Filters








138 Hits in 6.1 sec

BioContainers: an open-source and community-driven framework for software standardization

Felipe da Veiga Leprevost, Björn A Grüning, Saulo Alves Aflitos, Hannes L Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C Jimenez (+7 others)
2017 Bioinformatics  
Motivation: BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software.  ...  BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment.  ...  The BioContainers community is now working on new ways for testing containers and for workflow/pipelines integration.  ... 
doi:10.1093/bioinformatics/btx192 pmid:28379341 pmcid:PMC5870671 fatcat:gkrccbww7fgsnki5di42hwwupm

An overview of biomedical platforms for managing research data

Vivek Navale, Denis von Kaeppler, Matthew McAuliffe
2021 Journal of Data, Information and Management  
The use of the research community developed standards for data collection can foster the development of machine learning methods for data processing and analysis.  ...  AbstractBiomedical platforms provide the hardware and software to securely ingest, process, validate, curate, store, and share data.  ...  Open-source, modular, web-application framework, ontology-driven architecture, uti- lizes components of i2b2 for queries, exploration & analysis.  ... 
doi:10.1007/s42488-020-00040-0 fatcat:itiji5ifu5hjhhcjvtzwz6jq6e

D2.2 A Report On The Coordination With Wp1 On The Incorporation Of Monitoring Statistics And Benchmarking Results In Registry Releases

Josep Gelpi Ll., Jose Mª. Fernández, Vicky Sundesha, Repchevsky, Juergen Haas
2018 Zenodo  
Future developments of OpenEBench will focus in the generation of an automated platform for supporting scientific benchmarking activities driven by communities.  ...  This development will be largely related to the evolution of the ELIXIR platform for software deployment (Biocontainers), and the deployment for solutions for workflow specification and execution from  ...  The source of such metrics includes documents by the Software Sustainability Institute 12 , recommendations for open source software development 13 , or for software quality metrics 9 .  ... 
doi:10.5281/zenodo.1452560 fatcat:6zkiwkxwprdvhijwywptobt5vu

Using bio.tools to generate and annotate workbench tool descriptions

Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager
2017 F1000Research  
.: BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017; 33(16): 2580-2582. PubMed Abstract | Publisher Full Text 11.  ...  The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description.  ...  For instance, linking of the bioconda and biocontainers repositories to bio.tools will enable ToolDog to generate software requirements compatible with workbench platforms 25 .  ... 
doi:10.12688/f1000research.12974.1 pmid:29333231 pmcid:PMC5747335 fatcat:knz3bxbcbjf65haydr53vhz7di

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy [article]

Melanie Christine Foell, Lennart Moritz, Thomas Wollmann, Maren Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Bjoern Gruening, Oliver Schilling
2019 bioRxiv   pre-print
Open source software solutions that enable reproducible data analysis often require programming skills and are therefore not accessible to many MSI researchers.  ...  Conclusion: The Galaxy framework has emerged as a powerful analysis platform for the analysis of MSI data with ease of use and access together with high levels of reproducibility and transparency.  ...  Acknowledgement We thank the European Galaxy Instance for bioinformatics support (https://usegalaxy.eu/) and the Galaxy community for critically reviewing tools and training material.  ... 
doi:10.1101/628719 fatcat:hjguzwlusjhj3n34irysi5je44

Biology Needs Evolutionary Software Tools: Let's Build Them Right

Anton Nekrutenko, Galaxy Team, Jeremy Goecks, James Taylor, Daniel Blankenberg, Sudhir Kumar
2018 Molecular biology and evolution  
This situation makes algorithms and software tools developed by our community more important than ever before.  ...  Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole.  ...  Acknowledgments The authors are grateful to Bioconda, BioContainers, and Galaxy communities as without these resources this work would not be possible.  ... 
doi:10.1093/molbev/msy084 pmid:29688462 pmcid:PMC5967460 fatcat:odskxbbzkrdr3llir6sa4dlt2i

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Andreas Grüning, Oliver Schilling
2019 GigaScience  
Open source software solutions that enable reproducible data analysis often require programming skills and are therefore not accessible to many mass spectrometry imaging (MSI) researchers.  ...  Conclusion The Galaxy framework has emerged as a powerful analysis platform for the analysis of MSI data with ease of use and access, together with high levels of reproducibility and transparency.  ...  Acknowledgments We thank the European Galaxy Instance for bioinformatics support (https://usegalaxy.eu/) and the Galaxy community for critically reviewing tools and training material.  ... 
doi:10.1093/gigascience/giz143 pmid:31816088 pmcid:PMC6901077 fatcat:myc76yjrlfdibli362qpp4ut4m

Approaches for containerized scientific workflows in cloud environments with applications in life science

Ola Spjuth, Marco Capuccini, Matteo Carone, Anders Larsson, Wesley Schaal, Jon Ander Novella, Oliver Stein, Morgan Ekmefjord, Paolo Di Tommaso, Evan Floden, Cedric Notredame, Pablo Moreno (+5 others)
2021 F1000Research  
Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form  ...  A particular focus is placed on the workflow tool's interaction with the Kubernetes container orchestration framework.  ...  Recently, work to integrate and demonstrate Pachyderm in bioinformatics was published. 31 Luigi Luigi 32 is an open-source Python module for defining and running batch-like workflows.  ... 
doi:10.12688/f1000research.53698.1 fatcat:qy3gnqbsavcctctanch25ukgie

iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences

Ken Youens-Clark, Matt Bomhoff, Alise J Ponsero, Elisha M Wood-Charlson, Joshua Lynch, Illyoung Choi, John H Hartman, Bonnie L Hurwitz
2019 GigaScience  
Conclusions iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.  ...  To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community  ...  Ramona Walls at CyVerse; and Matt Vaughn and John Fonner at TACC.  ... 
doi:10.1093/gigascience/giz083 pmid:31289831 pmcid:PMC6615980 fatcat:cq4cvvg5mjfr3fzbtvt2yangwq

D1.3 Registry Release With Comprehensive Coverage Of Elixir Node Resources, Including Resource Data Format Curation And Analysis

Jon Ison, Hans Ienasescu, Piotr Chmura, Herve Menager, ELIXIR Tools Community
2018 Zenodo  
The objective of EXCELERATE Deliverable 1.3 is the development of a discovery portal (bio.tools ) built upon a federated curation of a registry of key software resources for 1 bioinformatics worldwide.  ...  Four reports (D1.1 - D1.4) describe the portal: ● M12: prototyping†of portal software and registry data model, addition of seed content ● M24: consolidation†of software features and content to a stable  ...  An article describing the work has been accepted for publication in The Journal of Open Source Software . 2 • biotoolsSum utility for search and browsing of local tool collections, embeddable on external  ... 
doi:10.5281/zenodo.1456754 fatcat:dk6t7laeynb2jfsu26hr5q4h6y

An intrinsically disordered proteins community for ELIXIR

Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas (+32 others)
2019 F1000Research  
The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.  ...  The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage  ...  A strategic meeting to identify the key priority areas for the roadmap was funded by ELIXIR, the research infrastructure for  ... 
doi:10.12688/f1000research.20136.1 pmid:31824649 pmcid:PMC6880265 fatcat:2rw2z5q3obgrllxjcthcqgoiyu

BioTracs: A transversal framework for computational workflow standardization and traceability [article]

Josephine Abi-Ghanem, Djomangan Adama Ouattara
2020 bioRxiv   pre-print
It leads to several community-driven initiatives to standardize the sharing of data and computational workflows.  ...  Results: We present here BioTracs, a transversal framework for computational workflow standardization and traceability.  ...  The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.16.951624 doi: bioRxiv preprint  ... 
doi:10.1101/2020.02.16.951624 fatcat:mqftjdsrp5fmjhwtwoqr7epzoe

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Björn A Grüning, Aysam Guerler, Jennifer Hillman-Jackson (+8 others)
2018 Nucleic Acids Research  
During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials.  ...  Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed.  ...  Our 2018 conference will be hosted jointly with the Bioinformatics Open Source Conference (BOSC) in an effort to promote and centralize discussion of open-source software for bioinformatics.  ... 
doi:10.1093/nar/gky379 pmid:29790989 pmcid:PMC6030816 fatcat:bfp64x6qizahzjj5yoybdkufku

Galaxy: A Decade of Realising CWFR Concepts

Beatriz Serrano-Solano, Anne Fouilloux, Ignacio Eguinoa, Matús Kalas, Björn A. Grüning, Frederik Coppens
2022 Data Intelligence  
We detail how Galaxy, an open-source workflow management system with a web-based interface, has implemented the concepts that are put forward by the Canonical Workflow Framework for Research (CWFR), whilst  ...  minimising changes to the practices of scientific communities.  ...  Software packages, especially in conjunction with a package manager, are very common in the open source community, with RPM and DPKG as prominent examples.  ... 
doi:10.1162/dint_a_00136 dblp:journals/dint/Serrano-SolanoF22 fatcat:ij5lrtzzkjcdtmg4q7fzjripfa

The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols

Denis Yuen, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen (+6 others)
2021 Nucleic Acids Research  
Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows.  ...  Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific  ...  support for workflow languages and execution platforms, adding integrations with several open source software development environments (making it easier to write reproducible, well tested workflows),  ... 
doi:10.1093/nar/gkab346 pmid:33978761 fatcat:zwvges37mva2hfc4aaa4w5dkyy
« Previous Showing results 1 — 15 out of 138 results