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Author(s): Gael Pérez Rodríguez
Daniel Glez Peña
Nuno F. Azevedo
Maria Olívia Pereira
Fiorentino Fdez Riverola
Anália Lourenco
Title: Enabling systematic, harmonised and large-scale biofilms data computation: The Biofilms Experiment Workbench
Issue Date: 2015
Abstract: Background and objective: Biofilms are receiving increasing attention from the biomedical community. Biofilm-like growth within human body is considered one of the key microbial strategies to augment resistance and persistence during infectious processes. The Biofilms Experiment Workbench is a novel software workbench for the operation and analysis of biofilms experimental data. The goal is to promote the interchange and comparison of data among laboratories, providing systematic, harmonised and large-scale data computation. Methods: The workbench was developed with AIBench, an open-source Java desktop application framework for scientific software development in the domain of translational biomedicine. Implementation favours free and open-source third-parties, such as the R statistical package, and reaches for the Web services of the BiofOmics database to enable public experiment deposition. Results: First, we summarise the novel, free, open, XML-based interchange format for encoding biofilms experimental data. Then, we describe the execution of common scenarios of operation with the new workbench, such as the creation of new experiments, the importation of data from Excel spreadsheets, the computation of analytical results, the on-demand and highly customised construction of Web publishable reports, and the comparison of results between laboratories. Conclusions:A considerable and varied amount of biofilms data is being generated, and there is a critical need to develop bioinformatics tools that expedite the interchange and comparison of microbiological and clinical results among laboratories. We propose a simple, open-source software infrastructure which is effective, extensible and easy to understand. The workbench is freely available for non-commercial use at under LGPL license.
Subject: Biotecnologia ambiental
Environmental biotechnology
Scientific areas: Ciências da engenharia e tecnologias::Biotecnologia ambiental
Engineering and technology::Environmental biotechnology
Related Information: info:eu-repo/grantAgreement/FCT - Fundação para a Ciência e a Tecnologia/Projetos Estratégicos/UID/EQU/00511/2013 - POCI-01-0145-FEDER-006939/Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia/LEPABE
Document Type: Artigo em Revista Científica Internacional
Rights: restrictedAccess
Appears in Collections:FEUP - Artigo em Revista Científica Internacional

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