GNomEx – genomic LIMS and data repository

GNomEx (Genomic LIMS and Data Repository) is an open-source genomics LIMS and analysis project center for organizing, annotating, tracking, and distributing raw genomic data and associated downstream analysis.

This application holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery.

Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing, Affy and Agilent Microarrays, Sequenom MassArray and Bioanalyzer.

Features include:

  • Submit an Experiment Order to a Core Facility and receive emails notifying you of progress.
  • Create an experiment and upload your own raw data files.
  • Fully annotate your experiment for each submitted sample.
  • Register downstream analysis performed on the Experiment, tracking all of the analysis pipeline details relevant to the data, for example, the Genome Build the sequence was aligned to.
  • Download the experiment results (raw data files) as well as analyzed data sets.
  • Organize analyzed data sets that can be viewed in a Genome Browser.
  • Organize experiments and analyses under Topics to aggregate data into unified view.
  • Dial in the access to your data – owner, lab members, institution, or public. Also, grant access to specific collaborators.
  • Search the repository for a key term or perform more advanced criteria based searches.
  • Configure different Experiment platforms based on the major categories of Next Gen Sequencing (Illumina HiSeq and MiSeq), Microarray, iScan, Capillary Sequencing, Sample Quality, Fragment Analysis, Mitochondrial DLoop Sequencing, and Plate Cherry Picking.
  • Configure annotations required for experiment samples and analyses. Handle wide range of annotations using text, checkbox, dropdowns, multi-select lists, and URLs.
  • For core facilities, manage experiment orders through the workflow and automate your billing.
  • For administrators, manage user accounts and labs.
  • Web tools to browse, search, modify, and download data files associated with datasets and meta-data.

Developer: David A. Nix, Tonya L. Di Sera, Brett A. Milash, and Samir J. Courdy
License: GNU General Public License v3.0


GNomEx is written in Java. Learn Java with our recommended free books and free tutorials.

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