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

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 ...

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

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.

Team for general BY-COVID contributions

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

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

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.

BioDT pipelines not associated with one of the BioDT use cases.

Part of T.4.1.1 Species response to environmental change (UFZ, GBIFS, UKCEH, JYU, MLU)

Part of T.4.1.3 Dynamics and threats from and for species of policy concern (UFZ, GBIFS, Naturalis, UKCEH, LifeWatchERIC)

Part of T.4.1.1 Species response to environmental change (UFZ, GBIFS, UKCEH, JYU, MLU)

Part of T.4.1.4 Species interactions with each other and with humans (GBIFS, UFZ, LifeWatchERIC, UiO)

Part of T.4.1.4 Species interactions with each other and with humans (GBIFS, UFZ, LifeWatchERIC, UiO)

Part of T.4.1.3 Dynamics and threats from and for species of policy concern (UFZ, GBIFS, Naturalis, UKCEH, LifeWatchERIC)

Part of T.4.1.2 Genetically detected biodiversity (GBIFS, UKCEH, UiO)

Part of T.4.1.2 Genetically detected biodiversity (GBIFS, UKCEH, UiO)

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.

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

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 ...

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:

1. To give visibility to the workflows created by the project and by the different networks and communities within the project
2. To give visibility to the workflows used by project that were created
3. To share workflows across the project, within project networks and externally
4. 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:

1. To give visibility to the workflows created by the project and by the different networks and communities within the project
2. To give visibility to the workflows used by project that were created
3. To share workflows across the project, within project networks and externally
4. To credit and cite the people making the workflows and the networks to which they belong
5. To track the versions of ...

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 ...

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.

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 ...

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.

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.

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