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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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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. |
format | Online Article Text |
id | pubmed-3123236 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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