Title

Authors

Affiliation

¹Department of Computer Science, Mail stop: MSC01 1130, 1 University of New Mexico, Albuquerque, NM 87131-0001; ²Center for Advanced Research Computing, University of New Mexico, Albuquerque, NM 87131; ³Systems Biology, Sandia National Laboratories, Mail Stop 9291, Livermore, CA 94550; ⁴Department of Biology, Mail stop: MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001; ⁵Security Systems Analysis, Sandia National Laboratories, Mail Stop 0757, Albuquerque, NM 87123; ⁶Computational Simulation Infrastructure, Sandia National Laboratories, Mail Stop 0845, Albuquerque, NM 87123

Email

ajpowel@sandia.gov; *Corresponding author

Article Type

Software

Date

Received October 11, 2014; Accepted March 16, 2015; Published April 30, 2015

Next-generation sequencing projects have underappreciated information management tasks requiring detailed attention to specimen curation, nucleic acid sample preparation and sequence production methods required for downstream data processing, comparison, interpretation, sharing and reuse. The few existing metadata management tools for genome-based studies provide weak curatorial frameworks for experimentalists to store and manage idiosyncratic, project-specific information, typically offering no automation supporting unified naming and numbering conventions for sequencing production environments that routinely deal with hundreds, if not thousands of samples at a time. Moreover, existing tools are not readily interfaced with bioinformatics executables, (e.g., BLAST, Bowtie2, custom pipelines). Our application, the Omics Metadata Management Software (OMMS), answers both needs, empowering experimentalists to generate intuitive, consistent metadata, and perform analyses and information management tasks via an intuitive web-based interface. Several use cases with short-read sequence datasets are provided to validate installation and integrated function, and suggest possible methodological road maps for prospective users. Provided examples highlight possible OMMS workflows for metadata curation, multistep analyses, and results management and downloading. The OMMS can be implemented as a stand alone-package for individual laboratories, or can be configured for web-based deployment supporting geographically-dispersed projects. The OMMS was developed using an open-source software base, is flexible, extensible and easily installed and executed.

Availability

The OMMS can be obtained at http://omms.sandia.gov.

Keywords

Bioinformatics, relational database management system, omics, next-generation sequencing, biological curation, open-source software, integrated workflow.

Citation

Arriaga et al.   Bioinformation 11(4): 165-172 (2015)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.