Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Jun 1;6(6):1-6.
doi: 10.1093/gigascience/gix025.

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs

Cassie Elizabeth Heinle, Nicolas Paul Eugène Gaultier, Dana Miller, Rikky Wenang Purbojati, Federico M Lauro

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs

Cassie Elizabeth Heinle et al. Gigascience. .

Abstract

As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers.

Keywords: GitHub; HTML; JavaScript; LIMS; customizable; mysql; open-source; php; sample management; web application.

PubMed Disclaimer

Figures

Figure 1:
Figure 1:
Database schema of MetaLIMS main sample tables. Please see Supplementary Fig. 1 for full database schema including auxiliary tables.
Figure 2:
Figure 2:
Sample recording workflow in MetaLIMS.
Figure 3:
Figure 3:
MetaLIMS sample input.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Genologics Clarity LIMS www.genologics.com/claritylims (15 February 2016, date last accessed).
    1. Starlims www.abbottinformatics.com/us/products/lims (15 February 2016, date last accessed).
    1. Scholtalbers J, Rossler J, Sorn P et al. . Galaxy LIMS for next-generation sequencing. Bioinformatics 2013; 29:1233–4. - PubMed
    1. SciGenom Labs www.scigenom.com (15 February 2016, date last accessed).
    1. MISO Managing Information for Sequencing Operations http://www.earlham.ac.uk/miso/ (9 November 2016, date last accessed).

Publication types