Informatics Educational Institutions & Programs
|Developer(s)||David A. Nix, Tonya L. Di Sera, Brett A. Milash, and Samir J. Courdy|
|Initial release||March 19, 2010|
(October 16, 2017 )
|Type||Laboratory informatics software|
|License(s)||GNU General Public License v3|
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.
GNomEx was developed by several researchers at the Huntsman Cancer Institute in Salt Lake City, Utah. It was created to:
- 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. 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.
Some of the features of GNomEx include
- 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
Installation requirements and instructions can be found in the SourceForge README file.
Videos, screenshots, and other media
Screenshots of GNomEx can be found at Softpedia.
Entities using GNomEx
- "GNomEx user guide". University of Utah. http://www.hci.utah.edu/internal/CSG/PublicDocs/SourceDocs/HCIApps/GNomEx/GNomEx.htm.
- "Several quick-start guides for GNomEx". University of Utah. http://b2b.hci.utah.edu/B2BWiki/index.php/GNomEx.
- Nix, David A.; Di Sera, Tonya L.; Dalley, Brian K.; Milash, Brett A.; Cundick, Robert M.; Quinn, Kevin S.; Courdy, Samir J. (2010). "Next generation tools for genomic data generation, distribution, and visualization". BMC Bioinformatics 11 (455). doi:10.1186/1471-2105-11-455. PMC PMC2944281. PMID 20828407. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=PMC2944281.
- GNomEx at GitHub
- GNomEx on University of Utah's "Bench to Bassinet" wiki
- GNomEx on University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources wiki
- 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 - Home/archive". SourceForge. 19 March 2010. http://sourceforge.net/projects/gnomex/files/archive/. Retrieved 6 April 2012.
- Nix, David A.; Tonya L. Di Sera; Brian K. Dalley; Brett A. Milash; Robert M. Cundick; Kevin S. Quinn; Samir J. Courdy (9 September 2010). "Next generation tools for genomic data generation, distribution, and visualization". BMC Bioinformatics (BioMed Central Ltd.) 11 (455). doi:10.1186/1471-2105-11-455. http://www.biomedcentral.com/1471-2105/11/455. Retrieved 6 April 2012.
- "GNomEx - Home". SourceForge. http://sourceforge.net/projects/gnomex/files/. Retrieved 6 April 2012.
- "Software:GNomEx". University of Utah's Bioinformatics and Microarray Next Generation Sequencing Shared Resources Wiki. University of Utah. http://bioserver.hci.utah.edu/BioInfo/index.php/Software:GNomEx. Retrieved 6 April 2012.