Expertise: High Performance Computing, Scientific workflow developement, Software Engineering, astronomy
Tools: Galaxy, Jupyter notebook, Python, Workflows, Git
Teams: Chemical Data Lab
Organizations: Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc
https://orcid.org/0000-0003-0285-6948Expertise: Cheminformatics
Tools: Jupyter notebook, Python, R, Workflows
Teams: Cluster Emergent del Cervell Humà, Workflows and Distributed Computing, WP6 - Tsunamis, WP7 - Earthquakes, WP8 - Anthropogenic geophysical extremes, WP5 - Volcanoes, Pillar I: Manufacturing, Pillar II: Climate, Pillar III: Urgent computing for natural hazards, eFlows4HPC general, COMPSs Tutorials
Organizations: Barcelona Supercomputing Center (BSC-CNS)
https://orcid.org/0000-0003-0606-2512Expertise: Workflows, Programming Models, High Performance Computing, Distributed Computing, Provenance
Tools: COMPSs
Established Researcher at Workflows and Distributed Computing Group, Computer Sciences department, Barcelona Supercomputing Center.
Expertise: Bioinformatics, Genomics, Metagenomics, Data Management
Tools: CWL, Jupyter notebook, Nextflow, Molecular Biology, Workflows, Microbiology, Transcriptomics, Perl, Python, R
Teams: EU-Openscreen
Organizations: Fraunhofer Institute for Translational Medicine and Pharmacology ITMP
https://orcid.org/0000-0002-8080-9170Expertise: Bioinformatics, Cheminformatics, Machine Learning
Tools: Workflows
Expertise: Metagenomics
Expertise: Bioinformatics, Computer Science, Data Management, Genetics, Genomics, Machine Learning, Metagenomics, NGS, Scientific workflow developement, Software Engineering
Tools: Databases, Galaxy, Genomics, Jupyter notebook, Machine Learning, Nextflow, nf-core, PCR, Perl, Python, R, rtPCR, Snakemake, Transcriptomics, Virology, Web, Web services, Workflows
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Teams: EU-Openscreen, OME
Organizations: Fraunhofer Institute for Translational Medicine and Pharmacology ITMP
https://orcid.org/0000-0002-1740-8390Expertise: Cheminformatics, Bioinformatics
Teams: MAB - ATGC
Organizations: Centre National de la Recherche Scientifique (CNRS)
https://orcid.org/0000-0003-3791-3973Expertise: Bioinformatics, Genomics, algorithm, Machine Learning, Metagenomics, NGS, Computer Science
Tools: Transcriptomics, Genomics, Python, C/C++, Web services, Workflows
Expertise: Bioinformatics, Biostatistics, Metabarcoding, Metagenomics
Teams: Harkany Lab
Organizations: Medical University of Vienna
https://orcid.org/0000-0001-5920-2190Expertise: Systems Biology, Bioengineering, Bioinformatics, Neuroscience
Tools: Workflows, Machine Learning, Transcriptomics
Expertise: Bioinformatics
Bioinformatician in Stockholm, Sweden. Lead for nf-core and MultiQC projects.
Teams: V-Pipe
Organizations: SIB - Swiss Institute of Bioinformatics
https://orcid.org/0000-0002-7561-0810Expertise: Bioinformatics, Software Engineering
Medical doctor and bioinformatician
Developer from the Swiss Institute of Bioinformatics (SIB) Working at the Computational Biology Group (CBG) of ETH Zurich.
Diplom in Medicine. MSc in Bioinformatics and Proteomics.
I am also a ski teacher as a hobby.
Teams: IBISBA Workflows
Organizations: Unspecified
Expertise: Bioinformatics
Tools: Workflows, Web services, Python
Teams: GalaxyProject SARS-CoV-2
Organizations: BC Centre for Disease Control
https://orcid.org/0000-0002-6178-3585Expertise: Bioinformatics, Data Management, Molecular Biology
Tools: Databases, PCR, Workflows, Web services
The EuroScienceGateway project is producing and maintaining workflows. We need to register those workflows in WorkflowHub:
- To give visibility to the workflows created by the project and by the different networks and communities within the project
- To give visibility to the workflows used by project that were created
- To share workflows across the project, within project networks and externally
- To credit and cite the people making the workflows and the ...
Creators: Stian Soiland-Reyes, Carole Goble, Finn Bacall
Submitter: Stian Soiland-Reyes
Provenance registration is becoming more and more important, as we increase the size and number of experiments performed using computers. In particular, when provenance is recorded in HPC environments, it must be efficient and scalable. In this paper, we propose a provenance registration method for scientific workflows, efficient enough to run in supercomputers (thus, it could run in other ...
Creator: Raül Sirvent
Submitter: Raül Sirvent
Keynote Presented at the ICTeSSH 2021 Conference to Social Science and Humanities. ICTeSSH 2021, 30th June 2021
https://ictessh.uns.ac.rs/ In data intensive science multi-step tool-chains are widely used to help scientists manage, analyze, and share increasing volumes of complex data. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the exchange of processing know-how, and ...
Creator: Carole Goble
Submitter: Carole Goble
Keynote JOBIM 2021 (French Bioinformatics Conference)
FAIR Computational Workflows https://jobim2021.sciencesconf.org/ 8 July 2021
Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for ...
Creator: Carole Goble
Submitter: Carole Goble
Calculates the Fibonacci series up to a specified length.
Type: COMPSs
Creator: Uploading this Workflow under the guidance of Raül Sirvent.
Submitter: Ashish Bhawel
ANNOTATO - Annotation workflow To Annotate Them Oll
Summary
This pipeline contains the following functions: (1) Data processing to handle the tansformations needed to obtain the original pathway scores of the samples according to single sample analysis GSEA (2) Model training based on the disease and healthy sample pathway scores, to classify them (3) Scoring matrix weights optimization according to a gold standard list of drugs (those that went on clinical trials or are approved for the disease).It tests the weights in a range of 0 to 30 (you ...
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...
Type: Common Workflow Language
Creators: Ekaterina Sakharova, Varsha Kale, Martin Beracochea, Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea