| 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. |
California Institute for Telecommunications and Information Technology
( Cal-(IT)2) |
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. |
Cell
Centered Database ( CCDB) |
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. |
| 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. |
| 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. |
| Classical light microscopy |
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. |
| 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. |
| Computer-aided 3D image reconstruction |
techniques that use computers to process data. |
Concurrent
Version System ( CVS) |
an open-source, network-transparent
program that allows developers to keep
track of different development versions
of source code. |
| 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. |
| Core facility |
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. |
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. |
| Database |
one or more large, structured sets of persistent data associated with software to update, access, reassemble, and query the data. |
| 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. |
| Dendritic
spines |
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.
|
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. |
| 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. |
| 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. |
| 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.
|
F-actin |
filamentous proteins that are the main constituent
of the cells and thin filaments of muscle fibers. |
| FlAsH |
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 |
|
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). |
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/ |
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. |
Home collection |
the default collection
where you start when initially logging
in or initializing a session. |
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. |
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. |
Information
Technology (IT) |
a broad subject concerned
with all aspects of managing and processing
information, but especially with computer
hardware and software. |
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. |
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 |
Internet protocol
version 4 (IPv4) |
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. |
Internet
protocol
version 6 ( IPv6) |
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/ |
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
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. |
JViewer |
a general-purpose 3D
viewer developed by NCMIR that is exposed
in the BIRN portal through Java Web Start. |
|
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. |
| |
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. |
| 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. |
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. |
| 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 |
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.)
|
Multi-photon microscopy |
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. |
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. |
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. |
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. |
National
Science Foundation ( NSF) |
independent agency
established by the U.S. government to
promote the progress of science through
grants, contracts, and fellowships. |
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. |
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. |
| 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. |
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. |
| Optical light microscopy |
see classical light microscopy. |
| 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/ |
|
Petabyte |
2 to the 50th power
(1,125,899,906,842,624) bytes. A petabyte
is equal to 1,024 terabytes. |
|
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 |
|
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. |
Provenance |
when referring to data,
indicates its origin and the record of
any transformations, changes in custody,
or other events of interest. |
| ReAsH |
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 |
| Recharge |
a process by which resource centers recover some costs of providing services. |
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. |
| Resolution |
in microscopy, the ability to distinguish adjacent objects as separate. |
San
Diego Supercomputer Center ( SDSC) |
an NSF-funded project
that, along with NPACI, creates computational
environments for future scientific discovery. |
| 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. |
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. |
| Secure Shell Handling
(SSH) |
a protocol for creating
a secure connection between two computers.
The secure SSH connection provides authentication,
encryption, and compression. |
| Service facility |
see core facility. |
| Service project |
involves use of existing NCMIR facilities or technologies but does not require extensive resource staff participation. |
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. |
Smart Atlas |
a spatial markup and
rendering tool that can create a spatial
database from a standard brain atlas for
data registration and querying. |
Space |
a collection of physical
and logical resources, users, and groups
that share information. Determined using
domain names and port numbers. |
| Spiny dendrite |
See dendritic spine. |
Structured
Query Language (SQL) |
an American National
Standards Institute (ANSI) standard query
language for requesting information from
a database. |
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. |
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. |
| Terabyte |
2 to the 40th power
(1,099,511,627,776) bytes. This is approximately
1 trillion bytes. |
| Transmission electron
microscope (TEM) |
microscope that uses electrons rather than
photons to view thin specimens. |
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. |
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. |
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. |
Voxel |
a volume pixel, which
is the smallest distinguishable part of
a 3D image. |
| Workflow |
the set of relationships among all the activities in a project, from start to finish; the scheduling of independent jobs on a computer. |
