ORCID Profile
0000-0001-6825-9439
Current Organisation
Health-RI
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Publisher: Ubiquity Press, Ltd.
Date: 26-10-2021
DOI: 10.5334/DSJ-2021-032
Publisher: Oxford University Press (OUP)
Date: 23-02-2011
DOI: 10.1093/BIOINFORMATICS/BTR094
Abstract: Summary: Warp2D is a novel time alignment approach, which uses the overlapping peak volume of the reference and s le peak lists to correct misleading peak shifts. Here, we present an easy-to-use web interface for high-throughput Warp2D batch processing time alignment service using the Dutch Life Science Grid, reducing processing time from days to hours. This service provides the warping function, the s le chromatogram peak list with adjusted retention times and normalized quality scores based on the sum of overlapping peak volume of all peaks. Heat maps before and after time alignment are created from the arithmetic mean of the sum of overlapping peak area rearranged with hierarchical clustering, allowing the quality control of the time alignment procedure. Taverna workflow and command line tool are provided for remote processing of local user data. Availability: online data processing service is available at www.nbpp.nl/warp2d.html. Taverna workflow is available at myExperiment with title ‘2D Time Alignment—Webservice and Workflow’ at orkflows/1283.html. Command line tool is available at www.nbpp.nl/Warp2D_commandline.zip. Contact: p.l.horvatovich@rug.nl Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: F1000 Research Ltd
Date: 13-06-2017
DOI: 10.12688/F1000RESEARCH.11407.1
Abstract: Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.
No related grants have been discovered for Rob Hooft.