title: 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.
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.
authors.affiliation: School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano Camerino 62032, Italy. kumar.saurabhsingh@unicam.it.
authors.forename: Kumar Saurabh
authors.initials: KS
authors.lastname: Singh
authors.affiliation: Next Generation Bioinformatics s.r.l Camerino 62032, Italy. dom_thual@yahoo.fr.
authors.forename: Dominique
authors.initials: D
authors.lastname: Thual
authors.affiliation: School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano Camerino 62032, Italy. roberto.spurio@unicam.it.
authors.forename: Roberto
authors.initials: R
authors.lastname: Spurio
authors.affiliation: School of Science and Technology, University of Camerino, Via Madonna delle Carceri Camerino 62032, Italy. nicola.cannata@gmail.com.
authors.forename: Nicola
authors.initials: N
authors.lastname: Cannata
mesh_terms: D004463:Ecology / Q000379:methods; D004783:Environmental Microbiology; D004784:Environmental Monitoring / Q000379:methods; D019451:Information Management / Q000379:methods*; D046228:Microarray Analysis; D012984:Software
keywords: LIMS; data management; ecological assessment; environmental studies; microarrays; open source system; software