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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.

Singh KS, Thual D, Spurio R, Cannata N - Int J Environ Res Public Health (2015)

Bottom Line: An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project.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.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano Camerino 62032, Italy. kumar.saurabhsingh@unicam.it.

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.

No MeSH data available.


(A) An image showing Microarray Experiments module. The display includes a unique microarray experiment and a list of oligonucleotides used in this particular microarray experiment; (B) Display of saved microarray experiments.
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ijerph-12-06352-f003: (A) An image showing Microarray Experiments module. The display includes a unique microarray experiment and a list of oligonucleotides used in this particular microarray experiment; (B) Display of saved microarray experiments.

Mentions: SaDA summarizes multiple microarray experiments under Microarray experiments section (Figure 3). In this section, user can keep track of the sample utilized in each microarray experiment. The Microarray experiment section further contains other sections encapsulating data associated with GAL (array data) and GPR (hybridization data) files. Users can manually upload and download files, check the summary and perform downstream data analysis.


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.

Singh KS, Thual D, Spurio R, Cannata N - Int J Environ Res Public Health (2015)

(A) An image showing Microarray Experiments module. The display includes a unique microarray experiment and a list of oligonucleotides used in this particular microarray experiment; (B) Display of saved microarray experiments.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4483705&req=5

ijerph-12-06352-f003: (A) An image showing Microarray Experiments module. The display includes a unique microarray experiment and a list of oligonucleotides used in this particular microarray experiment; (B) Display of saved microarray experiments.
Mentions: SaDA summarizes multiple microarray experiments under Microarray experiments section (Figure 3). In this section, user can keep track of the sample utilized in each microarray experiment. The Microarray experiment section further contains other sections encapsulating data associated with GAL (array data) and GPR (hybridization data) files. Users can manually upload and download files, check the summary and perform downstream data analysis.

Bottom Line: An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project.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.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano Camerino 62032, Italy. kumar.saurabhsingh@unicam.it.

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.

No MeSH data available.