-ReAsH, a novel, pulse-chase labeling approach for studying the life cycle of proteins, including assembly and internalization, by correlated light and electron microscopy. See also ReAsH. Pubmed |
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Global Grid Forum (GGF) |
a community promoting and supporting the development, deployment, and implementation of grid technologies and applications via the creation and documentation of "best practices" (i.e., technical specifications, user experiences, and implementation guidelines). |
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Globus Project |
a project 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. http://www.globus.org/ |
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Grid computing |
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. |
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Home collection |
the default collection where you start when initially logging in or initializing a session. |
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HyperText Markup Language (HTML) |
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. |
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HyperText Transport Protocol (HTTP) |
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. |
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Information Technology (IT) |
a broad subject concerned with all aspects of managing and processing information, but especially with computer hardware and software. |
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Intermediate voltage electron microscopy (IVEM) |
microscopy technique where higher accelerating voltage allows imaging of specimens thicker than those that can be imaged in the conventional electron microscope. |
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Internet2 consortium |
a consortium being led by more than 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. (Abilene is specifically the Internet2 proving ground for high-bandwidth technologies like the 10 gigabit/sec backbone used by the BIRN.) http://www.internet2.edu |
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Internet protocol |
an outdated version of the Internet protocol, created in the 1980s, that is still in use on the Internet to direct packets of information to their correct address. IPv4 uses a 32-bit addressing scheme, represented by four 8-bit (0-255) numbers separated by periods, such as 123.3.12.255. A newer protocol, IPv6 , has been created to meet the demand for more available addresses. |
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Internet
protocol |
replaces IPv4 and increases the Internet address space from 32 to 64 bits. It also adds many improvements to IPv4 in such areas as security, routing, and network autoconfiguration. http://www.ipv6.org/ |
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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. |
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Java Grid Interface (JGI) |
a platform-independent application that serves as a grid wrapper for specific biomedical applications as it brokers communications and information/data transfer between these desktop applications and the BIRN cyberinfrastructure. |
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JViewer |
a general-purpose 3D viewer developed by NCMIR that is exposed in the BIRN portal through Java Web Start. |
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a wavelength that can be sent along a single strand of optical fiber, increasing potential capacity to the point where bandwidth is no longer a bottleneck. See LambdaGrid. |
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grid system running over fiber wiring with lambda. The goal of this new architecture is to enable scientists who are generating terabytes and petabytes of data to interactively visualize, analyze, and correlate their data from multiple storage sites connected to optical networks. |
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Laser scanning |
the process of building up an image by scanning the specimen with a focused laser beam and recording the information detected at each point. Laser scanning microscope systems include CLSM and multiphoton systems. |
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Logical resource |
two or more physical resources that are grouped together and that act as one resource. Writing data to a logical resource means that copies of the data will be made on each of the physical resources in the logical resource. |
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Mesoscale |
dimensional range between 5 nm3 and 50 µ3. This range encompasses macromolecular complexes, organelles, and multi-component structures like synapses. Such structures have traditionally been difficult to study because they fall in the resolution gap between technologies, spanning X-ray crystallography, electron microscopy, and light microscopy |
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Metadata |
the classic definition is "data about data." More precisely, metadata comprises the details of how, 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.) |
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a type of 3D light microscopy that generates very thin optical sections using multi-photon excitation; two or more photons may be used. Link to a detailed description of multi-photon microscopy at Nikon's MicroscopyU Website. |
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National Center for Research Resources (NCRR) |
a component of the NIH. NCRR supports primary research to create and develop critical resources, models, and technologies. NCRR funding also provides biomedical researchers with access to diverse instrumentation, technologies, basic and clinical research facilities, animal models, genetic stocks, biomaterials, and more. |
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National Institutes of Health (NIH) |
the focal point for medical research in the U.S. The goal of NIH research is to acquire new knowledge to help prevent, detect, diagnose, and treat disease and disability. |
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National Partnership for Advanced Computational Infrastructure (NPACI) |
NSF-funded organization that works to advance science by creating a ubiquitous, continuous, and pervasive national computational infrastructure. |
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National Science Foundation (NSF) |
independent agency established by the U.S. government to promote the progress of science through grants, contracts, and fellowships. |
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National Science Foundation Middleware Initiative (NSF-NMI) |
an initiative focused on providing the software infrastructure to share instruments, laboratories, and data, as well as to enable collaboration among research colleagues. |
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NPACKage |
an NMI-enabled collection of software including NWS, VO-Grids, DataCutter, which is being tested, bundled, and released by NPACI to extend the cyberinfrastructure. |
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Ontology |
description of the concepts and relationships that can exist for a subject when constructing databases and other forms of knowledge sharing; the vocabulary with which queries and assertions are exchanged among users. |
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Open Grid Services Architecture (OGSA) |
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. |
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Optical light microscopy |
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OptIPuter |
NCMIR-affiliated project that is developing infrastructure to couple computational resources over parallel optical networks using Internet protocol communication. In the OptIPuter central architecture, optical networking replaces computers. http://www.optiputer.net/ |
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2 to the 50th power (1,125,899,906,842,624) bytes. A petabyte is equal to 1,024 terabytes. |
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the NCRR Biomedical Technology Resource Center Program designed to provide a multidisciplinary technological infrastructure primarily for NIH-funded researchers. http://www.ncrr.nih.gov/biotech/btguide2.pdf |
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actual electronic media that stores data. SRB space is made of many such physical resources of various types including hard disks and tape drives. Although these physical resources are distributed geographically, they perform as a single, sizeable storage repository. |
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Provenance |
when referring to data, indicates its origin and the record of any transformations, changes in custody, or other events of interest. |
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a biarsenical derivative of the red fluorophore resorufin; becomes fluorescent red upon binding to tetracysteine motifs. NCMIR introduced F1AsH-ReAsH, a novel, pulse-chase labeling approach for studying the life cycle of proteins, including assembly and internalization, by correlated light and electron microscopy. See also FlAsH. Pubmed |
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Recharge |
a process by which resource centers recover some costs of providing services. |
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Remote Procedure Call (RPC) |
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. |
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Resolution |
in microscopy, the ability to distinguish adjacent objects as separate. |
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an NSF-funded project that, along with NPACI, creates computational environments for future scientific discovery. |
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Scanning electron microscopy (SEM) |
process in which an image is formed by a beam synchronized with an electron probe scanning the object. The intensity of the image-forming beam is proportional to the scattering or secondary emission of the specimen where the probe strikes it. |
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Secure Sockets Layer (SSL) |
a technology developed originally by Netscape to enable 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. |
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Secure Shell Handling (SSH) |
a protocol for creating a secure connection between two computers. The secure SSH connection provides authentication, encryption, and compression. |
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Service facility |
see core facility. |
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Service project |
involves use of existing NCMIR facilities or technologies but does not require extensive resource staff participation. |
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Single Sign-On (SSO) |
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. |
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Smart Atlas |
a spatial markup and rendering tool that can create a spatial database from a standard brain atlas for data registration and querying. |
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Space |
a collection of physical and logical resources, users, and groups that share information. Determined using domain names and port numbers. |
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Spiny dendrite |
See dendritic spine. |
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an American National Standards Institute (ANSI) standard query language for requesting information from a database. |
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Telescience |
an alpha project of the National Partnership for Advanced Computational Infrastructure (NPACI) that provides remote access to rare, high-energy electron microscopes and powerful information technology resources. Telescience provides through one web interface a suite of tools for end-to-end electron tomography including remote microscopy, bioinformatics, distributed computing, and collaborative visualization. |
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Telescience Portal |
the interface for the Telescience Project; consolidates access for controlling instruments remotely, managing data, and controlling batch jobs with a single login and password. |
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2 to the 40th power (1,099,511,627,776) bytes. This is approximately 1 trillion bytes. |
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Transmission electron microscope (TEM) |
microscope that uses electrons rather than photons to view thin specimens. |
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Unfolding |
in the sense of views that expose data sources and relations, the process by which a complex expression is progressively expanded until it reaches its most simple terms. |
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Unified Medical Language System (UMLS) |
a set of knowledge sources, thesauri, and lexical programs intended to aid biomedical researchers in linking information across disparate sources and systems. |
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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. |
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Voxel |
a volume pixel, which is the smallest distinguishable part of a 3D image. |
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Workflow |
the set of relationships among all the activities in a project, from start to finish; the scheduling of independent jobs on a computer. |
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