SEEK ID: https://workflowhub.eu/people/2
Location: United Kingdom
ORCID: https://orcid.org/0000-0001-9842-9718
Joined: 6th Apr 2020
Expertise: Not specified
Tools: Not specified
Roles
Admin
PAL
- BioDT Use Case 4.1.2.2 DNA detected biodiversity, poorly known habitats
- BioDT Use Case 4.1.2.1 Crop wild relatives and genetic resources for food security
- BioDT Use Case 4.1.3.1 Invasive species
- BioDT Use Case 4.1.3.2 Endangered species
- BioDT Use Case 4.1.4.1 Disease outbreaks
- BioDT Use Case 4.1.4.2 Pollinators
- BioDT Use Case 4.1.1.2 Ecosystem services
Team Administrator
- BioBB Building Blocks
- Common Workflow Language (CWL) community
- BioExcel Best Practice Guides
- Specimen Data Refinery
- Vertebrate Genomes Pipelines in Galaxy
- TRE-FX
- EuroScienceGateway
- Biodiversity Genomics Europe (general)
- BY-COVID (general)
- BioDT additional pipelines
- BioDT Use Case 4.1.1.1 Biodiversity dynamics
- BioDT Use Case 4.1.2.2 DNA detected biodiversity, poorly known habitats
- BioDT Use Case 4.1.2.1 Crop wild relatives and genetic resources for food security
- BioDT Use Case 4.1.3.2 Endangered species
- BioDT Use Case 4.1.4.1 Disease outbreaks
- BioDT Use Case 4.1.4.2 Pollinators
- ELIXIR Tools platform
Asset housekeeper
Asset gatekeeper
Space Administrator
Related items
- Spaces (8)
- Teams (24)
- Organizations (2)
- SOPs (7)
- Publications (8)
- Presentations (5)
- Documents (3)
- Workflows (4+1)
- Collections (6)
Biodiversity Genomics Europe, funded by Horizon Europe call HORIZON-CL6-2021-BIODIV-01-01, aims at aligning the resources and research agendas of both DNA barcoding and reference genome generation, thus opening the door for a true quantum leap in biodiversity genomics research in Europe.
Despite ground-breaking developments in both DNA barcoding and full genome sequencing, there remains a critical need to develop and strengthen functioning communities of practice ...
Teams: Vertebrate Genomes Pipelines in Galaxy, Biodiversity Genomics Europe (general)
Web page: https://biodiversitygenomics.eu/
The Biodiversity Digital Twin prototype provides advanced models for simulation and prediction capabilities, through practical use cases addressing critical issues related to global biodiversity dynamics.
BioDT exploits the LUMI Supercomputer and employs FAIR data combined with digital infrastructure, predictive modelling and AI solutions, facilitating evidence-based solutions for biodiversity protection and restoration.
Funded by Horizon Europe call HORIZON-INFRA-2021-TECH-01-01 101057437, the ...
Teams: BioDT Use Case 4.1.1.2 Ecosystem services, BioDT Use Case 4.1.1.1 Biodiversity dynamics, BioDT Use Case 4.1.2.2 DNA detected biodiversity, poorly known habitats, BioDT Use Case 4.1.2.1 Crop wild relatives and genetic resources for food security, BioDT Use Case 4.1.3.1 Invasive species, BioDT Use Case 4.1.3.2 Endangered species, BioDT Use Case 4.1.4.1 Disease outbreaks, BioDT Use Case 4.1.4.2 Pollinators, BioDT additional pipelines
Web page: https://biodt.eu/
The Distributed System of Scientific Collections is a new world-class Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI aims to create a new business model for one European collection that digitally unifies all European natural science assets under common access, curation, policies and practices that ensure that all the data is easily Findable, Accessible, Interoperable and Reusable (FAIR principles).
DiSSCo represents the largest ever formal agreement between natural ...
Teams: Specimen Data Refinery
Web page: https://www.dissco.eu/
ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers.
The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. Ultimately, it will help them gain new insights into how living ...
Teams: ELIXIR Training, FAIR Computational Workflows, EuroScienceGateway, BY-COVID (general), ELIXIR Tools platform, ELIXIR Metabolomics
Web page: https://elixir-europe.org/
The BeYond-COVID project (BY-COVID) aims to make COVID-19 data accessible to scientists in laboratories but also to anyone who can use it, such as medical staff in hospitals or government officials.
Pursuing to go beyond SARS-CoV-2 data, the project will serve as the groundwork to make data from other infectious diseases open and accessible to everyone.
The BY-COVID project strives to simplify data access and reuse through four key ‘pillars’:
- Mobilise data: ensuring ...
Teams: BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection
Web page: https://by-covid.org/
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, MOLGENIS, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, OLCF-WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF, Jackson Laboratory NGS-Ops, Schwartz Lab, BRAIN - Biomedical Research on Adult Intracranial Neoplasms, Cancer Therapeutics and Drug Safety, Deepdefense, Mid-Ohio Regional Planning Commission, MGSSB, Institute for Human Genetics and Genomic Medicine Aachen, FengTaoSMU, EGA, Plant-Food-Research-Open, KrauthammerLab, Geo Workflows, grassland pDT, FunGIALab, CRIM - Computer Research Institute of Montréal, Medvedeva Lab, Metagenlab, FAIR-EASE, Protein-protein and protein-nucleic acid binding site prediction research, Culhane Lab, IDUN - Drug Delivery and Sensing, Edge Computing DAG Task Scheduling Research Group, Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment, COPO, Taudière group, ErasmusMC Clinical Bioinformatics, interTwin, fluid flow modeling, EnrichDO, WorkflowResearch, Application Security - Test Crypt4GH solutions, RenLabBioinformatics, Yongxin's team
Web page: Not specified
The goal of COVID-19-Biohackathon 2020 (COVID-19-BH20) is to develop and gather computational tools that can be useful for studying the biology of the virus and the disease.
The COVID-19 Programme in Workflow Hub aims to gather workflows for the analysis of COVID-19 molecular biology data and their metadata. In this programme, all workflows and their metadata will be curated and made interoperable, reusable and reproducible. All workflows and their metadata will be easily accessible to everyone ...
Teams: Connor Lab, GalaxyProject SARS-CoV-2, InSaFLU, nf-core viralrecon, CWL workflow SARS-CoV-2, V-Pipe, Test team
Web page: https://github.com/virtual-biohackathons/covid-19-bh20
This is a general team for the BGE project for any members affiliated directly or indirectly with the BGE project.
To request joining this team, make sure sure your WorkflowHub institution matches one of the listed BGE partners.
Space: Biodiversity Genomics Europe (BGE)
Public web page: https://biodiversitygenomics.eu/
Start date: 1st Sep 2022
End date: 28th Feb 2026
Organisms: Not specified
Team for general BY-COVID contributions
Space: ELIXIR
Public web page: Not specified
Organisms: Not specified
EuroScienceGateway will leverage a distributed computing network across 13 European countries, accessible via 6 national, user-friendly web portals, facilitating access to compute and storage infrastructures across Europe as well as to data, tools, workflows and services that can be customized to suit researchers’ needs.EuroScienceGateway will deliver a robust, scalable, seamlessly integrated open infrastructure for data-driven research, contributing an innovative and customizable service for ...
Space: ELIXIR
Public web page: https://eurosciencegateway.eu/
Start date: 1st Oct 2022
End date: 31st Aug 2025
Organisms: Not specified
Presentations and events associated with work in FAIR Guiding Principles for Computational Workflows.
Space: ELIXIR
Public web page: https://workflows.community/groups/fair/
Organisms: Not specified
A team that gathers the workflow and workflow-related training activities related to ELIXIR, run by ELIXIR or affiliated to ELIXIR; its Hub, Nodes, platforms and communities
Space: ELIXIR
Public web page: https://elixir-europe.org
Organisms: Not specified
The ELIXIR Tools Platform helps communities find, register and benchmark software tools. These tools help researchers access, analyse and integrate biological data, and so drive scientific discovery across the life sciences.We maintain information standards for these tools, and produce, adopt and promote best practices for their development.
Space: ELIXIR
Public web page: https://elixir-europe.org/platforms/tools
Organisms: Not specified
BioDT pipelines not associated with one of the BioDT use cases.
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Part of T.4.1.1 Species response to environmental change (UFZ, GBIFS, UKCEH, JYU, MLU)
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Part of T.4.1.3 Dynamics and threats from and for species of policy concern (UFZ, GBIFS, Naturalis, UKCEH, LifeWatchERIC)
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Part of T.4.1.1 Species response to environmental change (UFZ, GBIFS, UKCEH, JYU, MLU)
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Part of T.4.1.4 Species interactions with each other and with humans (GBIFS, UFZ, LifeWatchERIC, UiO)
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Part of T.4.1.4 Species interactions with each other and with humans (GBIFS, UFZ, LifeWatchERIC, UiO)
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Part of T.4.1.3 Dynamics and threats from and for species of policy concern (UFZ, GBIFS, Naturalis, UKCEH, LifeWatchERIC)
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Part of T.4.1.2 Genetically detected biodiversity (GBIFS, UKCEH, UiO)
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Part of T.4.1.2 Genetically detected biodiversity (GBIFS, UKCEH, UiO)
Space: BioDT
Public web page: Not specified
Organisms: Not specified
Workflows from the Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA 1.0) project, which is funded by the European Union Horizon 2020 program INRAIA-02 under grant agreement 730976.
The workflows also appear on https://hub.ibisba.eu
Space: Independent Teams
Public web page: https://www.ibisba.eu
Organisms: Homo sapiens, SARS-CoV-2
Background information
Task 5.2 aims to demonstrate how mobilisation of real-world population, health and care data across national borders can provide answers to policy-relevant research questions. Eventually, it aims to prototype a workflow that is standard for population health research. Here, the research question is approached by identifying a causal effect that allows to evaluate a public health intervention. As such, a methodology for approaching causal inference when conducting ...
Space: BeYond-COVID (BY-COVID)
Public web page: https://doi.org/10.5281/zenodo.7551181
Start date: 13th Oct 2021
End date: 30th Oct 2024
Organisms: SARS-CoV-2
TRE-FX is assembling leading technology providers from ELIXIR-UK and HDR UK, with three TRE providers and two leading analysis platforms to show through a real reference implementation how we can use secure Research Objects to move between TREs while still supporting the Five Safes principles that govern and protect patient data; all overseen by patient representatives.
Space: Independent Teams
Public web page: https://trefx.uk/
Start date: 1st Mar 2023
End date: 31st Oct 2023
Organisms: Not specified
Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org
Space: COVID-19 Biohackathon
Public web page: https://github.com/galaxyproject/SARS-CoV-2
Organisms: Homo sapiens, SARS-CoV-2
The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database
Space: Biodiversity Genomics Europe (BGE)
Public web page: https://galaxyproject.org/projects/vgp/workflows/
Organisms: Not specified
If your research project is producing workflows, they should be registered 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
- To share workflows across the project, within project networks and externally
- To credit and cite the people making the workflows, and the networks to which they belong
- To track the new versions of workflows as they are ...
Creators: Stian Soiland-Reyes, Carole Goble, Finn Bacall, Johan Gustafsson, Rafael Andrade Buono
Submitter: Stian Soiland-Reyes
This is a project specific guide for the Bioiversity Genomics Europe (BGE project use of WorkflowHub.
The BioDT 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 networks to which they ...
The BY-COVID project is producing 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 networks to which they belong
- To track the versions of ...
Creators: Carole Goble, Finn Bacall, Stian Soiland-Reyes, Andrew Stubbs, Helena Rasche
Submitter: Stian Soiland-Reyes
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
Tutorial and specification for packaging IEEE 2791-2020 (BioCompute Objects/BCOs) as RO-Crate Research Objects.
BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.
RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.
BCO RO-Crate is the combination ...
Creators: Stian Soiland-Reyes, Jonathon Keeney, Hadley King, Janisha Patel, Alex Coleman
Submitter: Stian Soiland-Reyes
This BioExcel best practice guide outlines the development process for writing a workflow using the Common Workflow Language (CWL), from creating and selecting tools like BioBB, through early experimentation, reuse and testing, to optimization and ensuring reproducibility before publication in workflow repositories.
Creators: Stian Soiland-Reyes, Douglas Lowe, Robin Long
Submitter: Stian Soiland-Reyes
Abstract (Expand)
Authors: Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble
Date Published: 24th Mar 2022
Publication Type: Journal
DOI: 10.1371/journal.pcbi.1009823
Citation: PLoS Comput Biol 18(3):e1009823
Abstract (Expand)
Authors: Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes
Date Published: 7th Mar 2022
Publication Type: Journal
DOI: 10.1162/dint_a_00134
Citation: Data Intelligence:1-19
Abstract (Expand)
Authors: Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Ilkay Altintas, Rosa M Badia, Bartosz Balis, Taina Coleman, Frederik Coppens, Frank Di Natale, Bjoern Enders, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Daniel Garijo, Carole Goble, Dorran Howell, Shantenu Jha, Daniel S. Katz, Daniel Laney, Ulf Leser, Maciej Malawski, Kshitij Mehta, Loic Pottier, Jonathan Ozik, J. Luc Peterson, Lavanya Ramakrishnan, Stian Soiland-Reyes, Douglas Thain, Matthew Wolf
Date Published: 1st Nov 2021
Publication Type: Journal
DOI: 10.1109/WORKS54523.2021.00016
Citation: 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS),pp.81-90,IEEE
Abstract (Expand)
Authors: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Carole Goble
Date Published: 14th May 2021
Publication Type: Unpublished
Citation: arXiv 2105.07028 [cs.DC]
Abstract (Expand)
Authors: Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital
Date Published: 7th Mar 2021
Publication Type: Journal
DOI: 10.1162/dint_a_00135
Citation:
Abstract (Expand)
Authors: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft
Date Published: 2021
Publication Type: Journal
DOI: 10.12688/f1000research.54159.1
Citation: F1000Res 10:897
Abstract (Expand)
Authors: Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
Date Published: 2020
Publication Type: Journal
DOI: 10.1162/dint_a_00033
Citation: Data Intellegence 2(1-2):108-121
Abstract (Expand)
Authors: Pau Andrio, Adam Hospital, Javier Conejero, Luis Jordá, Marc Del Pino, Laia Codo, Stian Soiland-Reyes, Carole Goble, Daniele Lezzi, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpi
Date Published: 1st Dec 2019
Publication Type: Journal
DOI: 10.1038/s41597-019-0177-4
Citation: Sci Data 6(1),169
To make your workflow FAIR (Findable, Accessible, Interoperable, Reusable), register it in WorkflowHub, a workflow registry with rich metadata capture for workflow discovery and sharing, and value-added services, for workflow testing (LifeMonitor), execution and publication.
The EuroScienceGateway, Biodiversity Genomics Europe and BioDT projects will use WorkflowHub to organise, share and publish their workflows.
This was Ask Me Anything and Bring Your Own Workflow (AMA & BYOW) specifically ...
Creators: Nick Juty, Finn Bacall
Submitter: Stian Soiland-Reyes
EOSC-Life FAIR hackathon 2021 Session 3: Workflow & Tools FAIRification
Creators: Carole Goble, Stuart Owen, Simone Leo, Finn Bacall, Stian Soiland-Reyes, Douglas Lowe
Submitter: Carole Goble
BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.
RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.
BCO RO-Crate is the combination of these two approaches, packaging a BCO and the workflow it describes in a RO-Crate.
This webinar describes ...
Creator: Stian Soiland-Reyes
Submitter: Stian Soiland-Reyes
Presented at the BioExcel Summer School 2021 this lecture introduces the BioExcel Building Blocks (BioBB).
See also part 2.
Creators: Adam Hospital, Pau Andrio, Genís Bayarri
Submitter: Stian Soiland-Reyes
Presented at the BioExcel Summer School 2021 this lecture shows how to use BioExcel Building Blocks (BioBB).
See also part 1.
Creator: Adam Hospital
Submitter: Stian Soiland-Reyes
The results of the mentimeter for the FAIR workflows section of the EOSC-Life 3rd Open Call projects pre-hackathon induction
Creators: Carole Goble, Stian Soiland-Reyes, Stuart Owen, Finn Bacall, Simone Leo, Douglas Lowe
Submitter: Carole Goble
This BioExcel best practice guide discusses the workflow engines available for the Common Workflow Language (CWL).
Creators: Robin Long, Douglas Lowe, Stian Soiland-Reyes
Submitter: Stian Soiland-Reyes
In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields ...
Creators: Pau Andrio, Genís Bayarri, Adam Hospital
Submitter: Stian Soiland-Reyes
rquest-omop-worker-workflows
Source for workflow definitions for the open source RQuest OMOP Worker tool developed for Hutch/TRE-FX
Note: ARM workflows are currently broken. x86 ones work.
Inputs
### Body Sample input payload:
{
"task_id": "job-2023-01-13-14: 20: 38-",
"project": "",
"owner": "",
"cohort": {
"groups": [
{
"rules": [
{
"varname": "OMOP",
"varcat": "Person",
"type": "TEXT",
"oper": "=",
"value": "8507"
}
],
"rules_oper": "AND"
}
],
"groups_oper": "OR"
},
"collection":
...
Type: Common Workflow Language
Creator: Vasiliki Panagi
Submitters: Stian Soiland-Reyes, Vasiliki Panagi, Jon Couldridge
Type: Common Workflow Language
Creators: Pjotr Prins, Andrea Guarracino, Peter Amstutz, Thomas Liener, Adam M. Novak, Bonface Munyoki, Tazro Inutano, Michael Heuer, Michael R. Crusoe, Stian Soiland-Reyes
Submitter: Michael R. Crusoe
This is an experimental KNIME workflow of using the BioExcel building blocks to implement the Protein MD Setup tutorial for molecular dynamics with GROMACS.
Note that this workflow won't import in KNIME without the experimental KNIME nodes for BioBB - contact Adam Hospital for details.
This PyCOMPSs workflow tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.
Workflows developed by or used by BY-COVID project.
Collection of workflows used or developed by the EuroScienceGateway project.
This is a general collection of workflows used by or developed by members of the BGE project.
The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database.
Selection of BioExcel Building Blocks (BioBB) Workflows, across three workflow languages (jupyter notebooks, CWL, and Galaxy), demonstrating the use of BioBB tool descriptors for each of these systems.
Maintainers: Douglas Lowe, Stian Soiland-Reyes, Adam Hospital, Genís Bayarri, Pau Andrio
Number of items: 5
Tags: Not specified
Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.