Proceedings of the EuBIC developer's meeting 2018

Willems, Sander; Bouyssié, David; Deforce, Dieter; Dorfer, Viktoria; Gorshkov, Vladimir; Kopczynski, Dominik; Laukens, Kris; Locard‐Paulet, Marie; Schwämmle, Veit; Uszkoreit, Julian; Valkenborg, Dirk; Vaudel, Marc; Bittremieux, Wout

doi:10.1016/j.jprot.2018.05.015

Cited by 8 publications

(6 citation statements)

References 14 publications

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“…Next year's EuBIC conference will again be a Developer's Meeting, like the one in 2018 [2], with a more hackathon-like program comprising more hands-on coding and less keynote talks. The meeting will take place in Denmark in January 2020 and the planning of the program is already underway.…”

Section: Discussionmentioning

confidence: 99%

“…The 2019 EuBIC Winter School on proteomics bioinformatics, held from January 15th to January 18th 2019 in Zakopane, Poland, was the third conference of its kind organised by the European Bioinformatics Community (EuBIC, [1,2]), an initiative of the European Proteomics Association (EuPA) for user-oriented bioinformatics. The Winter School brought together scientists from both academia and industry in the field of computational mass spectrometry (MS)-based proteomics to present and discuss their research in workshops, keynote lectures, flash talks and poster presentations.…”

Section: Introductionmentioning

confidence: 99%

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Proceedings of the EuBIC Winter School 2017

Willems

Bouyssié

David

et al. 2017

Journal of Proteomics

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The EUPA bioinformatics community (EuBIC) organized its first winter school in January 2017. This successful event illustrates the growing need of the bioinformatics community in proteomics to gather and discuss current and future challenges in the field. In addition to the organization of yearly meetings, the young and active EuBIC community aims to develop new collaborative open source projects, spread bioinformatics knowledge in Europe, and actively promote data sharing through public repositories.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Proceedings of the EuBIC Winter School 2017

Willems

Bouyssié

David

et al. 2017

Journal of Proteomics

Self Cite

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“…In an effort to simplify proteomics data analysis and provide fully reproducible data analysis workflows, we launched the ProtProtocols project () under the umbrella of the European Bioinformatics Community (EuBIC). 15 On the basis of the Biocontainers project, 2 the protocols are shipped in containerized Docker images that include all necessary software tools. Docker containers are lightweight virtual machines that encapsulate all the software required for the protocol to run.…”

Section: Introductionmentioning

confidence: 99%

IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments

2019

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Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Hence, a manuscript’s methods section is often insufficient to completely describe and reproduce a data analysis workflow. Here we present IsoProt: A complete and reproducible bioinformatic workflow deployed on a portable container environment to analyze data from isobarically labeled, quantitative proteomics experiments. The workflow uses only open source tools and provides a user-friendly and interactive browser interface to configure and execute the different operations. Once the workflow is executed, the results including the R code to perform statistical analyses can be downloaded as an HTML document providing a complete record of the performed analyses. IsoProt therefore represents a reproducible bioinformatics workflow that will yield identical results on any computer platform.

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“…In an effort to simplify proteomics data analysis and provide fully reproducible data analysis workflows we launched the ProtProtocols project ( https://protprotocols.github.io ) under the umbrella of the European Bioinformatics Community (EuBIC) 10 . Based on the Biocontainers project 2 the protocols are shipped in containerized Docker images that include all necessary software tools.…”

Section: Introductionmentioning

confidence: 99%

IsoProt: A complete and reproducible workflow to analyse iTRAQ/TMT experiments

Griss

Vinterhalter

Schwämmle

2018

Preprint

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Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Hence a manuscript’s methods section is often insufficient to completely describe and reproduce a data analysis workflow. Here we present IsoProt: A complete and reproducible bioinformatic workflow deployed on a portable container environment to analyse data from isobarically-labeled, quantitative proteomics experiments. The workflow uses only open source tools and provides a user-friendly and interactive browser interface to configure and execute the different operations. Once the workflow is executed, the results including the R code to perform statistical analyses can be downloaded as an HTML or PDF document providing a complete record of the performed analyses. IsoProt therefore represents a reproducible bioinformatics workflow that will yield identical results on any computer platform.

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Proceedings of the EuBIC developer's meeting 2018

Cited by 8 publications

References 14 publications

Proceedings of the EuBIC Winter School 2017

Proceedings of the EuBIC Winter School 2017

IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments

IsoProt: A complete and reproducible workflow to analyse iTRAQ/TMT experiments

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