Difference between revisions of "User:Shawndouglas/sandbox/sublevel5"

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This page is dedicated to collections and compilations of material originating from this website. As often happens on a wiki, information becomes scattered, and at times it becomes difficult to find content. These compilations of LIMSwiki material have been created to provide more focus to a few selected topics.
{{Infobox journal article
|name        =
|image        =
|alt          = <!-- Alternative text for images -->
|caption      =
|title_full  = Generalized Procedure for Screening Free Software and Open Source Software Applications
|journal      =
|authors      = Joyce, John
|affiliations = Arcana Informatica; Scientific Computing
|contact      = Email:
|editors      =
|pub_year    = 2015
|vol_iss      =
|pages        =
|doi          =
|issn        =
|license      = [https://creativecommons.org/licenses/by-sa/4.0/ Creative Commons Attribution-ShareAlike 4.0 International]
|website      =
|download    =
}}


==The Complete Guide to LIMS & Lab Informatics==
This is the glossary for the article "Generalized Procedure for Screening Free Software and Open Source Software Applications," [[User:Shawndouglas/sandbox/sublevel4|found here]]. Some definitions have been pulled from ''Wikipedia'' in an attempt to keep all description nuances intact.
[[File:CompleteGuideLIMS14.png|120px|left]]
 
'''Title of publication:''' The Complete Guide to LIMS & Lab Informatics<br />
==Glossary==
'''Edition''': 2015
{|
<br />&nbsp;<br />
| STYLE="vertical-align:top;"|
'''Abstract''': The various fields of [[laboratory informatics|laboratory]], [[health informatics|health]], and other scientific informatics are constantly in flux. Discoveries are made, technology changes, and information gathers. This organized collection of LIMSwiki content tries to provide a thorough and modern overview of these various fields of informatics and the software systems that contribute to them, including the [[laboratory information management system]] (LIMS). Also covered  are important standards and compliance issues impacting those systems and the jobs of informaticians. It closes with numerous resources concerning laboratory informatics and the developers/vendors most prominent in the field.
{| class= border="0" cellpadding="5" cellspacing="0" width="100%"
<br />&nbsp;<br />
|-
'''PDF (digital) version''': To be created<br />
  ! Term
'''PediaPress (paper) version''': To be created
  ! Explanation
&nbsp;<br />&nbsp;<br />
|-
'''Contents''':  
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|.ogg
<ul>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|File extension for Ogg Vorbis, an open-source patent-free audio compression format
1. About the Content of This Guide
|-
:<li>[[LIMSwiki mission]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[21 CFR Part 11]]
2. Introduction to Informatics in the Laboratory
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|United States Food and Drug Administration electronic records and electronic signatures rule
:<li>[[Information]]</li>
|-
:<li>[[Informatics (academic field)]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[https://www.academia.edu/ Academia.edu]
:<li>[[Laboratory informatics]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A web site that allows academics to share research papers and exchange information
3. Informatics Across Several Industries
|-
:<li>[[Bioinformatics]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|accuracy
::<li>[[Cancer informatics]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Defines how well the results of an analysis or measurement conforms to the actual or "correct" value
::<li>[[Evolutionary informatics]]</li>
|-
:<li>[[Chemical informatics]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|AEQ
:<li>[[Environmental informatics]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Analytical equipment qualification
:<li>[[Geoinformatics]]</li>
|-
:<li>[[Health informatics]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|agnostic
::<li>[[Imaging informatics]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A term applied to both hardware and software that indicates that the item is interoperable with different systems (The correct term should probably be "technology-independent" or "technology-neutral," but the use of the term "agnostic" appears to be well entrenched.)
::<li>[[Public health informatics]]</li>
|-
4. All about LIMS and LIS
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|AHP
:<li>[[Laboratory information management system]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Analytic hierarchy process (AHP), a structured technique developed by Thomas Saaty in the 1970s for organizing and analyzing complex decisions
:<li>[[LIMS feature]]</li>
|-
:<li>[[Laboratory information system]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|AIQ
:<li>[[LIS feature]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Analytical instrument qualification (AIQ), a term used in the pharmaceutical industry for the process of ensuring that an instrument meets the requirements for its intended application
:<li>[[LIMS and laboratory informatics questionnaire]]</li>
|-
5: More Laboratory Informatics Applications
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Apache Hadoop YARN
:<li>[[Electronic laboratory notebook]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Yet Another Resource Negotiator (YARN), a technology for managing resources on a cluster of computers
:<li>[[Laboratory execution system]]</li>
|-
:<li>[[Scientific data management system]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Apache Lucene
:<li>[[Chromatography data management system]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A software library for information retrieval from fields of text contained within document files
6: Related Standards and Compliance
|-
:<li>[[21 CFR Part 11]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|ASE
:<li>[[21 CFR Part 11/Audit guidelines and checklist]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Adaptive Server Enterprise
:<li>[[40 CFR Part 3]]</li>
|-
:<li>[[Good Automated Laboratory Practices]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[Audit trail]]
:<li>[[Good Automated Manufacturing Practice]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A log of records documenting the sequence of activities that have been performed on a system
:<li>[[Health Insurance Portability and Accountability Act]]</li>
|-
:<li>[[Health Insurance Portability and Accountability Act/Audit guidelines and checklist]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|binary package distribution
:<li>[[Clinical Laboratory Improvement Amendments]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A compilation of the compiled version of a program and all related documentation designed for release to the end user
:<li>[[Health Level 7]]</li>
|-
:<li>[[ISO 9000]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|BREW
:<li>[[ISO/IEC 17025]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Binary Runtime Environment for Wireless (BREW), a runtime and application development environment from Qualcomm that isolates portable applications from the hardware interface of mobile phones employing code division multiplex access (CDMA)
:<li>[[ISO/TS 16949]]</li>
|-
:<li>[[The American Society of Crime Laboratory Directors/Laboratory Accreditation Board]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|BRR
:<li>[[The NELAC Institute]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Business readiness rating
7: Laboratory Informatics Resources
|-
:<li>[[LIMSWiki:LIMSforum and LIMS/LI forum posts]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[Chromatography data management system|CDMS]]
:<li>[[Laboratory, Scientific, and Health Informatics Buyer's Guide]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Chromatography data management system (CDMS)
8: Key Laboratory Informatics Vendors
|-
:<li>[[LabLynx, Inc.]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|CFR
:<li>[[LABVANTAGE Solutions, Inc.]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|United States Code of Federal Regulations
:<li>[[LabWare, Inc.]]</li>
|-
:<li>[[STARLIMS Corporation]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|change log
:<li>[[Thermo Scientific]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A log documenting the changes made to a software product, which may include a list of new features, changes to behavior, or elimination of software bugs
9: Laboratory Informatics Vendor Directory
|-
:<li>[[LIMS vendor]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[Chain of custody|COC]]
:<li>[[LIS vendor]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Chain of custody (COC), a paper or electronic documentation trail that documents responsibility of a sample (This is required for legal reasons under various regulatory programs, and it also provides information used to track faulty or contaminated items back to their source.)
:<li>[[ELN vendor]]</li>
|-
:<li>[[SDMS vendor]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|committer
:<li>[[CDMS vendor]]</li>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|The person that represents the quality control of the community, controlling what changes are included in the originally licensed version, though users are free to make any changes they want in their own copies of the program
:<li>[[:Category:Laboratory informatics software (open source)|Open-source laboratory informatics software]]</li>
|-
</ul>
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[Compiere]]
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A suite of open-source applications (for small- to medium-sized businesses) that provides a number of business support applications
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|copyleft
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|[https://en.wikipedia.org/w/index.php?title=Copyleft&oldid=674443822 Per ''Wikipedia'']:
<blockquote>Copyleft (a play on the word "copyright") is the practice of offering people the right to freely distribute copies and modified versions of a work with the stipulation that the same rights be preserved in derivative works down the line.
 
Copyleft is a form of licensing, and can be used to maintain copyright conditions for works ranging from computer software, to documents, to art. In general, copyright law is used by an author to prohibit recipients from reproducing, adapting, or distributing copies of their work. In contrast, under copyleft, an author may give every person who receives a copy of the work permission to reproduce, adapt, or distribute it, with the accompanying requirement that any resulting copies or adaptations are also bound by the same licensing agreement.
 
Copyleft licenses (for software) require that information necessary for reproducing and modifying the work must be made available to recipients of the binaries. The source code files will usually contain a copy of the license terms and acknowledge the author(s).
 
Copyleft type licenses are a novel use of existing copyright law to ensure a work remains freely available. The GNU General Public License, originally written by Richard Stallman, was the first software copyleft license to see extensive use, and continues to dominate in that area. Creative Commons, a non-profit organization founded by Lawrence Lessig, provides a similar license provision condition called ShareAlike.</blockquote>
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Cosmos
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|C# Open Source Managed Operating System
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|COTS
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Commercial, off-the-shelf
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[40 CFR Part 3|CROMERR]]
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Cross-Media Electronic Reporting Rule (CROMERR) (or typically 40 CFR Part 3), an Environmental Protection Agency (EPA) rule specifying how electronic reporting should be performed for the EPA's various regulatory programs
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Cygwin
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A collection of tools that emulate a Linux environment, allowing Linux applications to be compiled for and executed in a MS Windows environment
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|data loading
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|The loading of data into static tables, including test definitions, sample container descriptions, location information, etc.
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|database-agnostic
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Indicates an application capable of running with database systems from any vendor
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|digital commons
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Name given to a collaboratively developed online resource that is managed by a community of people
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|DMOZ
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Also known as the Open Directory Project (ODP), an attempt to create the largest human curated open-content directory of web links (Originates from one of its earlier domain names, directory.mozilla.org)
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Docker
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A system designed to package an application with all of its dependencies into a standardized software container using an alternate architectural approach than a virtual machine, while providing similar resource isolation in a smaller footprint
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Documentation, Administrator
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Documentation for a system designed to be issued to a system administrator, providing information on configuring and operating the application
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Documentation, Developer
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Documentation for a system designed to be issued to a system developer, providing detailed information on how the system operates and is structured as well as how to alter the system code and extract data from the system in an ''ad hoc'' manner
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Documentation, User
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Documentation for a system designed to be issued to a user, helping to guide the user through using the application
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|DOI
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Digital object identifier (DOI), a character string identifier used to uniquely identify an electronic document (In many instances a scientific/technical publication will have a DOI printed on it, allowing you to access or purchase the article on-line; standardized under ISO 26324.)
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Drizzle
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A MySQL 6.0-derived database optimized for cloud computing
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Drupal
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|An open-source application designed for creating and managing a variety of web sites
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Eclipse
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A Java-based integrated development environment that can be customized via use of community-developed plug-ins
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|EDD
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Electronic data delivery or electronic data deliverable
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[Electronic health record|EHR]]
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Electronic health record
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Elasticsearch
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|An open-source search engine employing a RESTful (see REST) interface, built on Apache Lucene
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[Electronic laboratory notebook|ELN]]
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Electronic laboratory notebook
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[[Electronic medical record|EMR]]
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Electronic medical record
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[http://www.epa.gov/ EPA]
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|United States Environmental Protection Agency
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|ERP
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Enterprise resource planning, typically constituting a variety of integrated applications, with a shared database, that integrates critical business functions such as accounting, human resources, customer relationship management, inventory and order tracking, etc. into a single system
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|F/OSS
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Free/open-source software (See FOSS)
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|FAME
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|Filter, Analyze, Measure, and Evaluate (FAME) methodology for evaluating open-source applications
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|[http://www.fda.gov/ FDA]
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|United States Food and Drug Administration
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Fedora
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|A version of the Linux operating system sponsored by Red Hat
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Firefox
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|One of a number of open-source web browsers that can be highly customized via the use of member-developed "plug-ins"
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|FLOSS
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|[https://en.wikipedia.org/w/index.php?title=Alternative_terms_for_free_software&oldid=679497590 Per ''Wikipedia'']:
<blockquote>The acronym FLOSS was coined in 2001 by Rishab Aiyer Ghosh for "free/libre and open-source software." Later that year, the European Commission (EC) used the phrase when they funded a study on the topic.
 
Unlike "libre software," which aimed to solve the ambiguity problem, FLOSS aimed to avoid taking sides in the debate over whether it was better to say "free software" or to say "open-source software"</blockquote>
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|FLOSShub
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|[http://flosshub.org/node/9 Per FLOSS Research Group]:
<blockquote>FLOSShub is a portal for free/libre and open source software (FLOSS) research resources and discussion. FLOSShub's goal is to provide a central location for connecting researchers and FLOSS community members to research papers, data, tools, and most importantly, community.</blockquote>
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Forge
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|[https://en.wikipedia.org/w/index.php?title=Forge_%28software%29&oldid=674218812 Per ''Wikipedia'']:
<blockquote>In FLOSS development communities, a forge is a web-based collaborative software platform for both developing and sharing computer applications. (The word derives from the metalworking forge, used for shaping metal parts.) A forge platform is generally able to host multiple independent projects.
 
For software developers it is a place to host, among others, source code (often version-controlled), bug database and documentation for their projects. For users, a forge is a repository of computer applications.
 
Software forges have become popular, and have proven successful as a software development model for a large number of software projects.
 
The term forge refers to a common prefix or suffix adopted by various platforms created after the example of SourceForge (such as GForge and FusionForge).</blockquote>
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Forking
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|The process where a group takes an open-source application's source code and starts developing it in an independent direction from the original program
|-
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|FOSS
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|[https://en.wikipedia.org/w/index.php?title=Free_and_open-source_software&oldid=673395320 Per ''Wikipedia'']:
<blockquote>Free and open-source software (FOSS) is computer software that can be classified as both free software and open-source software. That is, anyone is freely licensed to use, copy, study, and change the software in any way, and the source code is openly shared so that people are encouraged to voluntarily improve the design of the software. This is in contrast to proprietary software, where the software is under restrictive copyright and the source code is usually hidden from the users.</blockquote>
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  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px; vertical-align: text-top;"|Free software
  | style="background-color:white; padding-left:10px; padding-right:10px; padding-bottom:10px;"|See Software, Free
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Revision as of 19:12, 9 October 2015

Full article title Generalized Procedure for Screening Free Software and Open Source Software Applications
Author(s) Joyce, John
Author affiliation(s) Arcana Informatica; Scientific Computing
Primary contact Email:
Year published 2015
Distribution license Creative Commons Attribution-ShareAlike 4.0 International

This is the glossary for the article "Generalized Procedure for Screening Free Software and Open Source Software Applications," found here. Some definitions have been pulled from Wikipedia in an attempt to keep all description nuances intact.

Glossary

Term Explanation
.ogg File extension for Ogg Vorbis, an open-source patent-free audio compression format
21 CFR Part 11 United States Food and Drug Administration electronic records and electronic signatures rule
Academia.edu A web site that allows academics to share research papers and exchange information
accuracy Defines how well the results of an analysis or measurement conforms to the actual or "correct" value
AEQ Analytical equipment qualification
agnostic A term applied to both hardware and software that indicates that the item is interoperable with different systems (The correct term should probably be "technology-independent" or "technology-neutral," but the use of the term "agnostic" appears to be well entrenched.)
AHP Analytic hierarchy process (AHP), a structured technique developed by Thomas Saaty in the 1970s for organizing and analyzing complex decisions
AIQ Analytical instrument qualification (AIQ), a term used in the pharmaceutical industry for the process of ensuring that an instrument meets the requirements for its intended application
Apache Hadoop YARN Yet Another Resource Negotiator (YARN), a technology for managing resources on a cluster of computers
Apache Lucene A software library for information retrieval from fields of text contained within document files
ASE Adaptive Server Enterprise
Audit trail A log of records documenting the sequence of activities that have been performed on a system
binary package distribution A compilation of the compiled version of a program and all related documentation designed for release to the end user
BREW Binary Runtime Environment for Wireless (BREW), a runtime and application development environment from Qualcomm that isolates portable applications from the hardware interface of mobile phones employing code division multiplex access (CDMA)
BRR Business readiness rating
CDMS Chromatography data management system (CDMS)
CFR United States Code of Federal Regulations
change log A log documenting the changes made to a software product, which may include a list of new features, changes to behavior, or elimination of software bugs
COC Chain of custody (COC), a paper or electronic documentation trail that documents responsibility of a sample (This is required for legal reasons under various regulatory programs, and it also provides information used to track faulty or contaminated items back to their source.)
committer The person that represents the quality control of the community, controlling what changes are included in the originally licensed version, though users are free to make any changes they want in their own copies of the program
Compiere A suite of open-source applications (for small- to medium-sized businesses) that provides a number of business support applications
copyleft Per Wikipedia:

Copyleft (a play on the word "copyright") is the practice of offering people the right to freely distribute copies and modified versions of a work with the stipulation that the same rights be preserved in derivative works down the line.

Copyleft is a form of licensing, and can be used to maintain copyright conditions for works ranging from computer software, to documents, to art. In general, copyright law is used by an author to prohibit recipients from reproducing, adapting, or distributing copies of their work. In contrast, under copyleft, an author may give every person who receives a copy of the work permission to reproduce, adapt, or distribute it, with the accompanying requirement that any resulting copies or adaptations are also bound by the same licensing agreement.

Copyleft licenses (for software) require that information necessary for reproducing and modifying the work must be made available to recipients of the binaries. The source code files will usually contain a copy of the license terms and acknowledge the author(s).

Copyleft type licenses are a novel use of existing copyright law to ensure a work remains freely available. The GNU General Public License, originally written by Richard Stallman, was the first software copyleft license to see extensive use, and continues to dominate in that area. Creative Commons, a non-profit organization founded by Lawrence Lessig, provides a similar license provision condition called ShareAlike.

Cosmos C# Open Source Managed Operating System
COTS Commercial, off-the-shelf
CROMERR Cross-Media Electronic Reporting Rule (CROMERR) (or typically 40 CFR Part 3), an Environmental Protection Agency (EPA) rule specifying how electronic reporting should be performed for the EPA's various regulatory programs
Cygwin A collection of tools that emulate a Linux environment, allowing Linux applications to be compiled for and executed in a MS Windows environment
data loading The loading of data into static tables, including test definitions, sample container descriptions, location information, etc.
database-agnostic Indicates an application capable of running with database systems from any vendor
digital commons Name given to a collaboratively developed online resource that is managed by a community of people
DMOZ Also known as the Open Directory Project (ODP), an attempt to create the largest human curated open-content directory of web links (Originates from one of its earlier domain names, directory.mozilla.org)
Docker A system designed to package an application with all of its dependencies into a standardized software container using an alternate architectural approach than a virtual machine, while providing similar resource isolation in a smaller footprint
Documentation, Administrator Documentation for a system designed to be issued to a system administrator, providing information on configuring and operating the application
Documentation, Developer Documentation for a system designed to be issued to a system developer, providing detailed information on how the system operates and is structured as well as how to alter the system code and extract data from the system in an ad hoc manner
Documentation, User Documentation for a system designed to be issued to a user, helping to guide the user through using the application
DOI Digital object identifier (DOI), a character string identifier used to uniquely identify an electronic document (In many instances a scientific/technical publication will have a DOI printed on it, allowing you to access or purchase the article on-line; standardized under ISO 26324.)
Drizzle A MySQL 6.0-derived database optimized for cloud computing
Drupal An open-source application designed for creating and managing a variety of web sites
Eclipse A Java-based integrated development environment that can be customized via use of community-developed plug-ins
EDD Electronic data delivery or electronic data deliverable
EHR Electronic health record
Elasticsearch An open-source search engine employing a RESTful (see REST) interface, built on Apache Lucene
ELN Electronic laboratory notebook
EMR Electronic medical record
EPA United States Environmental Protection Agency
ERP Enterprise resource planning, typically constituting a variety of integrated applications, with a shared database, that integrates critical business functions such as accounting, human resources, customer relationship management, inventory and order tracking, etc. into a single system
F/OSS Free/open-source software (See FOSS)
FAME Filter, Analyze, Measure, and Evaluate (FAME) methodology for evaluating open-source applications
FDA United States Food and Drug Administration
Fedora A version of the Linux operating system sponsored by Red Hat
Firefox One of a number of open-source web browsers that can be highly customized via the use of member-developed "plug-ins"
FLOSS Per Wikipedia:

The acronym FLOSS was coined in 2001 by Rishab Aiyer Ghosh for "free/libre and open-source software." Later that year, the European Commission (EC) used the phrase when they funded a study on the topic. Unlike "libre software," which aimed to solve the ambiguity problem, FLOSS aimed to avoid taking sides in the debate over whether it was better to say "free software" or to say "open-source software"

FLOSShub Per FLOSS Research Group:

FLOSShub is a portal for free/libre and open source software (FLOSS) research resources and discussion. FLOSShub's goal is to provide a central location for connecting researchers and FLOSS community members to research papers, data, tools, and most importantly, community.

Forge Per Wikipedia:

In FLOSS development communities, a forge is a web-based collaborative software platform for both developing and sharing computer applications. (The word derives from the metalworking forge, used for shaping metal parts.) A forge platform is generally able to host multiple independent projects.

For software developers it is a place to host, among others, source code (often version-controlled), bug database and documentation for their projects. For users, a forge is a repository of computer applications.

Software forges have become popular, and have proven successful as a software development model for a large number of software projects.

The term forge refers to a common prefix or suffix adopted by various platforms created after the example of SourceForge (such as GForge and FusionForge).

Forking The process where a group takes an open-source application's source code and starts developing it in an independent direction from the original program
FOSS Per Wikipedia:

Free and open-source software (FOSS) is computer software that can be classified as both free software and open-source software. That is, anyone is freely licensed to use, copy, study, and change the software in any way, and the source code is openly shared so that people are encouraged to voluntarily improve the design of the software. This is in contrast to proprietary software, where the software is under restrictive copyright and the source code is usually hidden from the users.

Free software See Software, Free