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

• Published in: International journal of environmental research and public health Vol. 12; no. 6; pp. 6352 - 6366
• Main Authors: Singh, Kumar, Thual, Dominique, Spurio, Roberto, Cannata, Nicola
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 03.06.2015; MDPI
• Subjects: Data analysis; Data collection; Ecology - methods; Environmental Microbiology; Environmental Monitoring - methods; Information management; Information Management - methods; Microarray Analysis; Sampling; Software; LIMS; data management; open source system; software; ecological assessment; environmental studies; microarrays
• ISSN: 1660-4601; 1661-7827; 1660-4601
• DOI: 10.3390/ijerph120606352

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.