Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench

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 summarize 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 http://sing.ei.uvigo.es/bew under LGPL license.Project PTDC/SAU-ESA/646091/2006/ FCOMP-01-0124-FEDER-007480FCT, theStrategic Project PEst-OE/EQB/LA0023/2013, the Project “Bio-Health – Biotechnology and Bioengineering approachesto improve health quality”, Ref. NORTE-07-0124-FEDER-000027, co-funded by the Programa Operacional Regionaldo Norte (ON.2 – O Novo Norte), QREN, FEDER, the project“RECI/BBB-EBI/0179/2012 – Consolidating Research Expertiseand Resources on Cellular and Molecular Biotechnology atCEB/IBB”, Ref. FCOMP-01-0124-FEDER-027462, FEDER, andthe Agrupamento INBIOMED from DXPCTSUG-FEDER unhamaneira de facer Europa (2012/273). The research leading tothese results has received funding from the European Union’s Seventh Framework Programme FP7/REGPOT-2012-2013.1under Grant Agreement N◦316265 (BIOCAPS) and the [14VI05]Contract-Programme from the University of Vigo