Computers and computing glossary

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Computers & computing glossary
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions? mchitty@healthtech.com
Last revised December 26, 2001
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Related glossaries include Informatics Algorithms & data management, Bioinformatics, Molecular Modeling Biology Protein Structures

ASP: Active Server Pages: A scripting technology for dynamic interactive webpages.

Beowulf computing: A method of ganging lots of Linux- based computers together to tackle heavy- duty calculation jobs. It's sort of a do- it- yourself, low- budget supercomputer that's proven popular at universities and government labs. Now, the broadening appeal of the technique has led companies such as IBM and Compaq Computer to see Beowulf as a possible product to add to the computing lineup. The move parallels the adoption of the Linux operating system in other parts of the corporate world. [Stephen Shankland "Beowulf Computing Method Makes Business Inroads" Cnet News.com Aug. 5, 1999] http://news.cnet.com/news/0,10000,0-1003-200-345757,00.html

biomedical computing (biomedical information science and technology): Includes database design, graphical interfaces, querying approaches, data retrieval, data visualization and manipulation, data integration through the development of integrated analytical tools, synthesis, and tools for electronic collaboration, as well as computational research including the development of structural, functional, integrative, and analytical models and simulations. [Innovations in biomedical information science and technology: SBIR/ STTR Initiative, NIH program announcement, June 29, 2000] http://grants.nih.gov/grants/guide/pa-files/PA-00-118.html

CML Chemical Markup Language: Chemoinformatics glossary

CORBA Common Object Request Broker Architecture: A set of core specifications proposed by the Object Management Group (OMG) CORBA is designed to be object- oriented. [CHI Bioinformatics] Related term object- oriented

OMG's showcase specification for application interoperability, independent of platform, operating system, programming language - even of network and protocol ... integrates Enterprise Java Beans, and a new specification will provide the most robust support in the industry for application interoperability using XML. [OMG Specifications and Process, June 2000] http://sisyphus.omg.org/gettingstarted/overview.htm

computational genomics: Computational methods for gene identification and characterization from DNA sequence data. The course focuses on approaches for extracting the maximum amount of information from protein and DNA sequence similarity through sequence database searches, statistical analysis, and multiple sequence alignment, gene recognition (exon/ intron prediction), identifying signals in unaligned sequences, and integration of genetic and sequence information in biological databases. [William Pearson, Randall Smith instructors; Cold Spring Harbor Laboratory "Computational Genomics" course, October 26 - 31, 2000] http://nucleus.cshl.org/meetings/_archive/2000/2000c-ecg.htm Related terms Molecular Modeling glossary.

compute farm: Network- centric compute farms (also known as server farms or ranches) have emerged as an effective method to boost productivity for design teams. Well designed compute farms provide a scalable computational resource and a seamless engineering environment that enables true twenty four hour, seven day per week global engineering. Compute farms are ideal for design automation disciplines such as Electronic Design Automation (EDA), Mechanical Computer Aided Engineering (MCAE), and Computational Fluid Dynamics (CFD). In all of these areas, engineers need to bring large amounts of power to bear on computationally-intensive problems in order to increase productivity. [Sun Microsystems "Maximizing Productivity: Compute Farms for EDA", 1998] http://www.sun.com/technical-computing/Publications/cfarm.html#1 Related terms compute server farm, ranch, server farm.

computing: Related terms include ASP Active Server Pages, compute farm, DCE Distributed Computing Environment, informatics, MPP Massively Parallel Processing, parallel processing, petaflop, teraflop, server farm, supercomputer. Narrower terms DNA computing, high performance computing, molecular computing, molecular computing, quantum computing

controlled vocabulary: Robin Cover's XML Cover Pages is described as "a collection of references on matters of Subject Classification, Taxonomies, Ontologies, Indexing, Metadata, Metadata Registries, Controlled Vocabularies, Terminology, Thesauri, Business Semantics" [last updated April 21, 2000] http://xml.coverpages.org/classification.html

A limited number of words or phrases used in an indexing system (subject headings) or database, to ensure reliable, consistent retrieval. Long used to enhance retrievability and consistency. Ontologies and/or taxonomies certainly sound sexier than "controlled vocabularies" but continue to have a good deal in common.

Broader term ontology Bioinformatics glossary Related term taxonomies

DAML DARPA Agent Markup Language: The goal of the DAML effort is to develop a language and tools to facilitate the concept of the semantic web. http://www.daml.org/

DNA computing: This research project is aimed at the development and characterization of complex mixtures of DNA molecules attached to surfaces. The attachment chemistry, hybridization chemistry and enzymatic activity of the adsorbed DNA molecules will be characterized by a variety of spectroscopic and biochemical methods, and subsequently optimized for use in (i) the manipulation of DNA sequences in molecular computing strategies and (ii) the high density storage and retrieval of information by DNA hybridization chemistry. [Robert M. Corn, Lloyd M. Smith "DNA Computing and Informatics at Surfaces" Dept. of Chem., Univ. of Wisconsin, US, 2001] http://www.corninfo.chem.wisc.edu/writings/DNAcomputing.html Related terms molecular computing, quantum computing Or are these the same?

deep web: Those parts of the web which are inaccessible to current search engines. A straightforward example is PubMed/ Medline. You won't pick up PubMed abstracts through a search engines, unless your query corresponds with summaries posted on other webpages. And of course you won't be able to access proprietary (fee- based) databases except directly. Until recently PDF documents were inaccessible to search engines, and as far as I know only Google.com indexes them now. Also known as the invisible web. Related term: semantic web

Deep web related links
Complete Planet, US http://www.completeplanet.com/index.asp

Direct Search, Gary Price, George Washington Univ. US http://gwis2.circ.gwu.edu/%7Egprice/direct.htm

Invisible Web: Database contents rarely found in Search Engines, Univ. of California- Berkeley, Spring 2001 http://www.lib.berkeley.edu/TeachingLib/Guides/Internet/InvisibleWeb.html

Directed Acyclic Graph DAG: A directed graph where no path starts and ends at the same vertex.See also directed graph, acyclic graph, cycle.Note: Also called a DAG or acyclic digraph. Also called an oriented acyclic graph. [Paul E. Black, NIST, Dictionary of Algorithms, Data Structures and Problems, 2001] http://hissa.nist.gov/dads/HTML/directAcycGraph.html

The difference between a DAG and a hierarchy is that in the latter each child can only have one parent; a DAG allows a child to have more than one parent. A child term may be an "instance" of its parent term (is a relationship) or a component of its parent term (part- of relationship). A child term may have more than one parent term and may have a different class of relationship with its different parents. [Gene Ontology Consortium, General Documentation" 2001] http://www.geneontology.org/GO.doc.html

disambiguate: Make less ambiguous, clarify, elucidate.

Distributed Computing Environment DEC: From the Open Software Foundation. (The Open Software Foundation is now called the Open Group.) DCE consists of multiple components which have been integrated to work closely together. ... DCE is called "middleware" or "enabling technology." It is not intended to exist alone, but instead should be bundled into a vendor's operating system offering, or integrated in by a third- party vendor. DCE's security and distributed filesystem, for example, can completely replace their current, non-network, analogs. DCE is not an application in itself, but is used to build custom applications or to support purchased applications. [Open Software Foundation Distributed Computing Environment FAQ, Oct. 1998 ] http://www.faqs.org/faqs/dce/faq/

Related terms CORBA, OMG; nanocomputer Miniaturization glossary

Dublin Core Metadata Initiative: An open forum engaged in the development of interoperable online metadata standards that support a broad range of purposes and business models. The original workshop for the Initiative was held in Dublin, Ohio [OCLC] in 1995. Hence the term "Dublin Core" in the name of the Initiative http://dublincore.org/

evolutionary computation: Encompasses methods of simulating EVOLUTION on a computer. The term is relatively new and represents an effort bring together researchers who have been working in closely related fields but following different paradigms. The field is now seen as including research in GENETIC ALGORITHMs, EVOLUTION STRATEGIEs,Evolutionary PROGRAMMING, ARTIFICIAL LIFE, and so forth. For a good overview see the editorial introduction to Vol. 1, No. 1 of "Evolutionary Computation" (MIT Press, 1993). That, along with the papers in the issue, should give you a good idea of representative research [Evolutionary computing glossary, Hitch Hiker's Guide to Evolutionary Computation Issue 8.1, released 29 March 2000] .http://www.cs.bham.ac.uk/Mirrors/ftp.de.uu.net/EC/clife/www/Q99_E.htm

Narrower terms genetic algorithms Algorithms & data management, genetic programming

genetic programming: A type of programming that utilizes the same properties of natural selection found in biological evolution. The general idea behind genetic programming is to start with a collection of functions and randomly combine them into programs; then run the programs and see which gives the best results; keep the best ones (natural selection), mutate some of the others, and test the new generation; repeat this process until a clear best program emerges. LISP is a popular language for genetic programming. [Lycos Tech Glossary] http://webopedia.lycos.com/TERM/G/genetic_programming.html.

granularity: Imposing different quality criteria on models built by homology from representative, experimentally determined [protein] structures [NIGMS Structural Genomics Targets Workshop February 11-12, 1999] http://www.nigms.nih.gov/news/meetings/structural_genomics_targets.html

<jargon, parallel> The size of the units of code under consideration in some context. The term generally refers to the level of detail at which code is considered, e.g. "You can specify the granularity for this profiling tool". The most common computing use is in parallelism where "fine grain parallelism" means individual tasks are relatively small in terms of code size and execution time, "coarse grain" is the opposite. You talk about the "granularity" of the parallelism. The smaller the granularity, the greater the potential for parallelism and hence speed-up but the greater the overheads of synchronisation and communication. [FOLDOC 1997]

The extent to which a system contains separate components (like granules). The more components in a system - or the greater the granularity - the more flexible it is. [ZD Webopedia]

high performance computing: A branch of computer science that concentrates on developing supercomputers and software to run on supercomputers. A main area of this discipline is developing parallel processing algorithms and software programs that can be divided into little pieces so that each piece can be executed simultaneously by separate processors. [ZD Webopedia]

The success of the drug discovery process is now directly related to a company's computation capabilities. Results and research projects that were unimaginable a few years ago are accessible with today's supercomputers. Industry sources expect the IT life- science market to explode to more than $9 billion by 2003. Major IT companies have made significant investments and formed partnerships, with IBM and Compaq each committing $100 million. Data overload from automation and robust database technology means that companies have an immense amount of data on both drug targets and lead compounds. The downside is that these companies are not equipped in infrastructure or organization to take full advantage efficiently of this gold mine.

Related terms include Distributed Computing Environment DCE, petaflop, supercomputers, teraflop.

integration: Bioinformatics glossary

interoperability:The ability of two or more systems or components to exchange information and to use the information that has been exchanged. [Institute of Electrical and Electronics Engineers. IEEE Standard Computer Dictionary: A Compilation of IEEE Standard Computer Glossaries. New York, NY: 1990] http://www.sei.cmu.edu/str/indexes/glossary/interoperability.html

Enabling heterogeneous databases to function in an integrated way, sometimes refers to cross platform functionality and operability across relational, object- oriented, and non- standard types of databases.

Related term ontology

invisible web: See under deep web

Linux clusters:Network multiple processors together to form a unified and more powerful computing system, are becoming a major technology in the bioinformatics industry. ... dozens, if not hundreds of these processors or "nodes" [are used] for the explicit purpose of gene sequencing, proteomic research, or drug discovery and development. [Joshua Harr, Linux NetworX, "Linux clusters - The New Workhorse of Gene Sequencing, Proteomics and Drug Development" Genome Link, Nov. 2001] http://www.chiresource.com/newsarticles/issue12_2.asp

A node within a Linux cluster is the basic unit of processing.

MatML Materials Markup Language: Biomaterials glossary

MPP Massively Parallel Processing: The coordinated processing of a program by multiple processors that work on different parts of the program, using their own operating systems and memory. Typically, MPP processors communicate using some messaging interface. Up to 200 or more processors can work on the same application. An "interconnect" arrangement of data paths allows messages to be sent between processors. Typically, the setup for MPP is more complicated, requiring thought about how to partition a common database among processors and how to assign work among the processors. An MPP system is also known as a "loosely coupled" or "shared nothing" system. MPP systems are considered better than SMP systems for applications that allow a number of databases to be searched in parallel. These include decision support system and data warehouse applications. [whatis.com]

metadata: One of the major issues of the World Wide Web as it exists today is that it is really hard to automate any tasks which one has to perform on the web. So far, the web is mainly built as a forum for human interaction; because most web documents are written for human consumption, the only available form of searching on the web (for example) is to simply match words or sentences contained in documents. Anyone who has used a web search service like AltaVista or HotBot knows that typing in a few keywords and receiving a couple of thousand "hits" is not necessarily very useful. A lot of manual "weeding" of information has to happen after that; it may also happen that the keywords for which you are searching are not prominent in the relevant document itself.

A possible solution for the search problem - and for the general issue of letting automated "agents" roam the web performing useful tasks - is to provide a mechanism which allows a more precise description of things on the web. This, in turn, could elevate the status of the web from machine- readable to something we might call machine- understandable.

Metadata is "data about data" or specifically in our current context "data describing web resources." The distinction between "data" and "metadata" is not an absolute one; it is a distinction created primarily by a particular application ("one application's metadata is another application's data"). [W3C, "Introduction to RDF Metadata" 1997] http://www.w3.org/TR/NOTE-rdf-simple-intro

Information about data that enables intelligent, efficient access and management of data. … metadata is always less than the data. [Robyne M. Sumpter “Whitepaper on Data Management” Lawrence Livermore National Laboratory, February 10, 1994] http://www.llnl.gov/liv_comp/metadata/papers/whitepaper-draft.html

Related terms RDF, semantic web

micro-theories: An ontology about a specific domain, that fits within, and for the most part is consistent with, an ontology with a broader scope. For example, structural biology fits within the larger context of biology. Structural biology will have its own terminology and specific algorithms that apply within the specific domain, but may not be useful or identical to, for example, the genome community. [Lawrence Berkeley Lab "Advanced Computational Structural Genomics" Glossary] http://cbcg.lbl.gov/ssi-csb/Meso.html#anchor597905

middleware: A technology for defining objects and creating interfaces between software systems. [CHI Bioinformatics]

An example of middleware is CORBA. Integrated applications can be built on top of middleware to produce a federated database approach.

Related term DCE Distributed Computing Environment

molecular computing: The core advantage of molecular computing is the potential to pack vastly more circuitry onto a microchip than silicon will ever be capable of—and to do it cheaply. [David Rotman "Molecular Computing" Technology Review May/ June 2000] http://www.technologyreview.com/magazine/may00/rotman.asp

Related terms DNA computing, quantum computing. Or are any of these the same?

Moore's Law: The observation by Gordon Moore, co-founder of Intel, that data density doubles about every 18 months.

natural language processing: <artificial intelligence> (NLP) Computer understanding, analysis, manipulation, and/or generation of natural language. This can refer to anything from fairly simple string- manipulation tasks like stemming, or building concordances of natural language texts, to higher- level AI-like tasks like processing user>queries in natural language. [FOLDOC]

OMG Object Management Group: Distributed object computing industry standards group founded in 1989. The OMG is moving forward in establishing CORBA as the "Middleware that's Everywhere" through its worldwide standard specifications: CORBA/IIOP, Object Services, Internet Facilities and Domain Interface specifications, UML and other specifications supporting Analysis and Design. http://www.omg.org/

Object- oriented modeling OOM: A method for designing software and databases that combines programs and data into self- contained packages called classes, and organizes these classes into a type/ subtype hierarchy. It is an excellent way to design software and databases that have to cope with a lot of picayune detail and many "exceptions to the rule," so long as the basic structure of the problem can be well- represented by a type/ subtype hierarchy, easily distributed, language- independent, and hardware- neutral. [CHI Bioinformatics]

ontology: A classification methodology for formalizing a subject's knowledge or belief system in a structured way (typically for consumption by a computer database). Dictionaries and encyclopedias are examples of ontologies, as are many Web- based entities, such as Yahoo or Excite, and so is the schema for a database. [National Center for Genome Research "Ontologies for Comparing Gene Expression Across Species Dec. 2000] http://www.ncgr.org/genex/ontology.html

The subject of ontology is the study of the categories of things that exist or may exist in some domain. The product of such a study, called an ontology, is a catalog of the types of things that are assumed to exist in a domain of interest D from the perspective of a person who uses a language L for the purpose of talking about D. The types in the ontology represent the predicates, word senses, or concept and relation types of the language L when used to discuss topics in the domain D. [John Sowa, Principles of ontology, Dec 3 1997 ANSI Ad Hoc Group on Ontology Standards mail archive] http://www-ksl.stanford.edu/onto-std/mailarchive/0136.html

Narrower term Gene Ontology^TM GORelated term interoperability

parallel processing: The processing of program instructions by dividing them among multiple processor with the objective of running a program in less time [whatis.com] http://whatis.techtarget.com/definition/0,289893,sid9_gci212747,00.html

pervasive computing: An emerging trend in which computing devices are increasingly ubiquitous, numerous and mobile. [NIST "Pervasive Computing 2001" May 1-2, 2001, Gaithersburg MD] http://www.nist.gov/pc2001/

peta: 10 ¹⁵quadrillions.SI unit prefixes beyond peta are exa 10^{18 (}quintillions), zetta 10²¹(sextillions) and yotta 10²⁴ (septillions) .

petaflop: Computer architects have begun to envision how a petaflop computer might work. A petaflop is a theoretical measure of a computer's speed and can be expressed as: A thousand trillion floating point operations per second; A thousand teraflop; 10 to the 15th power floating point operations per second; 2 to the 50th power FLOPS. Today's fastest parallel computing operations are capable of teraflop speeds. The National Science Foundation, together with NASA and DARPA, has funded eight research projects for envisioning a petaflop computer. A petaflop computer would actually require a massive number of computers working in parallel on the same problem. Applications might include real- time nuclear magnetic resonance imaging during surgery, computer based drug design, astrophysical simulation, the modeling of environmental pollution, and the study of long- term climate changes. [whatis.com]

portal:An entry or starting point on the web, with a mixture of content and services, usually capable of personalization.

precision: Percentage of unrelated material excluded by a specific query or search statement.

Related term Clinical genomics specificity Compare recall

quantum computing: The area of study focused on developing computer technology based on the principles of quantum theory, which explains the nature and behavior of energy and matter on the quantum (atomic and subatomic) level. Development of a quantum computer, if practical, would mark a leap forward in computing capability... with performance gains in the billion fold realm and beyond. The quantum computer, following the laws of quantum physics, would gain enormous processing power through the ability to be in multiple states, and to perform tasks using all possible permutations simultaneously. Current centers of research in quantum computing include MIT, IBM, Oxford University, and the Los Alamos National Laboratory.

The essential elements of quantum computing originated with Paul Benioff, working at Argonne National Labs, in 1981. He theorized a classical computer operating with some quantum mechanical principles. But it is generally accepted David Deutsch of Oxford University provided the critical impetus for quantum computing research. In 1984, he was at a computation theory conference and began to wonder about the possibility of designing a computer that was based exclusively on quantum rules, then published his breakthrough paper a few months later. [whatis.com] Related terms DNA computing, molecular computing, nanocomputer. Or are any of these the same?

qubit: A key concept in the very new field of quantum computing. The aim is to produce a device which is the quantum equivalent of the digital computer. The qubit (pronounced exactly the same was as the Old Testament measurement) is a 'quantum bit', the analogue at quantum dimensions of the ordinary computer's 1 or 0, on or off, heads or tails binary digit or bit. Unlike such digital representations, a qubit remains in an indeterminate state until it is observed, like a tossed coin that is still spinning. It was shown recently that in theory a quantum computer could solve certain mathematical problems, such as factoring large numbers, much faster than conventional ones, and so could be used, for example, in codebreaking. It might even be possible to employ the 'action at a distance' properties of quantum mechanics to transport information instantaneously over great distances without loss. This may all sound like S[cience] F[iction], but the first two- bit quantum logic gates were actually demonstrated at the end of 1995. [World Wide Words, 1996] http://www.quinion.com/words/turnsofphrase/tp-qub1.htm

RDF Resource Description Framework: Integrates a variety of web- based metadata activities including sitemaps, content ratings, stream channel definitions, search engine data collection (web crawling), digital library collections, and distributed authoring, using XML as an interchange syntax. The RDF specifications provide a lightweight ontology system to support the exchange of knowledge on the Web. [W3C, Semantic Web Activity: Resource Description Framework (RDF) Mar. 2001] http://www.w3.org/RDF/

recall: The percentage of applicable material retrieved by a specific query or search statement. Compare precision Related term Clinical genomics sensitivity

relevance: Percentage of truly related material retrieved by a specific query or search statement. Related term: precision Clinical genomics specificity Compare recall

SMP Symmetric MultiProcessing: Multiple processors (two or more) share the same memory and operating system. SMP systems are scalable, as more processors can be added as needed. Related term MMP.

semantic web: The Semantic Web is a vision: the idea of having data on the Web defined and linked in a way that it can be used by machines not just for display purposes, but for automation, integration and reuse of data across various applications. In order to make this vision a reality for the Web, supporting standards, technologies and policies must be designed to enable machines to make more sense of the Web, with the result of making the Web more useful for humans. Facilities and technologies to put machine- understandable data on the Web are rapidly becoming a high priority for many communities. For the Web to scale, programs must be able to share and process data even when these programs have been designed totally independently. The Web can reach its full potential only if it becomes a place where data can be shared and processed by automated tools as well as by people. [W3C, Semantic Web Activity Statement, Apr. 2001] http://www.w3.org/2001/sw/Activity Broader term web.

server farm: A server farm is a group of networked servers that are housed in one location. A server farm streamlines internal processes by distributing the workload between the individual components of the farm and expedites computing processes by harnessing the power of multiple servers. The farms rely on load- balancing software that accomplishes such tasks as tracking demand for processing power from different machines, prioritizing the tasks and scheduling and rescheduling them depending on priority and demand that users put on the network. When one server in the farm fails, another can step in as a backup. [ZD Webopedia] Related term compute farm.

supercomputer: A computer that performs at or near the currently highest operational rate for computers... typically used for scientific and engineering applications that must handle very large databases or do a great amount of computation (or both) .... At the lower end of supercomputing, a new trend, called clustering, suggests more of a build- it- yourself approach to supercomputing. [whatis.com]

Very expensive and employed for specialized applications that require immense amounts of mathematical calculations ... weather forecasting ... animated graphics, fluid dynamic calculations, nuclear energy research, and petroleum exploration. The chief difference between a supercomputer and a mainframe is that a supercomputer channels all its power into executing a few programs as fast as possible, whereas a mainframe uses its power to execute many programs concurrently. [ZD Webopaedia]

Related terms high performance computing, petaflop, teraflop; Blue gene Protein structure glossary

taxonomies: Taxonomy (from Greek taxis meaning arrangement or division and nomos meaning law) is the science of classification according to a pre- determined system, with the resulting catalog used to provide a conceptual framework for discussion, analysis, or information retrieval. In theory, the development of a good taxonomy takes into account the importance of separating elements of a group (taxon) into subgroups (taxa) that are mutually exclusive, unambiguous, and taken together, include all possibilities. In practice, a good taxonomy should be simple, easy to remember, and easy to use.

One of the best known taxonomies is the one devised by the Swedish scientist, Carl Linnaeus, whose classification for biology is still widely used (with modifications). In Web portal design, taxonomies are often created to describe categories and subcategories of topics found on the Web site. The categorization of words on whatis.com is similar to any Web portal taxonomy [whatis.com]

Frustrations with search engine and information retrieval have led to increased interest in specialized taxonomies. A form of controlled vocabulary, hierarchical relationships (broader terms, narrower terms) provide additional suggestions for browsing, as do lateral relationships (related terms) and preferred terms. While there is theoretical interest in natural language processing, a very small percentage of web search engine searching actually uses natural language processing successfully.

However the major aspect distinguishing taxonomies from "controlled vocabularies" is that taxonomies are intended to facilitate the interoperability of machine readable databases, in addition to aiding human computer interfaces.