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SaDA: From Sampling to Data Analysis—An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data

Author

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  • Kumar Saurabh Singh

    (School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano Camerino 62032, Italy)

  • Dominique Thual

    (Next Generation Bioinformatics s.r.l Camerino 62032, Italy)

  • Roberto Spurio

    (School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano Camerino 62032, Italy)

  • Nicola Cannata

    (School of Science and Technology, University of Camerino, Via Madonna delle Carceri Camerino 62032, Italy)

Abstract

One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies.

Suggested Citation

  • Kumar Saurabh Singh & Dominique Thual & Roberto Spurio & Nicola Cannata, 2015. "SaDA: From Sampling to Data Analysis—An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data," IJERPH, MDPI, vol. 12(6), pages 1-15, June.
    • Handle: RePEc:gam:jijerp:v:12:y:2015:i:6:p:6352-6366:d:50662
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    References listed on IDEAS

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    1. Dahl, David B. & Crawford, Scott, 2009. "RinRuby: Accessing the R Interpreter from Pure Ruby," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 29(i04).
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    Cited by:

    1. Stefania Marcheggiani & Roberto Spurio & Lucia Cimarelli & Duarte Tito & Laura Mancini, 2015. "Scientific Symposium “Small Solution for Big Water-Related Problems: Innovative Microarrays and Small Sensors to Cope with Water Quality and Food Security”," IJERPH, MDPI, vol. 12(12), pages 1-9, December.
    2. Lucia Cimarelli & Kumar Saurabh Singh & Nguyen Thi Nhu Mai & Bidhan Chandra Dhar & Anna Brandi & Letizia Brandi & Roberto Spurio, 2015. "Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels," IJERPH, MDPI, vol. 12(5), pages 1-20, May.

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