SeqWare - Revision history

Shawndouglas: Spacing

2022-11-28T20:42:42Z

Spacing

← Older revision		Revision as of 20:42, 28 November 2022
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	* {{cite journal \|journal=BMC Bioinformatics \|year=2010 \|volume=11 \|issue=Suppl. 12 \|pages=S2 \|title=SeqWare Query Engine: storing and searching sequence data in the cloud \|author=O'Connor, Brian D.; Merriman, Barry; Nelson, Stanley F. \|url=http://www.biomedcentral.com/1471-2105/11/S12/S2 \|doi=10.1186/1471-2105-11-S12-S2}}		* {{cite journal \|journal=BMC Bioinformatics \|year=2010 \|volume=11 \|issue=Suppl. 12 \|pages=S2 \|title=SeqWare Query Engine: storing and searching sequence data in the cloud \|author=O'Connor, Brian D.; Merriman, Barry; Nelson, Stanley F. \|url=http://www.biomedcentral.com/1471-2105/11/S12/S2 \|doi=10.1186/1471-2105-11-S12-S2}}
	* {{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}		* {{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}

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

Shawndouglas: /* Further reading */ Spacing

2022-11-28T20:42:25Z

Morgantaschuk: Corrected website links

2022-11-23T22:26:11Z

Corrected website links

Morgantaschuk: Remove Ontario Institute for Cancer Research from current institutions using SeqWare

2022-05-19T14:36:35Z

Remove Ontario Institute for Cancer Research from current institutions using SeqWare

← Older revision		Revision as of 14:36, 19 May 2022
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	Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>		Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>

	As of May 2021, the seqware.io website is dead, and no work has been ~~perfomed~~ on the project for over five years. The project is presumably abandoned.		As of May 2021, the seqware.io website is dead, and no work has been performed on the project for over five years. The project is presumably abandoned.

	The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:		The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:

	{\|		{\|
	\| ~~STYLE~~="vertical-align:top;"\|		\| style="vertical-align:top;" \|
	{\| class="wikitable"		{\| class="wikitable"
	\|- valign="top"		\|- valign="top"
	! Version		!Version
	! Release date		!Release date
	\|- valign="top"		\|- valign="top"
	\| 0.12.1		\|0.12.1
	\| Unknown<ref name="BIGeek">{{cite web \|url=https://boconnor.is-a-geek.com/pmwiki/index.php?n=Main.HomePage?logdate=201206 \|title=BOConnor's Wiki - Research Blog \|publisher=Brian O'Connor \|accessdate=02 October 2012}}</ref>		\|Unknown<ref name="BIGeek">{{cite web \|url=https://boconnor.is-a-geek.com/pmwiki/index.php?n=Main.HomePage?logdate=201206 \|title=BOConnor's Wiki - Research Blog \|publisher=Brian O'Connor \|accessdate=02 October 2012}}</ref>
	\|- valign="top"		\|- valign="top"
	\| 0.12.0		\|0.12.0
	\| Unknown<ref name="BIGeek" />		\|Unknown<ref name="BIGeek" />
	\|- valign="top"		\|- valign="top"
	\| 0.11.4		\|0.11.4
	\| 11 May 2012<ref name="BISFMain" />		\|11 May 2012<ref name="BISFMain" />
	\|- valign="top"		\|- valign="top"
	\| 0.11.2		\|0.11.2
	\| Unknown<ref name="BIDatabase" />		\|Unknown<ref name="BIDatabase" />
	\|- valign="top"		\|- valign="top"
	\| 0.10.2		\|0.10.2
	\| Unknown<ref name="BIDatabase" />		\|Unknown<ref name="BIDatabase" />
	\|- valign="top"		\|- valign="top"
	\| 0.10.1		\|0.10.1
	\| Unknown<ref name="BIDatabase" />		\|Unknown<ref name="BIDatabase" />
	\|- valign="top"		\|- valign="top"
	\| 0.10.0		\|0.10.0
	\| 12 January 2012<ref name="BISFMain" />		\|12 January 2012<ref name="BISFMain" />
	\|- valign="top"		\|- valign="top"
	\| 0.9.1		\|0.9.1
	\| Unknown<ref name="BIDatabase">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_MetaDB#Upgrading_your_Database_Version \|title=Setup SeqWare MetaDB - Upgrading your Database Version \|publisher=SourceForge \|date=10 July 2012 \|accessdate=02 October 2012}}</ref>		\|Unknown<ref name="BIDatabase">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_MetaDB#Upgrading_your_Database_Version \|title=Setup SeqWare MetaDB - Upgrading your Database Version \|publisher=SourceForge \|date=10 July 2012 \|accessdate=02 October 2012}}</ref>
	\|- valign="top"		\|- valign="top"
	\| 0.9.0		\|0.9.0
	\| Unknown<ref name="BIDatabase" />		\|Unknown<ref name="BIDatabase" />
	\|- valign="top"		\|- valign="top"
	\| 0.8.0		\|0.8.0
	\| Unknown<ref name="BIDatabase" />		\|Unknown<ref name="BIDatabase" />
	\|}		\|}
	\| ~~STYLE~~="vertical-align:top; padding-right:10px;"\|		\| style="vertical-align:top; padding-right:10px;" \|
	{\| class="wikitable"		{\| class="wikitable"
	\|- valign="top"		\|- valign="top"
	! Version		!Version
	! Release date		!Release date
	\|- valign="top"		\|- valign="top"
	\| 0.7.0		\|0.7.0
	\| 03 May 2010<ref name="BIMeetNotes1">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=20100426 \|title=SeqWare - 20100426 \|publisher=SourceForge \|date=26 April 2010 \|accessdate=02 October 2012}}</ref>		\|03 May 2010<ref name="BIMeetNotes1">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=20100426 \|title=SeqWare - 20100426 \|publisher=SourceForge \|date=26 April 2010 \|accessdate=02 October 2012}}</ref>
	\|- valign="top"		\|- valign="top"
	\| 0.6.1		\|0.6.1
	\| 24 February 2010<ref name="SWStart" />		\|24 February 2010<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.6.0		\|0.6.0
	\| 19 February 2010<ref name="SWStart" />		\|19 February 2010<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.5.0		\|0.5.0
	\| 18 February 2010<ref name="SWStart" />		\|18 February 2010<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.4.0		\|0.4.0
	\| 14 January 2010<ref name="SWStart" />		\|14 January 2010<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.3.0		\|0.3.0
	\| 11 December 2009 (public)<ref name="SWStart" />		\|11 December 2009 (public)<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.2.0		\|0.2.0
	\| 11 December 2009 (public)<ref name="SWStart" />		\|11 December 2009 (public)<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.1.2		\|0.1.2
	\| 11 December 2009 (public)<ref name="SWStart" />		\|11 December 2009 (public)<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.1.1		\|0.1.1
	\| 11 December 2009 (public)<ref name="SWStart" />		\|11 December 2009 (public)<ref name="SWStart" />
	\|}		\|}
	\|}		\|}
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	Features of SeqWare included<ref name="SWAbout" />:		Features of SeqWare included<ref name="SWAbout" />:

	* a database for storing metadata		*a database for storing metadata
	* sample management		*sample management
	* data analysis and retrieval		*data analysis and retrieval
	* worflow management		*worflow management
	* extensibility		*extensibility
	* query		*query

	==Hardware/software requirements==		==Hardware/software requirements==
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	Requirements for proper installation of SeqWare included:		Requirements for proper installation of SeqWare included:

	* a 64-bit Linux environment		*a 64-bit Linux environment
	* VirtualBox (if willing to run a local VM on Windows or MacOS)		*VirtualBox (if willing to run a local VM on Windows or MacOS)

	More information about installation can be found on [http://seqware.github.com/docs/2-installation/ the GitHub site].		More information about installation can be found on [http://seqware.github.com/docs/2-installation/ the GitHub site].
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	Current users included<ref name="SWPart">{{cite web \|url=http://seqware.github.com/partners/ \|title=SeqWare - Partners \|publisher=Brian O’Connor \|accessdate=02 October 2012}}</ref>:		Current users included<ref name="SWPart">{{cite web \|url=http://seqware.github.com/partners/ \|title=SeqWare - Partners \|publisher=Brian O’Connor \|accessdate=02 October 2012}}</ref>:

	Lineberger Comprehensive Cancer Center, Nimbus Informatics~~, Ontario Institute for Cancer Research~~		Lineberger Comprehensive Cancer Center, Nimbus Informatics

	==Further reading==		==Further reading==
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	==External links==		==External links==

	* [http://code.google.com/p/seqware/ SeqWare on Google Projects] (deprecated)		*[http://code.google.com/p/seqware/ SeqWare on Google Projects] (deprecated)
	* [https://github.com/SeqWare/seqware SeqWare GitHub repository] (current)		*[https://github.com/SeqWare/seqware SeqWare GitHub repository] (current)

	==References==		==References==

Shawndouglas: Abandoned

2021-05-04T17:47:42Z

Abandoned

← Older revision		Revision as of 17:47, 4 May 2021
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	\| developer = [http://seqware.github.com/partners/ SeqWare development team]		\| developer = [http://seqware.github.com/partners/ SeqWare development team]
	\| released = {{Start date\|2009\|12\|11}} (0.3.0)<ref name="SWStart">{{cite web \|url=http://code.google.com/p/seqware/source/browse/trunk/seqware-queryengine/backend/dist/?r=601 \|title=trunk/seqware-queryengine/backend/dist/ - SeqWare \|publisher=Google Project Hosting \|accessdate=02 October 2012}}</ref>		\| released = {{Start date\|2009\|12\|11}} (0.3.0)<ref name="SWStart">{{cite web \|url=http://code.google.com/p/seqware/source/browse/trunk/seqware-queryengine/backend/dist/?r=601 \|title=trunk/seqware-queryengine/backend/dist/ - SeqWare \|publisher=Google Project Hosting \|accessdate=02 October 2012}}</ref>
	\| discontinued =		\| discontinued = Yes
	\| 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! -->
	\| programming language = Java		\| programming language = Java
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	}}		}}

	'''SeqWare''' is a free open-source suite of software tools designed to act as a framework for building analysis workflows using the analysis tools you choose to implement. The software is targeted primarily at entities needing to analyze massive genomics datasets, especially those generated from next-generation sequencing (NGS) platforms.		'''SeqWare''' was a free open-source suite of software tools designed to act as a framework for building analysis workflows using the analysis tools you choose to implement. The software was targeted primarily at entities needing to analyze massive genomics datasets, especially those generated from next-generation sequencing (NGS) platforms.

	==Product history==		==Product history==

	Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>		Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>

			As of May 2021, the seqware.io website is dead, and no work has been perfomed on the project for over five years. The project is presumably abandoned.

	The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:		The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:
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	==Features==		==Features==

	Features of SeqWare ~~include~~<ref name="SWAbout" />:		Features of SeqWare included<ref name="SWAbout" />:

	* a database for storing metadata		* a database for storing metadata
Line 115:		Line 117:
	==Hardware/software requirements==		==Hardware/software requirements==

	Requirements for proper installation of SeqWare ~~include~~:		Requirements for proper installation of SeqWare included:

	* a 64-bit Linux environment		* a 64-bit Linux environment
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	==Videos, screenshots, and other media==		==Videos, screenshots, and other media==

	Screenshots ~~are~~ provided in the [http://seqware.github.com/docs/3-getting-started/user-tutorial/ user tutorial] as well as much of the current [http://seqware.github.com/docs/ documentation].		Screenshots were provided in the [http://seqware.github.com/docs/3-getting-started/user-tutorial/ user tutorial] as well as much of the current [http://seqware.github.com/docs/ documentation].

	==Entities using SeqWare==		==Entities using SeqWare==

	Current users ~~include~~<ref name="SWPart">{{cite web \|url=http://seqware.github.com/partners/ \|title=SeqWare - Partners \|publisher=Brian O’Connor \|accessdate=02 October 2012}}</ref>:		Current users included<ref name="SWPart">{{cite web \|url=http://seqware.github.com/partners/ \|title=SeqWare - Partners \|publisher=Brian O’Connor \|accessdate=02 October 2012}}</ref>:

	Lineberger Comprehensive Cancer Center, Nimbus Informatics, Ontario Institute for Cancer Research		Lineberger Comprehensive Cancer Center, Nimbus Informatics, Ontario Institute for Cancer Research
Line 147:		Line 149:

	<!---Place all category tags here-->		<!---Place all category tags here-->
	[[Category:~~Bioinformatics software (open source)]]~~		[[Category:Discontinued or abandoned software (open source)]]
	~~[[Category:Laboratory informatics~~ software (open source)]]

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

2015-06-15T19:32:21Z

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

← Older revision		Revision as of 19:32, 15 June 2015
Line 140:		Line 140:
	==External links==		==External links==

	* [http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page SeqWare on SourceForge] (deprecated)
	* [http://code.google.com/p/seqware/ SeqWare on Google Projects] (deprecated)		* [http://code.google.com/p/seqware/ SeqWare on Google Projects] (deprecated)
	* [https://github.com/SeqWare/seqware SeqWare GitHub repository] (current)		* [https://github.com/SeqWare/seqware SeqWare GitHub repository] (current)

Shawndouglas: /* Product history */ Fixed version

2014-09-02T19:04:03Z

Product history: Fixed version

← Older revision		Revision as of 19:04, 2 September 2014
Line 28:		Line 28:
	Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>		Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>

	The following table shows the dates of releases up to 0.12.5. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:		The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:

	{\|		{\|

Shawndouglas: /* Product history */ Updated release history info

2014-09-02T19:03:33Z

Product history: Updated release history info

← Older revision		Revision as of 19:03, 2 September 2014
Line 28:		Line 28:
	Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>		Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>

	The following table shows the dates of ~~various~~ releases. Some dates may be approximate:		The following table shows the dates of releases up to 0.12.5. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:

	{\|		{\|
	\| STYLE="vertical-align:top;"\|		\| STYLE="vertical-align:top;"\|
Line 35:		Line 36:
	! Version		! Version
	! Release date		! Release date
	~~\|- valign="top"~~
	~~\| 0.13.6~~
	~~\| 06 December 2012<ref name="BIGitNotes">{{cite web \|url=http://seqware.github.com/release-notes/ \|title=SeqWare - Release Notes \|publisher=GitHub, Inc. \|accessdate=01 February 2013}}</ref>~~
	~~\|- valign="top"~~
	~~\| 0.13.5~~
	~~\| 13 November 2012<ref name="BIGitNotes" />~~
	~~\|- valign="top"~~
	~~\| 0.13.4~~
	~~\| 22 October 2012<ref name="BIGitNotes" />~~
	~~\|- valign="top"~~
	~~\| 0.13.3~~
	~~\| 09 October 2012<ref name="BIGitNotes" />~~
	~~\|- valign="top"~~
	~~\| 0.13.2~~
	~~\| 20 September 2012<ref name="BIGitNotes" />~~
	~~\|- valign="top"~~
	~~\| 0.13.1~~
	~~\| 03 September 2012<ref name="BIGitNotes" />~~
	~~\|- valign="top"~~
	~~\| 0.13.0~~
	~~\| 20 August 2012<ref name="BIGitNotes" />~~
	~~\|- valign="top"~~
	~~\| 0.12.5~~
	~~\| 6 August 2012<ref name="BIGitNotes" />~~
	\|- valign="top"		\|- valign="top"
	\| 0.12.1		\| 0.12.1
Line 77:		Line 54:
	\| 0.10.1		\| 0.10.1
	\| Unknown<ref name="BIDatabase" />		\| Unknown<ref name="BIDatabase" />
	\|}
	~~\| STYLE="vertical-align:top; padding-right:10px;"\|~~
	~~{\| class="wikitable"~~
	~~\|- valign="top"~~
	~~! Version~~
	~~! Release date~~
	\|- valign="top"		\|- valign="top"
	\| 0.10.0		\| 0.10.0
Line 95:		Line 66:
	\| 0.8.0		\| 0.8.0
	\| Unknown<ref name="BIDatabase" />		\| Unknown<ref name="BIDatabase" />
			\|}
			\| STYLE="vertical-align:top; padding-right:10px;"\|
			{\| class="wikitable"
			\|- valign="top"
			! Version
			! Release date
	\|- valign="top"		\|- valign="top"
	\| 0.7.0		\| 0.7.0

Shawndouglas: Grammar

2013-10-03T16:53:37Z

Grammar

← Older revision		Revision as of 16:53, 3 October 2013
Line 26:		Line 26:
	==Product history==		==Product history==

	Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late-2007 or early-2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>		Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>

	The following table shows the dates of various releases. Some dates may be approximate:		The following table shows the dates of various releases. Some dates may be approximate:

Shawndouglas: /* Product history */ Update releases table.

2013-02-01T22:45:15Z

Product history: Update releases table.

← Older revision		Revision as of 22:45, 1 February 2013
Line 29:		Line 29:

	The following table shows the dates of various releases. Some dates may be approximate:		The following table shows the dates of various releases. Some dates may be approximate:
			{\|
			\| STYLE="vertical-align:top;"\|
	{\| class="wikitable"		{\| class="wikitable"
	\|- valign="top"		\|- valign="top"
Line 35:		Line 36:
	! Release date		! Release date
	\|- valign="top"		\|- valign="top"
	\| 0.1.1		\| 0.13.6
	\| 11 December ~~2009 (public)~~<ref name="~~SWStart~~" />		\| 06 December 2012<ref name="BIGitNotes">{{cite web \|url=http://seqware.github.com/release-notes/ \|title=SeqWare - Release Notes \|publisher=GitHub, Inc. \|accessdate=01 February 2013}}</ref>
			\|- valign="top"
			\| 0.13.5
			\| 13 November 2012<ref name="BIGitNotes" />
			\|- valign="top"
			\| 0.13.4
			\| 22 October 2012<ref name="BIGitNotes" />
	\|- valign="top"		\|- valign="top"
	\| 0.1.2		\| 0.13.3
	\| ~~11 December 2009 (public)~~<ref name="~~SWStart~~" />		\| 09 October 2012<ref name="BIGitNotes" />
	\|- valign="top"		\|- valign="top"
	\| 0.2.0		\| 0.13.2
	\| ~~11 December 2009 (public)~~<ref name="~~SWStart~~" />		\| 20 September 2012<ref name="BIGitNotes" />
	\|- valign="top"		\|- valign="top"
	\| 0.3.0		\| 0.13.1
	\| ~~11 December 2009 (public)~~<ref name="~~SWStart~~" />		\| 03 September 2012<ref name="BIGitNotes" />
	\|- valign="top"		\|- valign="top"
	\| 0.4.0		\| 0.13.0
	\| ~~14 January 2010~~<ref name="~~SWStart~~" />		\| 20 August 2012<ref name="BIGitNotes" />
	\|- valign="top"		\|- valign="top"
	\| 0.5.0		\| 0.12.5
	\| ~~18 February 2010~~<ref name="~~SWStart~~" />		\| 6 August 2012<ref name="BIGitNotes" />
	\|- valign="top"		\|- valign="top"
	\| 0.6.0		\| 0.12.1
	\| ~~19 February 2010~~<ref name="~~SWStart~~" />		\| Unknown<ref name="BIGeek">{{cite web \|url=https://boconnor.is-a-geek.com/pmwiki/index.php?n=Main.HomePage?logdate=201206 \|title=BOConnor's Wiki - Research Blog \|publisher=Brian O'Connor \|accessdate=02 October 2012}}</ref>
	\|- valign="top"		\|- valign="top"
	\| 0.6.1		\| 0.12.0
	\| ~~24 February 2010~~<ref name="~~SWStart~~" />		\| Unknown<ref name="BIGeek" />
	\|- valign="top"		\|- valign="top"
	\| 0.7.0		\| 0.11.4
	\| 03 May ~~2010~~<ref name="~~BIMeetNotes1~~"~~>{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware~~/~~index.php?title=20100426 \|title=SeqWare - 20100426 \|publisher=SourceForge \|date=26 April 2010 \|accessdate=02 October 2012}}</ref~~>		\| 11 May 2012<ref name="BISFMain" />
	\|- valign="top"		\|- valign="top"
	\| 0.8.0		\| 0.11.2
	\| Unknown<ref name="BIDatabase"~~>{{cite web \|url=http://sourceforge.net~~/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_MetaDB#Upgrading_your_Database_Version \|title=Setup SeqWare MetaDB - Upgrading your Database Version \|publisher=SourceForge \|date=10 July 2012 \|accessdate=02 October 2012}}</ref>		\| Unknown<ref name="BIDatabase" />
	\|- valign="top"		\|- valign="top"
	\| 0.9.0		\| 0.10.2
	\| Unknown<ref name="BIDatabase" />		\| Unknown<ref name="BIDatabase" />
	\|- valign="top"		\|- valign="top"
	\| 0.9.1		\| 0.10.1
	\| Unknown<ref name="BIDatabase" />		\| Unknown<ref name="BIDatabase" />
			\|}
			\| STYLE="vertical-align:top; padding-right:10px;"\|
			{\| class="wikitable"
			\|- valign="top"
			! Version
			! Release date
	\|- valign="top"		\|- valign="top"
	\| 0.10.0		\| 0.10.0
	\| 12 January 2012<ref name="BISFMain" />		\| 12 January 2012<ref name="BISFMain" />
	\|- valign="top"		\|- valign="top"
	\| 0.10.1		\| 0.9.1
			\| Unknown<ref name="BIDatabase">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_MetaDB#Upgrading_your_Database_Version \|title=Setup SeqWare MetaDB - Upgrading your Database Version \|publisher=SourceForge \|date=10 July 2012 \|accessdate=02 October 2012}}</ref>
			\|- valign="top"
			\| 0.9.0
	\| Unknown<ref name="BIDatabase" />		\| Unknown<ref name="BIDatabase" />
	\|- valign="top"		\|- valign="top"
	\| 0.10.2		\| 0.8.0
	\| Unknown<ref name="BIDatabase" />		\| Unknown<ref name="BIDatabase" />
	\|- valign="top"		\|- valign="top"
	\| 0.11.2		\| 0.7.0
	\| ~~Unknown~~<ref name="~~BIDatabase~~" />		\| 03 May 2010<ref name="BIMeetNotes1">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=20100426 \|title=SeqWare - 20100426 \|publisher=SourceForge \|date=26 April 2010 \|accessdate=02 October 2012}}</ref>
			\|- valign="top"
			\| 0.6.1
			\| 24 February 2010<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.11.4		\| 0.6.0
	\| ~~11 May 2012~~<ref name="~~BISFMain~~" />		\| 19 February 2010<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.12.0		\| 0.5.0
	\| ~~Unknown~~<ref name="~~BIGeek~~"~~>{{cite web \|url=https://boconnor.is-a-geek.com/pmwiki/index.php?n=Main.HomePage?logdate=201206 \|title=BOConnor's Wiki - Research Blog \|publisher=Brian O'Connor \|accessdate=02 October 2012}}<~~/~~ref~~>		\| 18 February 2010<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.12.1		\| 0.4.0
	\| ~~Unknown~~<ref name="~~BIGeek~~" />		\| 14 January 2010<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.12.5		\| 0.3.0
	\| ~~6 August 2012~~<ref name="~~BIGitNotes~~"~~>{{cite web \|url=http:~~/~~/seqware.github.com/release-notes/ \|title=SeqWare - Release Notes \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref~~>		\| 11 December 2009 (public)<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.13.0		\| 0.2.0
	\| ~~20 August 2012~~<ref name="~~BIGitNotes~~" />		\| 11 December 2009 (public)<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
	\| 0.13.1		\| 0.1.2
	\| ~~03 September 2012~~<ref name="~~BIGitNotes~~" />		\| 11 December 2009 (public)<ref name="SWStart" />
	\|- valign="top"		\|- valign="top"
			\| 0.1.1
			\| 11 December 2009 (public)<ref name="SWStart" />
			\|}
	\|}		\|}

← Older revision		Revision as of 20:42, 28 November 2022
Line 135:		Line 135:

	==Further reading==		==Further reading==

	* {{cite journal \|journal=BMC Bioinformatics \|year=2010 \|volume=11 \|issue=Suppl. 12 \|pages=S2 \|title=SeqWare Query Engine: storing and searching sequence data in the cloud \|author=O'Connor, Brian D.; Merriman, Barry; Nelson, Stanley F. \|url=http://www.biomedcentral.com/1471-2105/11/S12/S2 \|doi=10.1186/1471-2105-11-S12-S2}}		* {{cite journal \|journal=BMC Bioinformatics \|year=2010 \|volume=11 \|issue=Suppl. 12 \|pages=S2 \|title=SeqWare Query Engine: storing and searching sequence data in the cloud \|author=O'Connor, Brian D.; Merriman, Barry; Nelson, Stanley F. \|url=http://www.biomedcentral.com/1471-2105/11/S12/S2 \|doi=10.1186/1471-2105-11-S12-S2}}

	* {{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}		* {{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}

← Older revision		Revision as of 22:26, 23 November 2022
Line 19:		Line 19:
	\| genre = [[Laboratory informatics]] software		\| genre = [[Laboratory informatics]] software
	\| license = GNU General Public License v3		\| license = GNU General Public License v3
	\| website = [http://seqware.github.~~com~~/ seqware.github.~~com~~]		\| website = [http://seqware.github.io/ seqware.github.io]
	}}		}}

Line 28:		Line 28:
	Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>		Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web \|url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf \|format=PDF \|title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production \|author=Marx, Vivien \|publisher=BioInform - Genomeweb LLC \|date=5 February 2010 \|accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web \|url=http://seqware.github.com/about/ \|title=SeqWare - About \|publisher=GitHub, Inc. \|accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web \|url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page \|title=SeqWare - Main Page \|publisher=SourceForge \|date=24 September 2012 \|accessdate=02 October 2012}}</ref>

	As of May 2021, ~~the seqware.io website is dead, and~~ no work has been performed on the project for over five years. The project is presumably abandoned.		As of May 2021, no work has been performed on the project for over five years. The project is presumably abandoned.

	The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:		The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:
Line 122:		Line 122:
	*VirtualBox (if willing to run a local VM on Windows or MacOS)		*VirtualBox (if willing to run a local VM on Windows or MacOS)

	More information about installation can be found on [~~http~~://seqware.github.~~com~~/docs/2-installation/ the GitHub site].		More information about installation can be found on [https://seqware.github.io/docs/2-installation/ the GitHub site].

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

	Screenshots were provided in the [http://seqware.github.~~com~~/docs/3-getting-started/user-tutorial/ user tutorial] as well as much of the current [http://seqware.github.~~com~~/docs/ documentation].		Screenshots were provided in the [http://seqware.github.io/docs/3-getting-started/user-tutorial/ user tutorial] as well as much of the current [http://seqware.github.io/docs/ documentation].

	==Entities using SeqWare==		==Entities using SeqWare==