GNomEx - Revision history

Shawndouglas at 20:06, 4 June 2019

2019-06-04T20:06:43Z

← Older revision		Revision as of 20:06, 4 June 2019
Line 61:		Line 61:
	==External links==		==External links==

	* [https://github.com/hci-gnomex/gnomex GNomEx at GitHub]		* [https://github.com/hci-gnomex/gnomex/ GNomEx at GitHub]
	* [http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx GNomEx] on University of Utah's "Bench to Bassinet" wiki		* [http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx GNomEx] on University of Utah's "Bench to Bassinet" wiki
	* [http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx GNomEx] on University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources wiki		* [http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx GNomEx] on University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources wiki

Shawndouglas at 19:23, 3 May 2018

2018-05-03T19:23:05Z

← Older revision		Revision as of 19:23, 3 May 2018
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://hci-bio-demo.hci.utah.edu/gnomexDocumentation/wordpress~~/ http:/~~/hci-bio-demo.hci.utah.edu]		\| website = [http://hci-bio-demo.hci.utah.edu/gnomexDocumentation/wordpress/ hci-bio-demo.hci.utah.edu]
	}}		}}

Shawndouglas: URL

2018-05-03T19:22:48Z

URL

← Older revision		Revision as of 19:22, 3 May 2018
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://~~b2b~~.hci.utah.edu/~~B2BWiki~~/~~index.php~~/~~GNomEx b2b~~.hci.utah.edu]		\| website = [http://hci-bio-demo.hci.utah.edu/gnomexDocumentation/wordpress/ http://hci-bio-demo.hci.utah.edu]
	}}		}}

Shawndouglas: /* External links */

2018-05-03T19:21:24Z

External links

← Older revision		Revision as of 19:21, 3 May 2018
Line 61:		Line 61:
	==External links==		==External links==

			* [https://github.com/hci-gnomex/gnomex GNomEx at GitHub]
	* [http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx GNomEx] on University of Utah's "Bench to Bassinet" wiki		* [http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx GNomEx] on University of Utah's "Bench to Bassinet" wiki
	* [http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx GNomEx] on University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources wiki		* [http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx GNomEx] on University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources wiki
	* [https://hci-as3.hci.utah.edu/gnomex/gnomex.html GNomEx] deployed at the University of Utah		* [https://hci-as3.hci.utah.edu/gnomex/gnomex.html GNomEx] deployed at the University of Utah

	GNomEx can also be found on SourceForge. However, use caution when downloading and installing from there; the install package may contain undesirable add-on software.		GNomEx can also be found on SourceForge. However, use caution when downloading and installing from there; the install package may contain undesirable add-on software.

	==References==		==References==

Shawndouglas: /* Further reading */ Updated citation

2015-12-23T19:03:07Z

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

2015-06-16T19:01:47Z

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

← Older revision		Revision as of 19:01, 16 June 2015
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://~~gnomex~~.~~sourceforge~~.~~net~~/ ~~gnomex~~.~~sourceforge~~.~~net~~]		\| website = [http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx b2b.hci.utah.edu]
	}}		}}

Line 45:		Line 45:
	==Hardware/software requirements==		==Hardware/software requirements==

	Installation requirements and instructions can be found in the ~~[http://iweb.dl.sourceforge.net/project/gnomex/README_INSTALL.txt~~ SourceForge README file].		Installation requirements and instructions can be found in the SourceForge README file.

	==Videos, screenshots, and other media==		==Videos, screenshots, and other media==
Line 61:		Line 61:
	==External links==		==External links==

	* [http://sourceforge.net/projects/gnomex/ GNomEx] on SourceForge
	* [http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx GNomEx] on University of Utah's "Bench to Bassinet" wiki		* [http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx GNomEx] on University of Utah's "Bench to Bassinet" wiki
	* [http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx GNomEx] on University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources wiki		* [http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx GNomEx] on University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources wiki
	* [https://hci-as3.hci.utah.edu/gnomex/gnomex.html GNomEx] deployed at the University of Utah		* [https://hci-as3.hci.utah.edu/gnomex/gnomex.html GNomEx] deployed at the University of Utah

			GNomEx can also be found on SourceForge. However, use caution when downloading and installing from there; the install package may contain undesirable add-on software.

	==References==		==References==

Shawndouglas: Added internal link.

2012-09-30T18:47:08Z

Added internal link.

← Older revision		Revision as of 18:47, 30 September 2012
Line 28:		Line 28:
	GNomEx was developed by several researchers at the Huntsman Cancer Institute in Salt Lake City, Utah. It was created to<ref name="Nix1" />:		GNomEx was developed by several researchers at the Huntsman Cancer Institute in Salt Lake City, Utah. It was created to<ref name="Nix1" />:

	* track samples for experimentation in Huntsman's microarray and next generation [[sequencing]] core facility		* track samples for experimentation in Huntsman's [[DNA microarray\|microarray]] and next generation [[sequencing]] core facility
	* associate raw data with biological samples		* associate raw data with biological samples
	* link downstream computational analysis with generated data		* link downstream computational analysis with generated data

Shawndouglas: Added internal link.

2012-09-30T18:46:06Z

Added internal link.

← Older revision		Revision as of 18:46, 30 September 2012
Line 28:		Line 28:
	GNomEx was developed by several researchers at the Huntsman Cancer Institute in Salt Lake City, Utah. It was created to<ref name="Nix1" />:		GNomEx was developed by several researchers at the Huntsman Cancer Institute in Salt Lake City, Utah. It was created to<ref name="Nix1" />:

	* track samples for experimentation in Huntsman's microarray and next generation sequencing core facility		* track samples for experimentation in Huntsman's microarray and next generation [[sequencing]] core facility
	* associate raw data with biological samples		* associate raw data with biological samples
	* link downstream computational analysis with generated data		* link downstream computational analysis with generated data

Shawndouglas: /* References */ Added cat.

2012-05-02T21:10:30Z

References: Added cat.

← Older revision		Revision as of 21:10, 2 May 2012
Line 70:		Line 70:

	<!---Place all category tags here-->		<!---Place all category tags here-->
			[[Category:Laboratory informatics software (open source)]]
	[[Category:Laboratory information management systems (open source)]]		[[Category:Laboratory information management systems (open source)]]

Shawndouglas: Created article.

2012-04-06T23:38:24Z

Created article.

New page

{{Infobox software
| name = GNomEx
| title = GNomEx
| logo = [[Image:GNomEx_logo.jpg‎]]
| screenshot = 
| caption =
| collapsible =
| author =
| developer = David A. Nix, Tonya L. Di Sera, Brett A. Milash, and Samir J. Courdy
| released = {{Start date|2010|03|19}}<ref name="GNom4.6">{{cite web |url=http://sourceforge.net/projects/gnomex/files/archive/ |title=GNomEx - Home/archive |publisher=SourceForge |date=19 March 2010 |accessdate=6 April 2012}}</ref>
| discontinued =
| frequently updated = yes
| programming language = Java
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU General Public License v3
| website = [http://gnomex.sourceforge.net/ gnomex.sourceforge.net]
}}

'''GNomEx''' is a free open-source [[genomics]] LIMS and analysis project center for organizing, annotating, tracking, and distributing raw genomic data and associated downstream analysis. It contains a genomics LIMS, an analysis project center, and programmatic data distribution server. It is designed for institutional core facilities and large research laboratories.<ref name="Nix1">{{cite journal |url=http://www.biomedcentral.com/1471-2105/11/455 |title=Next generation tools for genomic data generation, distribution, and visualization |journal=BMC Bioinformatics |author=Nix, David A.; Tonya L. Di Sera; Brian K. Dalley; Brett A. Milash; Robert M. Cundick; Kevin S. Quinn; Samir J. Courdy |publisher=BioMed Central Ltd. |date=9 September 2010 |volume=11 |issue=455 |accessdate=6 April 2012 |doi=10.1186/1471-2105-11-455}}</ref>

==Product history==

GNomEx was developed by several researchers at the Huntsman Cancer Institute in Salt Lake City, Utah. It was created to<ref name="Nix1" />:

* track samples for experimentation in Huntsman's microarray and next generation sequencing core facility
* associate raw data with biological samples
* link downstream computational analysis with generated data

On March 19, 2010, the researchers released the first public, open-source version of GNomEx on SourceForge as version 4.6.<ref name="GNom4.6" /> Since then, work on the software has been steady, with a 5.0.0 release on October 25, 2010; a 5.1.2 release on April 13, 2011; and a 5.3 release on September 27.<ref>{{cite web |url=http://sourceforge.net/projects/gnomex/files/ |title=GNomEx - Home |publisher=SourceForge |accessdate=6 April 2012}}</ref>

==Features==

Some of the features of GNomEx include<ref>{{cite web |url=http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx |title=Software:GNomEx |work=University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources Wiki |publisher=University of Utah |accessdate=6 April 2012}}</ref>

* a LIMS for making and tracking requests for genomic analysis
* ability to import externally generated genomic datasets in their native formats
* ability to enter and associate structured meta-data using MAGE ontologies for the samples and experimental parameters with the data
* Web tools to browse, search, modify, and download data files associated with datasets and meta-data

==Hardware/software requirements==

Installation requirements and instructions can be found in the [http://iweb.dl.sourceforge.net/project/gnomex/README_INSTALL.txt SourceForge README file].

==Videos, screenshots, and other media==

Screenshots of GNomEx can be found at [http://www.softpedia.com/progScreenshots/GNomEx-Screenshot-190452.html Softpedia].

==Entities using GNomEx==

==Further reading==

* {{cite web |url=http://www.hci.utah.edu/internal/CSG/PublicDocs/SourceDocs/HCIApps/GNomEx/GNomEx.htm |title=GNomEx user guide |publisher=University of Utah}}
* {{cite web |url=http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx |title=Several quick-start guides for GNomEx |publisher=University of Utah}}
* {{cite journal |url=http://www.biomedcentral.com/1471-2105/11/455 |title=Next generation tools for genomic data generation, distribution, and visualization |journal=BMC Bioinformatics |author=Nix, David A.; Tonya L. Di Sera; Brian K. Dalley; Brett A. Milash; Robert M. Cundick; Kevin S. Quinn; Samir J. Courdy |publisher=BioMed Central Ltd. |date=9 September 2010 |volume=11 |issue=455}}

==External links==

* [http://sourceforge.net/projects/gnomex/ GNomEx] on SourceForge
* [http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx GNomEx] on University of Utah's "Bench to Bassinet" wiki
* [http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx GNomEx] on University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources wiki
* [https://hci-as3.hci.utah.edu/gnomex/gnomex.html GNomEx] deployed at the University of Utah

==References==
<references />


[[Category:Laboratory information management systems (open source)]]

← Older revision		Revision as of 19:03, 23 December 2015
Line 57:		Line 57:
	* {{cite web \|url=http://www.hci.utah.edu/internal/CSG/PublicDocs/SourceDocs/HCIApps/GNomEx/GNomEx.htm \|title=GNomEx user guide \|publisher=University of Utah}}		* {{cite web \|url=http://www.hci.utah.edu/internal/CSG/PublicDocs/SourceDocs/HCIApps/GNomEx/GNomEx.htm \|title=GNomEx user guide \|publisher=University of Utah}}
	* {{cite web \|url=http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx \|title=Several quick-start guides for GNomEx \|publisher=University of Utah}}		* {{cite web \|url=http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx \|title=Several quick-start guides for GNomEx \|publisher=University of Utah}}
	* {{cite journal ~~\|url=http://www.biomedcentral.com/1471-2105/11/455~~ \|title=Next generation tools for genomic data generation, distribution, and visualization \|journal=BMC Bioinformatics \|author=Nix, David A.; Tonya L. ~~Di Sera~~; Brian K. ~~Dalley~~; Brett A. ~~Milash~~; Robert M. ~~Cundick~~; Kevin S. ~~Quinn~~; Samir J. ~~Courdy~~ \|~~publisher~~=~~BioMed Central Ltd.~~ \|~~date~~=~~9 September~~ 2010 \|~~volume~~=11 \|~~issue~~=~~455~~}}		* {{cite journal \|title=Next generation tools for genomic data generation, distribution, and visualization \|journal=BMC Bioinformatics \|author=Nix, David A.; Di Sera, Tonya L.; Dalley, Brian K.; Milash, Brett A.; Cundick, Robert M.; Quinn, Kevin S.; Courdy, Samir J. \|volume=11 \|issue=455 \|year=2010 \|doi=10.1186/1471-2105-11-455 \|pmid=20828407 \|pmc=PMC2944281}}

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