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).
Web page: https://www.eosc-life.eu/
Funding details:Related items
Teams: IBISBA Workflows, nf-core viralrecon, Testing, Defragmentation TS, EuroScienceGateway, ELIXIR Training
Organizations: The University of Manchester
Teams: EOSC-Life WP3
Organizations: CCMAR
Teams: GalaxyProject SARS-CoV-2, nf-core viralrecon, EOSC-Life - Demonstrator 7: Rare Diseases, iPC: individualizedPaediatricCure, EJPRD WP13 case-studies workflows, TransBioNet, OpenEBench, ELIXIR Proteomics
Organizations: Barcelona Supercomputing Center (BSC-CNS), ELIXIR
https://orcid.org/0000-0003-4929-1219Expertise: Bioinformatics, Computer Science, AI, Machine Learning
Computer Engineer in Barcelona Supercomputing Center (BSC)
Teams: IBISBA Workflows, EOSC-Life WP3, NGFF Tools, Euro-BioImaging, AI4Life OC
Organizations: Unspecified, EMBL-EBI, Euro-BioImaging
https://orcid.org/0000-0002-5862-6132Expertise: image analysis
Teams: EOSC-Life WP3 OC Team, cross RI project, EOSC-Life WP3, Euro-BioImaging
Organizations: EOSC-Life, Euro-BioImaging
Expertise: Bioengineering, Bioinformatics, Computer Science, Data Management
Tools: Databases, Jupyter notebook, Python
Biomedical Engineer working on preclinical image dataset repository and cross researching RIs
Teams: IBISBA Workflows, Test team, EOSC-Life WP3
Organizations: The University of Manchester
Space: EOSC-Life
Public web page: Not specified
Organisms: Not specified
An integrative analysis pipeline of genomic and transcriptomic human data for disentangling the genetic origin of a rare-disease in the context of the European Open Science Cloud.
Space: EOSC-Life
Public web page: https://www.eosc-life.eu/services/demonstrators/
Organisms: Not specified
This workflow has been created as part of Demonstrator 6 of the project EOSC-Life (within WP3) and is focused on reusing publicly available RNAi screens to gain insights into the nucleolus biology. The workflow downloads images from the Image Data Resource (IDR), performs object segmentation (of nuclei and nucleoli) and feature extraction of the images and objects identified.
Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.
This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...
Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.
This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...
Type: Common Workflow Language
Creators: José Mª Fernández, Laura Rodriguez-Navas
Submitter: Laura Rodriguez-Navas