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MicroGen: a MIAME compliant web system for microarray experiment information and workflow management

BACKGROUND: Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Althoug...

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Autores principales: Burgarella, Sarah, Cattaneo, Dario, Pinciroli, Francesco, Masseroli, Marco
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866379/
https://www.ncbi.nlm.nih.gov/pubmed/16351755
http://dx.doi.org/10.1186/1471-2105-6-S4-S6
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author Burgarella, Sarah
Cattaneo, Dario
Pinciroli, Francesco
Masseroli, Marco
author_facet Burgarella, Sarah
Cattaneo, Dario
Pinciroli, Francesco
Masseroli, Marco
author_sort Burgarella, Sarah
collection PubMed
description BACKGROUND: Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. RESULTS: We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. CONCLUSION: MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.
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spelling pubmed-18663792007-05-11 MicroGen: a MIAME compliant web system for microarray experiment information and workflow management Burgarella, Sarah Cattaneo, Dario Pinciroli, Francesco Masseroli, Marco BMC Bioinformatics Research Article BACKGROUND: Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. RESULTS: We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. CONCLUSION: MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production. BioMed Central 2005-12-01 /pmc/articles/PMC1866379/ /pubmed/16351755 http://dx.doi.org/10.1186/1471-2105-6-S4-S6 Text en Copyright © 2005 Burgarella et al; licensee BioMed Central Ltd http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Burgarella, Sarah
Cattaneo, Dario
Pinciroli, Francesco
Masseroli, Marco
MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
title MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
title_full MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
title_fullStr MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
title_full_unstemmed MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
title_short MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
title_sort microgen: a miame compliant web system for microarray experiment information and workflow management
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866379/
https://www.ncbi.nlm.nih.gov/pubmed/16351755
http://dx.doi.org/10.1186/1471-2105-6-S4-S6
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