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

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...

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Bibliographic Details
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
Online Access:Get full text
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Summary: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.
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ISSN:1660-4601
1661-7827
1660-4601
DOI:10.3390/ijerph120606352