Expertise: Machine Learning, R, Scientific workflow developement, Workflows, Agronomy, Biostatistics
Teams: NBIS, ERGA Assembly
Organizations: NBIS – National Bioinformatics Infrastructure Sweden
https://orcid.org/0000-0003-1675-0677Expertise: Bioinformatics, Genomics, Scientific workflow developement, Workflows
I'm a bioinformatician for the National Bioinformatics Infrastrure Sweden. I specialise in de novo genome assembly and workflow development with Nextflow. I'm also a Nextflow ambassador and nf-core maintainer.
Teams: CRIM - Computer Research Institute of Montréal
Organizations: CRIM
https://orcid.org/0000-0003-4862-3349Expertise: AI, Machine Learning, Python, Scientific workflow developement, Software Engineering, Workflows, Geospatial, Computer Vision
Tools: CWL, Databases, Jupyter notebook, Python, Workflows, Conda, OGC
Teams: RECETOX SpecDatRI, RECETOX, usegalaxy-eu, ELIXIR Metabolomics
Organizations: Masaryk University, RECETOX
https://orcid.org/0000-0001-6744-996XExpertise: Bioinformatics, Cheminformatics, Metabolomics, Python, R, Software Engineering, Workflows
Tools: Metabolomics, Python, R, Workflows, Mass spectrometry, Chromatography
Teams: Genome Data Compression Team
Organizations: Shenzhen University
https://orcid.org/0009-0007-9672-6728Expertise: Bioinformatics
Tools: Workflows
Teams: FAIR Computational Workflows
Organizations: Telespazio UK
Expertise: Software Engineering, Reproducible Science, ARD (Analysis Ready Data), Data Quality, Space Industry
Tools: Workflows
Ground Segment Architect specialising in Reproducible Science, AI (Artificial Intelligence), ARD (Analysis Ready Data) and Quality initiatives in the space industry. Heavily involved in the architecture of Open Source solutions, frameworks and platforms.
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
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
Nextflow Pipeline for DeepVariant
This repository contains a Nextflow pipeline for Google’s DeepVariant, optimised for execution on NCI Gadi.
Quickstart Guide
- Edit the
pipeline_params.yml
file to include:
samples
: a list of samples, where each sample includes the sample name, BAM file path (ensure corresponding .bai is in the same directory), path to an optional regions-of-interest BED file (set to''
if not required), and the model type.ref
: path to the reference FASTA (ensure ...
Name: PhysioNet CascadeCSVM Kfold Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
Kfold to evaluate CascadeCSVM accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0
Name: PhysioNet kNN Kfold Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
Kfold to evaluate kNN accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0
Name: PhysioNet RF Kfold Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
Kfold to evaluate RandomForest accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0
A R workflow for proteomics data analysis is reported. This pipeline was basing on protein expression projects, stored on the PRIDE database and reported on the COVID-19 Data portal. This is an R pipeline to analyze protein expression data, built on lung cell lines infected by SARS-CoV-2 variants: B.1, Delta, and Omicron BA.1 (Mezler et al. 2023) https://www.ebi.ac.uk/pride/archive/projects/PXD037265. This pipeline can obtain DEPs for each variant, starting from normalized protein expression ...
Name: GridSearchCV Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
GridSearch of kNN algorithm for the iris.csv dataset (https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad21398ea43cba4f7d537619d0e07d5ae3/iris.csv). This application used dislib-0.9.0
Name: GridSearchCV Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
GridSearch of kNN algorithm for the iris.csv dataset (https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad21398ea43cba4f7d537619d0e07d5ae3/iris.csv). This application used dislib-0.9.0
cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls. ...
Name: KMeans Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
KMEans for clustering the housing.csv dataset (https://github.com/sonarsushant/California-House-Price-Prediction/blob/master/housing.csv). This application used dislib-0.9.0
Variant Interpretation Pipeline (VIP) that annotates, filters and reports prioritized causal variants in humans, see https://github.com/molgenis/vip for more information.
Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.
Type: Common Workflow Language
Creators: Aishwarya Iyer, Friederike Ehrhart
Submitter: Aishwarya Iyer
JAX NGS Operations Nextflow DSL2 Pipelines
This repository contains production bioinformatic analysis pipelines for a variety of bulk 'omics data analysis. Please see the Wiki documentation associated with this repository for all documentation and available analysis workflows.
Type: Nextflow
Creators: Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Ardian Ferraj, Anuj Srivastava
Submitter: Michael Lloyd
Name: Incrementation and Fibonacci Access Level: public License Agreement: Apache2 Platform: COMPSs
Description
Brief Overview: Demonstrates COMPSs task parallelism with increment and Fibonacci computations. Helps to understand COMPSs.
Detailed Description:
- Performs multiple increments of input values in parallel using COMPSs.
- Concurrently calculates Fibonacci numbers using recursive COMPSs tasks.
- Demonstrates task synchronization via
compss_wait_on
.
Execution
...
Type: COMPSs
Creators: Ashish Bhawel, Ashish Bhawel, Uploading this Workflow under the guidance of Raül Sirvent.
Submitter: Ashish Bhawel
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