The University of Manchester
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Organizations: The University of Manchester
Teams: IBISBA Workflows
Organizations: The University of Manchester
Teams: IBISBA Workflows, nf-core viralrecon, Testing, Defragmentation TS, EuroScienceGateway, ELIXIR Training
Organizations: The University of Manchester
Teams: Specimen Data Refinery
Organizations: The University of Manchester
Teams: Nick-test-team
Organizations: The University of Manchester
https://orcid.org/0000-0002-2036-8350
Teams: BioBB Building Blocks, UX trial team
Organizations: The University of Manchester
https://orcid.org/0000-0003-2249-645X
Teams: ELIXIR Training
Organizations: The University of Manchester
https://orcid.org/0000-0002-4479-715X
Teams: IBISBA Workflows, GalaxyProject SARS-CoV-2, BioBB Building Blocks, Common Workflow Language (CWL) community, BioExcel Best Practice Guides, Specimen Data Refinery, FAIR Computational Workflows, Vertebrate Genomes Pipelines in Galaxy, TRE-FX, EuroScienceGateway, Biodiversity Genomics Europe (general), BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection, 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 4.1.3.1 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, ELIXIR Training, ELIXIR Tools platform
Organizations: The University of Manchester, ELIXIR-UK
https://orcid.org/0000-0001-9842-9718
Teams: Air Quality Prediction
Organizations: The University of Manchester
Teams: IBISBA Workflows, Test team, EOSC-Life WP3
Organizations: The University of Manchester
Teams: Specimen Data Refinery, Air Quality Prediction
Organizations: The University of Manchester
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/
EOSC-Life brings together the 13 Life Science ‘ESFRI’ research infrastructures (LS RIs) to create an open, digital and collaborative space for biological and medical research.
The project will publish ‘FAIR’ data and a catalogue of services provided by participating RIs for the management, storage and reuse of data in the European Open Science Cloud (EOSC).
Teams: EOSC-Life - Demonstrator 7: Rare Diseases, EOSC-Life WP3
Web page: https://www.eosc-life.eu/
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, 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
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
Team for general BY-COVID contributions
Space: ELIXIR
Public web page: 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
Presentations and events associated with work in FAIR Guiding Principles for Computational Workflows.
Space: ELIXIR
Public web page: https://workflows.community/groups/fair/
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
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
BioDT pipelines not associated with one of the BioDT use cases.
Space: BioDT
Public web page: 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
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
Part of T.4.1.1 Species response to environmental change (UFZ, GBIFS, UKCEH, JYU, MLU)
Space: BioDT
Public web page: 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
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
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
Part of T.4.1.2 Genetically detected biodiversity (GBIFS, UKCEH, UiO)
Space: BioDT
Public web page: Not specified
Part of T.4.1.2 Genetically detected biodiversity (GBIFS, UKCEH, UiO)
Space: BioDT
Public web page: Not specified
Junk/test data
Space: Independent Teams
Public web page: 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
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
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
Space: EOSC-Life
Public web page: Not specified
