Difference between revisions of "SeqWare"

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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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| 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]
}}
}}


'''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==
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:
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]:
 
{|  
{|  
  | STYLE="vertical-align:top;"|
  | style="vertical-align:top;" |
{| class="wikitable"
{| class="wikitable"
|- valign="top"
|- valign="top"
! 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"
|- valign="top"
| 0.13.5
|0.12.1
| 13 November 2012<ref name="BIGitNotes" />
|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"
| 0.13.4
|0.12.0
| 22 October 2012<ref name="BIGitNotes" />
|Unknown<ref name="BIGeek" />
|- valign="top"
|- valign="top"
| 0.13.3
|0.11.4
| 09 October 2012<ref name="BIGitNotes" />
|11 May 2012<ref name="BISFMain" />
|- valign="top"
|- valign="top"
| 0.13.2
|0.11.2
| 20 September 2012<ref name="BIGitNotes" />
|Unknown<ref name="BIDatabase" />
|- valign="top"
|- valign="top"
| 0.13.1
|0.10.2
| 03 September 2012<ref name="BIGitNotes" />
|Unknown<ref name="BIDatabase" />
|- valign="top"
|- valign="top"
| 0.13.0
|0.10.1
| 20 August 2012<ref name="BIGitNotes" />
|Unknown<ref name="BIDatabase" />
|- valign="top"
|- valign="top"
| 0.12.5
|0.10.0
| 6 August 2012<ref name="BIGitNotes" />
|12 January 2012<ref name="BISFMain" />
|- valign="top"
|- valign="top"
| 0.12.1
|0.9.1
| 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="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"
| 0.12.0
|0.9.0
| Unknown<ref name="BIGeek" />
|Unknown<ref name="BIDatabase" />
|- valign="top"
|- valign="top"
| 0.11.4
|0.8.0
| 11 May 2012<ref name="BISFMain" />
|Unknown<ref name="BIDatabase" />
|- valign="top"
| 0.11.2
| Unknown<ref name="BIDatabase" />
|- valign="top"
| 0.10.2
| Unknown<ref name="BIDatabase" />
|- valign="top"
| 0.10.1
| 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"
| 0.10.0
|0.7.0
| 12 January 2012<ref name="BISFMain" />
|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"
| 0.9.1
|0.6.1
| 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>
|24 February 2010<ref name="SWStart" />
|- valign="top"
|- valign="top"
| 0.9.0
|0.6.0
| Unknown<ref name="BIDatabase" />
|19 February 2010<ref name="SWStart" />
|- valign="top"
|- valign="top"
| 0.8.0
|0.5.0
| Unknown<ref name="BIDatabase" />
|18 February 2010<ref name="SWStart" />
|- valign="top"
|- valign="top"
| 0.7.0
|0.4.0
| 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>
|14 January 2010<ref name="SWStart" />
|- valign="top"
|- valign="top"
| 0.6.1
|0.3.0
| 24 February 2010<ref name="SWStart" />
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|- valign="top"
| 0.6.0
|0.2.0
| 19 February 2010<ref name="SWStart" />
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|- valign="top"
| 0.5.0
|0.1.2
| 18 February 2010<ref name="SWStart" />
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|- valign="top"
| 0.4.0
|0.1.1
| 14 January 2010<ref name="SWStart" />
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
| 0.3.0
| 11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
| 0.2.0
| 11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
| 0.1.2
| 11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
| 0.1.1
| 11 December 2009 (public)<ref name="SWStart" />
|}
|}
|}
|}
Line 127: Line 106:
==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
* 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==


Requirements for proper installation of SeqWare include:
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 [https://seqware.github.io/docs/2-installation/ the GitHub site].


==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.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==


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


==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}}
==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)


==References==
==References==
Line 171: Line 146:


<!---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)]]

Latest revision as of 20:42, 28 November 2022

SeqWare
Seqware logo.png
Developer(s) SeqWare development team
Initial release December 11, 2009 (2009-12-11) (0.3.0)[1]
Discontinued

1.1.2  (November 18, 2015; 9 years ago (2015-11-18))

[±]
Preview release [±]
Written in Java
Operating system Cross-platform
Type Laboratory informatics software
License(s) GNU General Public License v3
Website seqware.github.io

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

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.[2][3] 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.[1] 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."[2] 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."[2] Work progressed steadily, including a 2012 switch from SourceForge to GitHub.[4]

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 release notes:

Version Release date
0.12.1 Unknown[5]
0.12.0 Unknown[5]
0.11.4 11 May 2012[4]
0.11.2 Unknown[6]
0.10.2 Unknown[6]
0.10.1 Unknown[6]
0.10.0 12 January 2012[4]
0.9.1 Unknown[6]
0.9.0 Unknown[6]
0.8.0 Unknown[6]
Version Release date
0.7.0 03 May 2010[7]
0.6.1 24 February 2010[1]
0.6.0 19 February 2010[1]
0.5.0 18 February 2010[1]
0.4.0 14 January 2010[1]
0.3.0 11 December 2009 (public)[1]
0.2.0 11 December 2009 (public)[1]
0.1.2 11 December 2009 (public)[1]
0.1.1 11 December 2009 (public)[1]

Features

Features of SeqWare included[3]:

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

Hardware/software requirements

Requirements for proper installation of SeqWare included:

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

More information about installation can be found on the GitHub site.

Videos, screenshots, and other media

Screenshots were provided in the user tutorial as well as much of the current documentation.

Entities using SeqWare

Current users included[8]:

Lineberger Comprehensive Cancer Center, Nimbus Informatics

Further reading

External links

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 "trunk/seqware-queryengine/backend/dist/ - SeqWare". Google Project Hosting. http://code.google.com/p/seqware/source/browse/trunk/seqware-queryengine/backend/dist/?r=601. Retrieved 02 October 2012. 
  2. ↑ 2.0 2.1 2.2 Marx, Vivien (5 February 2010). "UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production" (PDF). BioInform - Genomeweb LLC. http://pegasus.isi.edu/publications/ucla-pegasus.pdf. Retrieved 02 October 2012. 
  3. ↑ 3.0 3.1 "SeqWare - About". GitHub, Inc.. http://seqware.github.com/about/. Retrieved 02 October 2012. 
  4. ↑ 4.0 4.1 4.2 "SeqWare - Main Page". SourceForge. 24 September 2012. http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page. Retrieved 02 October 2012. 
  5. ↑ 5.0 5.1 "BOConnor's Wiki - Research Blog". Brian O'Connor. https://boconnor.is-a-geek.com/pmwiki/index.php?n=Main.HomePage?logdate=201206. Retrieved 02 October 2012. 
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 "Setup SeqWare MetaDB - Upgrading your Database Version". SourceForge. 10 July 2012. http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_MetaDB#Upgrading_your_Database_Version. Retrieved 02 October 2012. 
  7. ↑ "SeqWare - 20100426". SourceForge. 26 April 2010. http://sourceforge.net/apps/mediawiki/seqware/index.php?title=20100426. Retrieved 02 October 2012. 
  8. ↑ "SeqWare - Partners". Brian O’Connor. http://seqware.github.com/partners/. Retrieved 02 October 2012. 
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