BASE - Revision history

Shawndouglas: /* Hardware/software requirements */ Updated

2016-03-14T21:02:24Z

Hardware/software requirements: Updated

← Older revision		Revision as of 21:02, 14 March 2016
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	==Hardware/software requirements==		==Hardware/software requirements==

	The following requirements exist for an installation of BASE version 3.2.4<ref name="BASEInst">{{cite web \|url=http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html \|title=20.2. Installation instructions \|work=BASE 3.2.4 Documentation \|publisher=Lund BASE team \|date=~~14 March 2013~~ \|accessdate=~~22 May 2014~~}}</ref>:		The following requirements exist for an installation of BASE version 3.6 to 3.7.1<ref name="BASEInst">{{cite web \|url=http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html \|title=21.2. Installation instructions \|work=BASE 3.7.1 Documentation \|publisher=Lund BASE team \|date=08 October 2015 \|accessdate=14 March 2016}}</ref>:

	* Java SE 6		* Java SE 8
	* [[Apache Tomcat]] ~~6.0.20~~ or any later 6.x release		* [[Apache Tomcat]] 8 or any later 8.x release
	* [[MySQL]] 5.1 or [[PostgreSQL]] 9.1		* [[MySQL]] 5.5 or [[PostgreSQL]] 9.3

	Note that requirements may be different for earlier or later versions. Consult [http://base.thep.lu.se/chrome/site/latest/html/index.html the documentation] for ~~more~~ installation information.		Note that requirements may be different for earlier or later versions. Consult [http://base.thep.lu.se/chrome/site/latest/html/index.html the documentation] for the latest installation information.

	==Videos, screenshots, and other media==		==Videos, screenshots, and other media==

Shawndouglas: /* Releases */ Updated release history

2016-03-14T20:57:16Z

Releases: Updated release history

← Older revision		Revision as of 20:57, 14 March 2016
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	! Version		! Version
	! Release date		! Release date
			\|- valign="top"
			\| 3.7.1
			\| 07 March 2016
			\|- valign="top"
			\| 3.7.0
			\| 11 January 2016
			\|- valign="top"
			\| 3.6.3
			\| 25 November 2015
			\|- valign="top"
			\| 3.6.2
			\| 12 November 2015
			\|- valign="top"
			\| 3.6.1
			\| 19 October 2015
			\|- valign="top"
			\| 3.6.0
			\| 08 October 2015
			\|- valign="top"
			\| 3.5.3
			\| 17 September 2015
			\|- valign="top"
			\| 3.5.3
			\| 05 May 2015
			\|- valign="top"
			\| 3.5.1
			\| 29 April 2015
			\|- valign="top"
			\| 3.5.0
			\| 21 April 2015
			\|- valign="top"
			\| 3.4.2
			\| 18 March 2015
			\|- valign="top"
			\| 3.4.1
			\| 10 February 2015
			\|- valign="top"
			\| 3.4.0
			\| 14 January 2015
			\|- valign="top"
			\| 3.3.4
			\| 04 December 2014
			\|- valign="top"
			\| 3.3.3
			\| 17 November 2014
			\|- valign="top"
			\|}
			\| STYLE="vertical-align:top; padding-right:10px;"\|
			{\| class="wikitable"
			\|- valign="top"
			! Version
			! Release date
			\|- valign="top"
			\| 3.3.2
			\| 22 October 2014
			\|- valign="top"
			\| 3.3.1
			\| 26 September 2014
	\|- valign="top"		\|- valign="top"
	\| 3.3.0		\| 3.3.0

Shawndouglas: /* Further reading */ Updated ref

2015-12-23T18:51:02Z

Shawndouglas: /* External links */ Removed standalone SF links so as to not encourage downloading from that site.

2015-06-16T18:26:12Z

External links: Removed standalone SF links so as to not encourage downloading from that site.

← Older revision		Revision as of 18:26, 16 June 2015
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	* [http://base.thep.lu.se/browser BASE code repository]		* [http://base.thep.lu.se/browser BASE code repository]
	* [http://sourceforge.net/projects/basedb/ BASE on Sourceforge] (deprecated)
	* [http://sourceforge.net/p/basedb/mailman/ BASE mailing list archives]		* [http://sourceforge.net/p/basedb/mailman/ BASE mailing list archives]

Shawndouglas: /* Releases */ Added item

2014-09-03T19:52:42Z

Releases: Added item

← Older revision		Revision as of 19:52, 3 September 2014
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	! Version		! Version
	! Release date		! Release date
			\|- valign="top"
			\| 3.3.0
			\| 18 August 2014
	\|- valign="top"		\|- valign="top"
	\| 3.2.4		\| 3.2.4
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	\|-		\|-
	\|}		\|}

	==Features==		==Features==

Shawndouglas: Added content.

2014-05-22T23:25:04Z

Added content.

Show changes

Shawndouglas: Added content.

2014-05-22T21:20:04Z

Added content.

← Older revision		Revision as of 21:20, 22 May 2014
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	\| author = Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, and Jari Häkkinen		\| author = Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, and Jari Häkkinen
	\| developer = The Lund BASE team		\| developer = The Lund BASE team
	\| released = {{Start date\|~~2006~~\|08\|31}} (2.0)<ref name="~~BASEStart~~">{{cite web \|url=http://base.thep.lu.se/~~log~~/~~tags~~/2.~~0?rev=6370~~ \|title=~~tags/2.0 @ 6370~~ \|publisher=Lund BASE team \|accessdate=22 May 2014}}</ref>		\| released = {{Start date\|2002\|05\|18}} (1.0)<ref name="BASENewsOld">{{cite web \|url=http://base.thep.lu.se/news_old.phtml \|archiveurl=https://web.archive.org/web/20050412201703/http://base.thep.lu.se/news_old.phtml \|title=BioArray Software Environment - Site news archive \|publisher=Lund BASE team \|date=21 October 2004 \|archivedate=12 April 2005 \|accessdate=22 May 2014}}</ref>
	\| discontinued =		\| discontinued =
	\| frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! -->		\| frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! -->
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	\| website = [http://base.thep.lu.se/ base.thep.lu.se]		\| website = [http://base.thep.lu.se/ base.thep.lu.se]
	}}		}}
	'''BASE''' is a free open-source [[laboratory informatics]] application "designed for laboratories looking for a single point of storage for all information related to their experimentation and for storing, managing, and analysing genomics/transcriptomics data."<ref name="BASEDoc">{{cite web \|url=http://base.thep.lu.se/chrome/site/latest/html/overview.html \|title=Part I. Overview \|work=BASE 3.2.4 Documentation \|publisher=Lund BASE team \|date=14 March 2013 \|accessdate=22 May 2014}}</ref>		'''BASE''' (BioArray Software Environment) is a free open-source [[laboratory informatics]] application "designed for laboratories looking for a single point of storage for all information related to their experimentation and for storing, managing, and analysing genomics/transcriptomics data."<ref name="BASEDoc">{{cite web \|url=http://base.thep.lu.se/chrome/site/latest/html/overview.html \|title=Part I. Overview \|work=BASE 3.2.4 Documentation \|publisher=Lund BASE team \|date=14 March 2013 \|accessdate=22 May 2014}}</ref>

	==Product history==		==Product history==
			Unable to find a unified informatics system "capable of organizing all the information surrounding microarray experimentation and which also integrate[s] this information with tools for the analysis of quantified microarray hybridization data,"<ref name="BASE10Paper">{{cite journal \|url=http://genomebiology.com/2002/3/8/software/0003 \|journal=Genome Biology \|title=BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data \|author=Saal, Lao H.; Troein, Carl; Vallon-Christersson, Johan; Gruvberger, Sofia; Borg, Åke; Peterson, Carsten \|volume=3 \|page=software0003-software0003.6 \|year=2002 \|doi=10.1186/gb-2002-3-8-software0003}}</ref> researchers at Lund University and its associated hospital set out to develop the BioArray Software Environment (BASE) sometime in 2001. After several beta releases in early 2002, the group released version 1.0 of the PHP-based open-source software to the public on May 18, 2002,.<ref name="BASENewsOld" />

			During the 7th International Meeting of the Microarray Gene Expression Data Society on September 8–10, 2004, the development team discussed among other things the transition to BASE 2.0<ref name="BASENewsOld" />, including a change from PHP to Java. "The switch to Java will make the source code structure more transparent and facilitate in-depth understanding of the software by advanced users and developers, thereby increasing accessibility to an even broader community,"<ref name="BASE20Abst">{{cite web \|url=http://www.microarrays.ca/MGED/Abstracts/Hakkinen.pdf \|archiveurl=https://web.archive.org/web/20050313163040/http://www.microarrays.ca/MGED/Abstracts/Hakkinen.pdf \|format=PDF \|title=Update on a Microarray Database and Analysis System: BioArray Software Environment (BASE) \|author=Häkkinen, J.; Nordborg, N.; Saal, L.; Troein, C.; Vallon-Christersson, J. \|date=06 September 2004 \|archivedate=13 March 2005 \|accessdate=22 May 2014}}</ref> stated the group. They anticipated the software would be ready by that fall<ref name="BASE20Abst" />; however, it wasn't until August 31, 2006 that version 2.0 of the software was released.<ref name="BASE20">{{cite web \|url=http://base.thep.lu.se/log/tags/2.0?rev=6370 \|title=tags/2.0 @ 6370 \|publisher=Lund BASE team \|accessdate=22 May 2014}}</ref>

	==Features==		==Features==

	Features of BASE include:		Features of BASE include<ref name="BASEFeats">{{cite web \|url=http://base.thep.lu.se/chrome/site/latest/html/features.html \|title=Chapter 2. BASE features \|work=BASE 3.2.4 Documentation \|publisher=Lund BASE team \|date=14 March 2013 \|accessdate=22 May 2014}}</ref>:

	* multi-user local data repository with a web-based interface		* multi-user local data repository with a web-based interface
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	* annotations for clinical other types of information		* annotations for clinical other types of information
	* hierarchical overview of analysis		* hierarchical overview of analysis
			* data grouping, sharing, and privacy policies
			* integrated file system
	* integrated tools like MultiExperiment Viewer		* integrated tools like MultiExperiment Viewer
			* plugin and extension infrastructure
			* batch upload and download of data
			* support for many array platforms and raw data formats
			* extended support for sequencing applications such as RNAseq

	==Hardware/software requirements==		==Hardware/software requirements==

			The following requirements exist for an installation of BASE version 3.2.4<ref name="BASEInst">{{cite web \|url=http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html \|title=20.2. Installation instructions \|work=BASE 3.2.4 Documentation \|publisher=Lund BASE team \|date=14 March 2013 \|accessdate=22 May 2014}}</ref>:

			* Java SE 6
			* [[Apache Tomcat]] 6.0.20 or any later 6.x release
			* [[MySQL]] 5.1 or [[PostgreSQL]] 9.1

			Note that requirements may be different for earlier or later versions. Consult [http://base.thep.lu.se/chrome/site/latest/html/index.html the documentation] for more installation information.

	==Videos, screenshots, and other media==		==Videos, screenshots, and other media==

			* [http://base.thep.lu.se/wiki/DownloadPage Newer BASE downloads]
			* [http://base.thep.lu.se/wiki/DownloadOld Older BASE downloads]
			* [http://base.thep.lu.se/chrome/site/latest/html/index.html BASE documentation]
			* [http://base2.thep.lu.se/demo/ BASE demo server] (Login and Password = base2)

	==Entities using BASE==		==Entities using BASE==
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	==Further reading==		==Further reading==

	* {{cite journal \|url=http://www.biomedcentral.com/1471-2105/10/330 \|journal=BMC Bioinformatics \|title=BASE - 2nd generation software for microarray data management and analysis \|author=Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari \|~~issue~~=10 \|page=330 \|year=2009 \|doi=10.1186/1471-2105-10-330}}		* {{cite journal \|url=http://genomebiology.com/2002/3/8/software/0003 \|journal=Genome Biology \|title=BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data \|author=Saal, Lao H.; Troein, Carl; Vallon-Christersson, Johan; Gruvberger, Sofia; Borg, Åke; Peterson, Carsten \|volume=3 \|page=software0003-software0003.6 \|year=2002 \|doi=10.1186/gb-2002-3-8-software0003}}

			* {{cite journal \|url=http://www.biomedcentral.com/1471-2105/10/330 \|journal=BMC Bioinformatics \|title=BASE - 2nd generation software for microarray data management and analysis \|author=Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari \|volume=10 \|page=330 \|year=2009 \|doi=10.1186/1471-2105-10-330}}

	==External links==		==External links==

Shawndouglas: Created page with "{{Infobox software | name = BASE | title = BASE | logo = File:BASE_os_logo.png | screenshot =

← Older revision		Revision as of 18:51, 23 December 2015
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	* {{cite journal \|url=http://genomebiology.com/2002/3/8/software/0003 \|journal=Genome Biology \|title=BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data \|author=Saal, Lao H.; Troein, Carl; Vallon-Christersson, Johan; Gruvberger, Sofia; Borg, Åke; Peterson, Carsten \|volume=3 \|page=software0003-software0003.6 \|year=2002 \|doi=10.1186/gb-2002-3-8-software0003}}		* {{cite journal \|url=http://genomebiology.com/2002/3/8/software/0003 \|journal=Genome Biology \|title=BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data \|author=Saal, Lao H.; Troein, Carl; Vallon-Christersson, Johan; Gruvberger, Sofia; Borg, Åke; Peterson, Carsten \|volume=3 \|page=software0003-software0003.6 \|year=2002 \|doi=10.1186/gb-2002-3-8-software0003}}

	* {{cite journal ~~\|url=http://www.biomedcentral.com/1471-2105/10/330 \|journal=BMC Bioinformatics~~ \|title=BASE - 2nd generation software for microarray data management and analysis \|author=Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari \|volume=10 \|page=330 \|year=2009 \|doi=10.1186/1471-2105-10-330}}		* {{cite journal \|title=BASE - 2nd generation software for microarray data management and analysis \|journal=BMC Bioinformatics \|author=Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari \|volume=10 \|page=330 \|year=2009 \|doi=10.1186/1471-2105-10-330 \|pmid=19822003 \|pmc=PMC2768720}}

	==External links==		==External links==