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 ...

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.

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 ...

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.

Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org

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

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

The SDR is concerned with digitisation pipelines for digital access to natural history collections

The SDR integrate machine learning, Artificial Intelligence, and human approaches to extract, enhance, and annotate data from digital images and records at scale. Many collections-holding institutions still need to digitise the bulk of their collections. Digitisation takes time and resources. One of the major challenges in digitising massive collections is finding ways of ensuring high-quality ...

Presentations and events associated with work in FAIR Guiding Principles for Computational Workflows.

Team developing BioExcel best practice guides

The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, High Energy Physics, and Machine Learning.CWL is developed by a multi-vendor working group consisting ...

The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...

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 ...

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.

EOSC-Life FAIR hackathon 2021 Session 3: Workflow & Tools FAIRification

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 ...

Presented at the BioExcel Summer School 2021 this lecture introduces the BioExcel Building Blocks (BioBB).

See also part 2.

Presented at the BioExcel Summer School 2021 this lecture shows how to use BioExcel Building Blocks (BioBB).

See also part 1.

The results of the mentimeter for the FAIR workflows section of the EOSC-Life 3rd Open Call projects pre-hackathon induction

This BioExcel best practice guide discusses the workflow engines available for the Common Workflow Language (CWL).

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 ...

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":
...

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.

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.

Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.