Difference between revisions of "SeqWare"

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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>


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]:


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Revision as of 19:04, 2 September 2014

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

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.com

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.

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]

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 include[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 include:

  • 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 are provided in the user tutorial as well as much of the current documentation.

Entities using SeqWare

Current users include[8]:

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

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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