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Life Sciences IT Infrastructure: hardware & software glossary & taxonomy
Evolving Terminologies for Emerging Technologies
Comments? Questions? Revisions? Mary Chitty
mchitty@healthtech.com
Last revised November 14, 2013

 



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Related glossaries include
Drug discovery & development  Genomics, Proteomics
Informatics Algorithms & data analysis   Bioinformatics   Clinical informatics  Drug discovery informatics  Information management & interpretation 
Technologies: Combinatorial libraries & synthesis   Sequencing 
Biology DNA   Gene definitions  RNA  Protein Structures

agent: Definitions for autonomous agents, intelligent agents, user- agent.  WebRobots FAQ http://www.robotstxt.org/wc/faq.html#agent 

Amazon Web Services AWS: Today's life science organizations must deal with increasingly complex network, storage and computational requirements. Next-generation lab instruments and protocols are changing faster than the underlying research IT infrastructures built to support them. Operating an efficient, scalable and agile research IT infrastructure in the face of such rapid change is a complex challenge we all encounter.

In late 2007 [Chris]  Dagdigian and his BioTeam colleagues realized that, without any managerial mandate, the whole group of consultants was independently experimenting with Amazon Web Services (AWS) to solve a customer problem. The cost of EC2 is ridiculously cheap, with almost infinite ways of controlling it. Bio-IT World Nov 18, 2009
http://www.bio-itworld.com/2009/11/18/c-word.html 

amorphous computing: 
Amorphous computing is inspired by the recent astonishing developments in molecular biology and in microfabrication. Each of these is the basis of a kernel technology that makes it possible to build or grow huge numbers of almost- identical information- processing units, with integral actuators and sensors (e.g. MEMS), at almost no cost. Microelectronic components are so inexpensive that we can imagine mixing them into materials that are produced in bulk, such as paints, gels, and concrete. Such ``smart materials'' will be used in structural elements and in surface coatings, such as skins or paints. Harold Abelson, Thomas F. Knight, Gerald Jay Sussman, and friends, Amorphous Computing Manifesto, MIT, 1996  http://www.swiss.ai.mit.edu/projects/amorphous/white-paper/amorph-new/amorph-new.html   
Amorphous Computing Homepage
, Artificial Intelligence, MIT, US http://groups.csail.mit.edu/mac/projects/amorphous/ 
"Amorphous computing"
Communications of the ACM, May 2000  http://www.swiss.ai.mit.edu/projects/amorphous/cacm-2000.html

autonomic computing: An approach to self-managed computing systems with a minimum of human interference. The term derives from the body's autonomic nervous system, which controls key functions without conscious awareness or involvement. IBM Corp, Autonomic Computing Glossary  http://www.research.ibm.com/autonomic/glossary.html

Beowulf computing: Wikipedia http://en.wikipedia.org/wiki/Beowulf_(computing)   

bikeshed:  Why should I care? [metaphor] http://www.unixguide.net/freebsd/faq/16.19.shtml  Thanks to World Wide Words 

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  

captology: The study of computers as persuasive technologies. This includes the design, research, and analysis of interactive computing products created for the purpose of changing people's attitudes or behaviors.  Key Concepts: Computers as Persuasive Technologies, Stanford Univ. Persuasive Technologies Lab, US  http://captology.stanford.edu/
Captology.org
http://captology.stanford.edu/http://captology.stanford.edu/    

cellular computing: Cell biology   

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This Insight Pharma Reports Market Study was conducted to further explore the usage of Cloud Computing within Biotech and Pharma.  Included in this Industry Market Study is survey data, analysis and industry articles. Cloud Computing Usage in Biotech & Pharma Market Study March 2012  


See also: Amazon Web Services AWS,  utility computing

computational linguistics: Information management & interpretation

computational video:  The study and application of the processing of streamed video data. This field of research is emerging from the convergence of two technologies: digital cameras and high performance computing and high bandwidth networks. In addition, past and current research in machine vision has provided some practical solutions to some of the fundamental processing problems inherent in processing video.  Institute for Information Technology, National Research Council, Canada, Research Programs Computational Video http://iit-iti.nrc-cnrc.gc.ca/templates/itiiit/itiiit2.cfm?CFID=33974&CFTOKEN=93356...  

compute farm: Related terms: compute server farm, ranch, server farm.  

computer virus: Virus Glossary of terms, McAfee,  100 + definitions, http://home.mcafee.com/VirusInfo/Glossary.aspx 

computers: Narrower terms include high performance computers, supercomputers

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

configurable:
Many out-of-the-box solutions claim to be easy to "customize," when in fact they are referring to configuration options, not true customizability.  Manufacturers have distinct challenges, some which can be addressed out of the box, but many of which cannot. Manufacturers also need the ability to capitalize on changing dynamics in the marketplace before their competitors do. That's why it's imperative to understand the differences between configuration and customization and the value of selecting a CRM system that offers the flexibility to adapt and model specific manufacturing business processes.  Why you need to know the difference between Customizable and Configurable CRM, CDC Software podcast, Intelligent Enterprise,  2006  http://www.blogmanno.com/?q=node/33   Configurable gives users the chance to modify options, without expensive programming.

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.  

Common Object Request Broker Architecture, OMG's open, vendor- independent architecture and infrastructure that computer applications use to work together over networks. Using the standard protocol IIOP, a CORBA- based program from any vendor, on almost any computer, operating system, programming language, and network, can interoperate with a CORBA- based program from the same or another vendor, on almost any other computer, operating system, programming language, and network. CORBA FAQ, OMG, 1997- 2002 http://www.omg.org/gettingstarted/corbafaq.htm  Related terms: interoperability, object- oriented     

customizable: Customized implies programming and expense.   Compare configurable

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FLOP: Floating point operations per second. A measure of how fast a computer is based on calculations per second. A floating point is a number representation consisting of a mantissa, an exponent, and an assumed radix. The number represented is M multiplied by R raised to the power of E (M*R^E) where R is the radix or base of the number system. (For example, 10 is the radix of the decimal system.) National Center for Supercomputing Applications, MetaComputer Glossary, Univ. of Illinois, Urbana- Champaign 1995 http://archive.ncsa.uiuc.edu/Cyberia/MetaComp/MetaGlossary.html   Related terms: petaflop, teraflop

geek: http://en.wikipedia.org/wiki/Geek  Compares with nerd but there are many nuances and variations.

Google Custom Search APIs and Tools Glossary  http://code.google.com/apis/customsearch/docs/glossary.html 

grid computing: Wikipedia http://en.wikipedia.org/wiki/Grid_computing  
Narrower term: desktop grids; Related terms:  utility grids, Information management & interpretation semantic grid   

Grid computing glossary, Israel Association of Grid Technologies  http://www.grid.org.il/?CategoryID=365 

Hadoop: The Apache™ Hadoop® project develops open-source software for reliable, scalable, distributed computing.  The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. Hadoop http://hadoop.apache.org/

high performance computing: Weboepedia definition http://www.webopedia.com/TERM/H/High_Performance_Computing.html   High Performance Computing DVD April 27, 2009 •  
Related terms: Distributed Computing Environment DCE, MPP Massively Parallel Processing, petaflop, supercomputers, teraflop  

Human Computer Interface HCI:  http://usableweb.com/authors/perlmangary.html

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legacy systems: Wikipedia http://en.wikipedia.org/wiki/Legacy_systems  

Linux:  A free Unix- type operating system originally created by Linus Torvalds with the assistance of developers around the world. Developed under the GNU General Public License , the source code for Linux is freely available to everyone.   
Wikipedia http://en.wikipedia.org/wiki/Linux 

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.chidb.com/newsarticles/issue12_2.asp 

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

machine-readable: See under metadata 

machine-understandable:  http://www.w3.org/DesignIssues/Semantic.html   See also under metadata  

markup languages:  XML  eXtensible Markup Language; Bioengineering & Biomaterials BIOML Biopolymer Markup Language, MatML Materials Markup Language; Bioinformatics BSML Bioinformatic Sequence Markup Language; Cheminformatics CML Chemical Markup Language; Information management DAML DARPA Agent Markup Language, DAML + OIL; Drug discovery informatics  VRML Virtual Reality Modeling Language; Microarrays GEML Gene Expression Markup Language, MAGE-ML MicroArray and Gene Expression Markup Language, MAML Microarray Markup Language [no longer supported]  

markup languages, standards core: Robin Cover, Core Standards for Markup Languages, 2002  http://xml.coverpages.org/coreStandards.html

metacomputer: A collection of computers held together by state- of- the- art technology and "balanced" so that, to the individual user, it looks and acts like a single computer. The constituent parts of the resulting "metacomputer" could be housed locally, or distributed between buildings, even continents. [MetaComputer HomePage, National Center for Supercomputing Applications, Univ. of Illinois Urbana- Champaign, US] http://archive.ncsa.uiuc.edu/Cyberia/MetaComp/MetaHome.html 
MetaComputer Glossary of Terms
http://archive.ncsa.uiuc.edu/Cyberia/MetaComp/MetaGlossary.html

metadata: Information management & interpretation

middleware:  Wikipedia  http://en.wikipedia.org/wiki/Middleware   Related term: DCE Distributed Computing Environment  

modularity:  Ensures that, for the particular task at hand, the data will be collected and stored in an appropriate manner - which differs greatly from one level of activity (simply gathering the raw data) to another (storing analyzed data) and from one type of high- throughput system to another. ... The best system is one that employs integration at those levels where it is an advantage but maintains enough modularity to ensure that (1) there are no major compromises regarding how any one type of data is handled and, (2) all the key elements in a researcher’s information system can be adjusted or updated independently.   Related terms: integration, interoperability 
Wikipedia http://en.wikipedia.org/wiki/Modularity    

molecular computers: Computers whose input, output and state transitions are carried out by biochemical interactions and reactions. MeSH 2003 
Wikipedia http://en.wikipedia.org/wiki/Molecular_computer   

molecular computing: Ruzena Bajcsy, Assistant Director for Computer and Information Science and Engineering at the National Science Foundation, was lead off witness at a September 12 [2000] House Science Committee Hearing on "Beyond Silicon Computing: Quantum and Molecular Computing" ... is currently supporting a number of researchers who are exploring physical processes can be exploited as computing substrates - chemical, biomolecular, optical computing via photonics, and quantum systems... Chairman Nick Smith pressed the panel for their visions of where this research would take us in 20 or 30 years. Witnesses suggested applications for non- silicon based computing, including cryptography, pharmaceutical development, protein folding, and data storage and mining. Dr. Bajcsy suggested that very small computers would provide portable devises that would enhance and extend of our sensory capabilities - the vision of an eagle, the olfaction of a dog, or the hearing of a rabbit. National Science Foundation, Hearing Summary: House Science Committee's Hearing on "Beyond Silicon Computing: Quantum and Molecular Computing" Sept. 12, 2000 http://www.nsf.gov/od/lpa/congress/106/hs_beyondsilicon.htm  Related terms: DNA computing, quantum computing. Or are any of these the same?  

Moore's Law: Intel co-founder Gordon Moore is a visionary. His prediction, popularly known as Moore's Law, states that the number of transistors on a chip will double about every two years. http://www.intel.com/technology/mooreslaw/   Wikipedia http://en.wikipedia.org/wiki/Moore's_law  Moore's original paper    

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open source: Open source definition annotated http://www.opensource.org/docs/definition.php   
open source software:
  Wikipedia http://en.wikipedia.org/wiki/Open_source_software 
The Cathedral and the bazaar
, Eric Steven Raymond http://catb.org/~esr/writings/cathedral-bazaar/    

open source programming languages: Python, R

peta: 1015 quadrillions. SI unit prefixes beyond peta are exa1018 (quintillions), zetta1021 (sextillions) and yotta1024 (septillions) Compare with prefixes for the smallest numbers: Ultrasensitivity atto, femto, micro, nano, pico, yocto, zepto 

petaflop: A petaflops computer is more powerful than all of the computers on today's Internet combined. If such a system incorporated a petabyte of memory, it could hold all 17 million books in the Library of Congress or several thousand years' worth of videotapes. To fabricate such a system today from the best price/ performance systems available requires up to 10 million processors and consumes more than one billion watts of power. Its cost would be approximately $25 billion dollars, and the supercomputer would fail every couple of minutes. The system would cover the flight decks of all existing Nimitz-class aircraft carriers or fill up most of the Empire State Building with its hardware. T. Sterling "In pursuit of a quadrillion operations per second" Insights, NASA, Apr. 1998  http://www.hq.nasa.gov/hpcc/insights/vol5/petaflop.htm    Related term: teraflop computing. Broader term: FLOP  

Python: Python is a remarkably powerful dynamic programming language that is used in a wide variety of application domains. Python is often compared to Tcl, Perl, Ruby, Scheme or Java. About Python http://www.python.org/about/
Wikipedia http://en.wikipedia.org/wiki/Python_(programming_language)

quantum computing:  The idea of a computational device based on quantum mechanics was first explored in the 1970's and early 1980's by physicists and computer scientists such as Charles H. Bennett of the IBM Thomas J. Watson Research CenterPaul A. Benioff of Argonne National Laboratory in Illinois, David Deutsch of the University of Oxford, and the late Richard P. Feynman of the California Institute of Technology (Caltech).  The idea emerged when scientists were pondering the fundamental limits of computation.  They understood that if technology continued to abide by Moore's Law, then the continually shrinking size of circuitry packed onto silicon chips would eventually reach a point where individual elements would be no larger than a few atoms.  Here a problem arose because at the atomic scale the physical laws that govern the behavior and properties of the circuit are inherently quantum mechanical in nature, not classical.  This then raised the question of whether a new kind of computer could be devised based on the principles of quantum physics.   Feynman was among the first to attempt to provide an answer to this question by producing an abstract model in 1982 that showed how a quantum system could be used to do computations.  He also explained how such a machine would be able to act as a simulator for quantum physics.  In other words, a physicist would have the ability to carry out experiments in quantum physics inside a quantum mechanical computer.   Later, in 1985, Deutsch realized that Feynman's assertion could eventually lead to a general purpose quantum computer and published a crucial theoretical paper showing that any physical process, in principle, could be modeled perfectly by a quantum computer.  Thus, a quantum computer would have capabilities far beyond those of any traditional classical computer.  After Deutsch published this paper, the search began to find interesting applications for such a machine.  Jacob West, The Quantum Computer, An introduction, 2000 http://www.cs.rice.edu/~taha/teaching/05F/210/news/2005_09_16.htm    Related terms: DNA computing, molecular computing, nanocomputer. Or are any of these the same?   

quantum information: http://en.wikipedia.org/wiki/Quantum_information

Our scientists are exploiting such quantum weirdness to build quantum logic gates as a step towards a super-powerful quantum computer. In other work they are inventing ultra-secure crytography systems in which data is coded in the quantum states of individual photons. IBM Almaden, Quantum Information http://www.almaden.ibm.com/st/past_projects/quantum_information/  

R: R is a language and environment for statistical computing and graphics. R Project for Statistical Computing http://www.r-project.org/index.html

robots: See Google definitions for WWW robot http://www.robotstxt.org/wc/faq.html#what other kinds of robots, and spiders, webcrawlers, worm, and ants http://www.robotstxt.org/wc/faq.html#kinds     Web robots http://www.robotstxt.org/wc/robots.html   

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supercomputer: FOLDOC definition http://foldoc.org/supercomputer
Webopedia definition http://www.webopedia.com/TERM/S/supercomputer.html
whatis.com definition http://www.swif.uniba.it/lei/foldop/foldoc.cgi?supercomputer

Very fast computers. Often used for graphics, modeling or simulations. 
Getting up to Speed: The Future of Supercomputing
, National Academies of Science, US, 2004  http://books.nap.edu/catalog/11148.html   
Related terms: high performance computing, petaflop, teraflop; Protein structure Blue gene 

teraFlop (Tflop): The development of massively parallel computers with teraflop speed and the mastering of the associated programming problems will clearly shape new computational solutions for biomedicine in coming years ... in the field of experimental structural biology. Techniques for the experimental determination of biological structure increasingly rely on advanced computational tools. X-ray crystallography, NMR structure determination, and single molecule electron microscopy all continue to make advances in capabilities following increases in computing power. Opportunities in Molecular Biomedicine in the Era of Teraflop Computing, March 3 & 4, 1999, Rockville, MD, NIH Resource for Macromolecular Modeling and Bioinformatics; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign 10 12 floating point operations per second  (trillions).  Related term: petaflop computing. Broader term: FLOP  

utility computing:  {Chris] Dagdigian [of BioTeam]  tries hard not to use the term ‘cloud,’ preferring instead utility computing or simply “The C word.” “Amazon Web Services is the cloud,” said Dagdigian  Bio-IT World Nov 18, 2009 http://www.bio-itworld.com/2009/11/18/c-word.html 

Computing power on demand (similar to electricity). Sun, HP [Hewlett Packard] and IBM have utility computing initiatives.   

Bibliography
ACM Computing Classification System, Association of Computing Machinery, 1998 http://www.acm.org/class/1998/ Valid through 2011 no definitions
Cnet glossary, http://www.cnet.com/Resources/Info/Glossary/index.html
FOLDOC Free On-line Dictionary of Computing, Denis Howe, 2010. 14,400+ terms.  http://foldoc.org/ 
Geek.com Technical Glossary, 1996-2002, 2000+ definitions.    http://www.geek.com/glossary/glossary_search.htm
Howe, Walt, Glossary of Internet Terms,  2002, 360 + terms http://www.walthowe.com/glossary/ 
IBM Terminology Website http://www-01.ibm.com/software/globalization/terminology/index.html
 
Insight Pharma Reports Cloud Computing in Life Sciences R&D 2010  
Jargon File 4.4.7, 2003  http://catb.org/esr/jargon/ 
McAfee Threat Glossary 2003-2011 http://www.mcafee. com/us/threat-center/ resources/threat-glossary.aspxMcAfee Online Security Glossary 2003-2010 http://home.mcafee.com/VirusInfo/Glossary.aspx  
National Center for Supercomputing Applications, MetaComputer Glossary, Univ. of Illinois, Urbana- Champaign 1995] 45 definitions. http://archive.ncsa.uiuc.edu/Cyberia/MetaComp/MetaGlossary.html
W3C Glossaries, http://www.w3.org/2003/glossary/  2003-2010 
Weboepedia, Quinstreet 2011  http://www.webopedia.com/
whatis.com Information Technology encyclopedia.  http://whatis.techtarget.com/
WordSpy, Paul McFedries 1995-2011  http://www.wordspy.com/ 

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How to look for other unfamiliar  terms

 

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