GNomEx

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GNomEx
GNomEx logo.jpg
Developer(s) David A. Nix, Tonya L. Di Sera, Brett A. Milash, and Samir J. Courdy
Initial release March 19, 2010 (2010-03-19)[1]
Stable release

5.39  (October 16, 2017; 13 months ago (2017-10-16))

[±]
Preview release none [±]
Written in Java
Operating system Cross-platform
Type Laboratory informatics software
License(s) GNU General Public License v3
Website hci-bio-demo.hci.utah.edu

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.[2]

Product history

GNomEx was developed by several researchers at the Huntsman Cancer Institute in Salt Lake City, Utah. It was created to[2]:

  • 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.[1] 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.[3]

Features

Some of the features of GNomEx include[4]

  • 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 SourceForge README file.

Videos, screenshots, and other media

Screenshots of GNomEx can be found at Softpedia.

Entities using GNomEx

Further reading

External links

  • 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.

References

  1. 1.0 1.1 "GNomEx - Home/archive". SourceForge. 19 March 2010. http://sourceforge.net/projects/gnomex/files/archive/. Retrieved 6 April 2012. 
  2. 2.0 2.1 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. 
  3. "GNomEx - Home". SourceForge. http://sourceforge.net/projects/gnomex/files/. Retrieved 6 April 2012. 
  4. "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.