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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}} | }} | ||
'''SeqWare''' | '''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 | Features of SeqWare included<ref name="SWAbout" />: | ||
* a database for storing metadata | * a database for storing metadata | ||
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==Hardware/software requirements== | ==Hardware/software requirements== | ||
Requirements for proper installation of SeqWare | 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 | 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 | 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 | ||
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<!---Place all category tags here--> | <!---Place all category tags here--> | ||
[[Category: | [[Category:Discontinued or abandoned software (open source)]] | ||
Revision as of 17:47, 4 May 2021
 | |
| Developer(s) | SeqWare development team |
|---|---|
| Initial release | December 11, 2009 (0.3.0)[1] |
| Discontinued |
1.1.2 (November 18, 2015) [±] |
| 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 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, 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 release notes:
|
|
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, Ontario Institute for Cancer Research
Further reading
- O'Connor, Brian D.; Merriman, Barry; Nelson, Stanley F. (2010). "SeqWare Query Engine: storing and searching sequence data in the cloud". BMC Bioinformatics 11 (Suppl. 12): S2. doi:10.1186/1471-2105-11-S12-S2. http://www.biomedcentral.com/1471-2105/11/S12/S2.
- 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.
External links
- SeqWare on Google Projects (deprecated)
- SeqWare GitHub repository (current)
References
- ↑ 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.
- ↑ 2.0 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.
- ↑ 3.0 3.1 "SeqWare - About". GitHub, Inc.. http://seqware.github.com/about/. Retrieved 02 October 2012.
- ↑ 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.
- ↑ 5.0 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.
- ↑ 6.0 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.
- ↑ "SeqWare - 20100426". SourceForge. 26 April 2010. http://sourceforge.net/apps/mediawiki/seqware/index.php?title=20100426. Retrieved 02 October 2012.
- ↑ "SeqWare - Partners". Brian O’Connor. http://seqware.github.com/partners/. Retrieved 02 October 2012.
