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Brunn: An open source laboratory information system for microplates with a graphical plate layout design process

BACKGROUND: Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a flexible lightweight open syste...

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Autores principales: Alvarsson, Jonathan, Andersson, Claes, Spjuth, Ola, Larsson, Rolf, Wikberg, Jarl ES
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123236/
https://www.ncbi.nlm.nih.gov/pubmed/21599898
http://dx.doi.org/10.1186/1471-2105-12-179
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author Alvarsson, Jonathan
Andersson, Claes
Spjuth, Ola
Larsson, Rolf
Wikberg, Jarl ES
author_facet Alvarsson, Jonathan
Andersson, Claes
Spjuth, Ola
Larsson, Rolf
Wikberg, Jarl ES
author_sort Alvarsson, Jonathan
collection PubMed
description BACKGROUND: Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a flexible lightweight open system for handling plate design, and validation and preparation of data. RESULTS: A Bioclipse plugin consisting of a client part and a relational database was constructed. A multiple-step plate layout point-and-click interface was implemented inside Bioclipse. The system contains a data validation step, where outliers can be removed, and finally a plate report with all relevant calculated data, including dose-response curves. CONCLUSIONS: Brunn is capable of handling the data from microplate assays. It can create dose-response curves and calculate IC(50 )values. Using a system of this sort facilitates work in the laboratory. Being able to reuse already constructed plates and plate layouts by starting out from an earlier step in the plate layout design process saves time and cuts down on error sources.
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spelling pubmed-31232362011-06-25 Brunn: An open source laboratory information system for microplates with a graphical plate layout design process Alvarsson, Jonathan Andersson, Claes Spjuth, Ola Larsson, Rolf Wikberg, Jarl ES BMC Bioinformatics Software BACKGROUND: Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a flexible lightweight open system for handling plate design, and validation and preparation of data. RESULTS: A Bioclipse plugin consisting of a client part and a relational database was constructed. A multiple-step plate layout point-and-click interface was implemented inside Bioclipse. The system contains a data validation step, where outliers can be removed, and finally a plate report with all relevant calculated data, including dose-response curves. CONCLUSIONS: Brunn is capable of handling the data from microplate assays. It can create dose-response curves and calculate IC(50 )values. Using a system of this sort facilitates work in the laboratory. Being able to reuse already constructed plates and plate layouts by starting out from an earlier step in the plate layout design process saves time and cuts down on error sources. BioMed Central 2011-05-20 /pmc/articles/PMC3123236/ /pubmed/21599898 http://dx.doi.org/10.1186/1471-2105-12-179 Text en Copyright © 2011 Alvarsson et al; licensee BioMed Central Ltd. https://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 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Alvarsson, Jonathan
Andersson, Claes
Spjuth, Ola
Larsson, Rolf
Wikberg, Jarl ES
Brunn: An open source laboratory information system for microplates with a graphical plate layout design process
title Brunn: An open source laboratory information system for microplates with a graphical plate layout design process
title_full Brunn: An open source laboratory information system for microplates with a graphical plate layout design process
title_fullStr Brunn: An open source laboratory information system for microplates with a graphical plate layout design process
title_full_unstemmed Brunn: An open source laboratory information system for microplates with a graphical plate layout design process
title_short Brunn: An open source laboratory information system for microplates with a graphical plate layout design process
title_sort brunn: an open source laboratory information system for microplates with a graphical plate layout design process
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123236/
https://www.ncbi.nlm.nih.gov/pubmed/21599898
http://dx.doi.org/10.1186/1471-2105-12-179
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