A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Abstract Summary Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA. The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission. A Galaxy wrap of the tool allows users with little or no bioinformatic knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment. Availability CLI ENA upload tool is available at github.com/usegalaxy-eu/ena-upload-cli (DOI 10.5281/zenodo.4537621); Galaxy ENA upload tool at toolshed.g2.bx.psu.edu/view/iuc/ena_upload/382518f24d6d and https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload (development) and; ENA upload Galaxy container at github.com/ELIXIR-Belgium/ena-upload-container (DOI 10.5281/zenodo.4730785) </jats:sec

Galaxy Training: A powerful framework for teaching!

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments

ELIXIR Toolkit Theme - Create a modern looking knowledge base using GitHub and Jekyll.

&lt;p&gt;Poster on the ELIXIR Toolkit Theme presented at the ELIXIR Belgium Conference, 2023: "ELIXIR Belgium: Your data, Our services, European success".&lt;/p&gt

ENA Data Submission Toolbox - submitting raw sequencing reads, assemblies and respective metadata to the European Nucleotide Archive (ENA)

&lt;p&gt;Poster on the ENA Data Submission Toolbox presented at the ELIXIR Belgium Conference, 2023: "ELIXIR Belgium: Your data, Our services, European success".&lt;/p&gt

ELIXIR-Belgium/elixir-toolkit-theme: 2.3.0 - Hide sidebar and integrated country support

What's Changed Add hide sidebar function by @bedroesb in https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/pull/205 Update countries automatically by @bedroesb in https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/pull/206 Fix topnav highlight bug when toc: false by @bedroesb in https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/pull/208 Full Changelog: https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/compare/2.2.2...2.3.

ELIXIR-Belgium/elixir-toolkit-theme: 2.4.0 - Support for custom headings

&lt;h2&gt;What's Changed&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;Add support for custom headings by @bedroesb in https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/pull/212&lt;/li&gt; &lt;li&gt;Update Bootstrap to 5.3.2 and fix warning in build by @bedroesb in https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/pull/213&lt;/li&gt; &lt;li&gt;Only show pagination and search in datatables when relevant by @bedroesb in https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/pull/214&lt;/li&gt; &lt;/ul&gt; &lt;h3&gt;:rotating_light: &lt;strong&gt;BREAKING&lt;/strong&gt; :rotating_light:&lt;/h3&gt; &lt;p&gt;The variables to specify the min of headings that need to appear for the table of contents to show up and what type it has to pick up is changed from &lt;code&gt;headers&lt;/code&gt; -&gt; &lt;code&gt;headings&lt;/code&gt; to be consistent and more correct.&lt;/p&gt; &lt;pre&gt;&lt;code class="language-yml"&gt;theme_variables: toc: min_headings: 2 headings: 'h2' &lt;/code&gt;&lt;/pre&gt; &lt;p&gt;&lt;strong&gt;Full Changelog&lt;/strong&gt;: https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/compare/2.3.0...2.4.0&lt;/p&gt

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA. The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission. A Galaxy wrap of the tool allows users with little or no bioinformatic knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment

ro-crate-py 0.8.0:RO-Crate metadata generator/parser

What's Changed Test to check the performance of adding a data entity by @simleo in https://github.com/ResearchObject/ro-crate-py/pull/134 Fix missing file by @simleo in https://github.com/ResearchObject/ro-crate-py/pull/136 Fix typos in notebooks by @kinow in https://github.com/ResearchObject/ro-crate-py/pull/144 Fix typo on README by @kinow in https://github.com/ResearchObject/ro-crate-py/pull/145 Add Autosubmit language by @kinow in https://github.com/ResearchObject/ro-crate-py/pull/143 Add methods for adding and updating JSON-LD directly (partials for WMS) by @kinow in https://github.com/ResearchObject/ro-crate-py/pull/149 Remove version from ComputerLanguage by @simleo in https://github.com/ResearchObject/ro-crate-py/pull/150 Add add_tree method by @simleo in https://github.com/ResearchObject/ro-crate-py/pull/151 Remove engine version default by @simleo in https://github.com/ResearchObject/ro-crate-py/pull/152 New Contributors @kinow made their first contribution in https://github.com/ResearchObject/ro-crate-py/pull/144 Full Changelog: https://github.com/ResearchObject/ro-crate-py/compare/0.7.0...0.8.0Cite a

ELIXIR biovalidator for semantic validation of life science metadata

SUMMARY: To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents. AVAILABILITY AND IMPLEMENTATION: Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

EOSC-Life Workflow Collaboratory for the Life Sciences

Workflows have become a major tool for the processing of Research Data, for example, data collection and data cleaning pipelines, data analytics, and data update feeds populating public archives. The EOSC-Life Research Infrastructure Cluster project brought together Europe’s Life Science Research Infrastructures to create an Open, Digital and Collaborative space for biological and medical research to develop a cloud-based Workflow Collaboratory. As adopting FAIR practices extends beyond data, the Workflow Collaboratory drives the implementation of FAIR computational workflows and tools. It fosters tool-focused collaborations and reuse via the sharing of data analysis workflows and offers an ecosystem of services for researchers and workflow specialists to find, use and reuse workflows. It’s web-friendly Digital Object Metadata Framework, based on RO-Crate and Bioschemas, supports the description and exchange of workflows across the services