ELIXIR

Team for general BY-COVID contributions

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 ...

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.

canonical record: https://zenodo.org/records/10405036

Source data (GSE182152) was analysed with WFHub:688 to generate these datasets

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 ...

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 ...

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 ...

Presented at Swedish eResearch Centre meeting, 13 may 2022

Keynote JOBIM 2021 (French Bioinformatics Conference)

FAIR Computational Workflows https://jobim2021.sciencesconf.org/ 8 July 2021

Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for ...

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

So, you want to build a pan-national digital space for bioscience data and methods? That works with a bunch of pre-existing data repositories and processing platforms? So you can share FAIR workflows and move them between services? Package them up with data and other stuff (or just package up data for that matter)? How? WorkflowHub (https://workflowhub.eu) and RO-Crate Research Objects (https://www.researchobject.org/ro-crate) that’s how! A step towards FAIR Digital Objects gets a workout. Keynote ...

Keynote presented at WORKS 2021 https://works-workshop.org/

16th Workshop on Workflows in Support of Large-Scale Science November 15, 2021 Held in conjunction with SC21: The International Conference for High Performance Computing, Networking, Storage and Analysis

Keynote at German Conference on Bioinformatics 2021 https://gcb2021.de/ FAIR Computational Workflows Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the ...

invited presentation at https://researchsoft.github.io/FAIReScience/, FAIReScience 2021 online workshop virtually co-located with the 17th IEEE International Conference on eScience (eScience 2021)

20th Sept 2021

Keynote Presented at the ICTeSSH 2021 Conference to Social Science and Humanities. ICTeSSH 2021, 30th June 2021

https://ictessh.uns.ac.rs/ In data intensive science multi-step tool-chains are widely used to help scientists manage, analyze, and share increasing volumes of complex data. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the exchange of processing know-how, and ...

EOSC-Life 3rd Open Call Biohackathon induction workshop

Reproducibility is a cornerstone of good scientific practice. Thanks to funding provided by ELIXIR Training Platform Task 2, we have brought together the biggest names in bioinformatics workflow management for a 3 day practical workshop. We have presentations from the development teams of CWL, Snakemake, Nextflow, nf-core and more. If you want to learn more about the workflow management concepts that will be addressed in this workshop, check out these articles:

Workflow systems turn raw data into ...

virtually co-located with the 17th IEEE International Conference on eScience (eScience 2021)

This discussion-focused workshop examines how the FAIR (Findable, Accessible, Interoperable, Reusable) principles are and can be applied to eScience research objects beyond data. Invited speakers will present the idea of FAIR and its application to objects such as software, workflows, machine learning models, and executable notebooks, and where FAIR is going. Invited talks will be followed by a panel ...

The public and the press already expect to assess the trustworthiness of research relevant to pressing social and public health issues in terms of transparency. While widely recognized as a critical component of research reproducibility in principle, the promise of making research fully transparent—and scientific claims easier to evaluate—via reliable provenance has yet to be realized in full. In particular, it is still far from routine for researchers in the natural, social, and data sciences ...

The FAIR Principles have two aspects: They were written specifically for research data and they also claim to be general for all research objects. In practice, this means that while the high-level concepts (findable, accessible, interoperable, and reusable) are generally applicable, the details of the wording, their context, and how they are applied is not. Different groups have been studying how the FAIR principles could be applied to other types of research objects, such as research software, ...

Date: Friday 11 June 2021, 10.00 CEST

Chairs: Carole Goble, Stian Soiland-Reyes, Salvador Capella-Gutiérrez, José María Fernández González and Frederik Coppens

In Life Sciences, experimental laboratory procedures usually have a lifespan since their first inception, wide adoption along the years, and later being superseded by others. The same applies to the analysis of the generated experimental data. Workflow Lifecycle represents the different states of workflows during their “life”. This workshop ...

Scientific workflows capture precise descriptions of the steps and data dependencies needed to carry out computational experiments in many areas of Science, ranging from Astrophysics to Bioinformatics or Geosciences. In order to promote long-term usability and uptake by the scientific community, workflows (as well as the tools that integrate them) should become findable, accessible, understandable, reusable, and citable so that author’s credit is attributed fairly and accurately.

The work on ...

In the age of computational science, researchers in the life sciences – just as in other domains – regularly face the need of composing several individual software tools into pipelines or workflows that perform the specific data analysis processes that they need in their research. For over 20 years now, dedicated scientific workflow management systems have been supporting scientists in this task, and they continue to gain popularity. In fact, recent years have seen significant progress in the ...

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

A R workflow for proteomics data analysis is reported. This pipeline was basing on protein expression projects, stored on the PRIDE database and reported on the COVID-19 Data portal. This is an R pipeline to analyze protein expression data, built on lung cell lines infected by SARS-CoV-2 variants: ​B.1, Delta, and Omicron BA.1 (Mezler et al. 2023) https://www.ebi.ac.uk/pride/archive/projects/PXD037265. This pipeline can obtain DEPs for each variant, starting from normalized protein expression ...

High-Performance Computing (HPC) environments are integral to quantum chemistry and computationally intense research, yet their complexity poses challenges for non-HPC experts. Navigating these environments proves challenging for researchers lacking extensive computational knowledge, hindering efficient use of domain specific research software. The prediction of mass spectra for in silico annotation is therefore inaccessible for many wet lab scientists. Our main goal is to facilitate non-experts ...

This workflow provides a calculaiton of the power spectrum of Stochastic Gravitational Wave Backgorund (SGWB) from a first-order cosmological phase transition based on the parameterisations of Roper Pol et al. (2023). The power spectrum includes two components: from the sound waves excited by collisions of bubbles of the new phase and from the turbulence that is induced by these collisions.

The cosmological epoch of the phase transition is described by the temperature, T_star and by the number(s) ...

The tool provides a calculation of the power spectrum of Stochastic Gravitational Wave Backgorund (SGWB) from a first-order cosmological phase transition based on the parameterisations of Roper Pol et al. (2023). The power spectrum includes two components: from the sound waves excited by collisions of bubbles of the new phase and from the turbulence that is induced by these collisions.

The cosmological epoch of the phase transition is described by the temperature, T_star and by the number(s) of ...

Protype demonstrator of a workflow reducing HESS and INTEGRAL/SPI-ACS data to common Light Curve format and combining the lightcurves into a multi-wavelength observation.

Refining Genome Annotations with Apollo

NDVI data with OpenEO to time series visualisation with HoloViz

Calculating and visualizing marine biodiversity indicators

Finding potential muon stopping sites in crystalline copper

From Copernicus Sentinel 5P data to panoply visualization of volcanic activity impact to atmosphere

Functional annotation of protein sequences

Structural and functional genome annotation with Funannotate

Masking repeats in a genome using RepeatMasker

Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA

This portion of the workflow produces sets of feature Counts ready for analysis by limma/etc.