ELIXIR-FR/IFB Galaxy News
This page contains announcements of interest to the Galaxy Community. These include items from the Galaxy Team or the Galaxy community and address anything that is of wide interest to the community.
Also see the Galactic Blog for more.
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To add a news item, create a new folder within the news folder with an index.md file. It's probably easiest to copy the format from one of the other existing news items as a template.
| 6 June 2023 | New Paper "An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy" | |
| 6 June 2023 | EU Maintenance Announcement 12th June | EU database maintenance, 8hrs downtime estimated |
| 22 May 2023 | Stronger together: first FAIR-EASE and EuroScienceGateway workshop | Presenting some outcomes from the first joined FAIR-EASE / EuroScienceGateway workshop |
| 21 May 2023 | New Paper "A panel of blood-derived miRNAs with a stable expression pattern as a potential pan-cancer detection signature" | Sabbaghian and colleagues have used the European Galaxy server to study miRNAs as biomarkers for cancer |
| 17 May 2023 | New Galaxy training: Genome-wide alternative splicing analysis | GTN hosts a new training for analyzing alternative splicing at genome-wide scale |
| 8 May 2023 | Replacing the Job Router with Zero Downtime on EU | Mothballing the Sorting Hat – how we migrated our dynamic job routing |
| 6 May 2023 | Galaxy taking part @ Applied Bioinformatics & Public Health Microbiology 2023 | From the 3rd to the 5th of May, Engy Nasr from the Freiburg Galaxy team travelled to Hinxton, England to join and present her work at the Applied Bioinformatics & Public Health Microbiology 2023 conference |
| 5 May 2023 | Joining forces in EOSC: OpenAIRE and EuroScienceGateway sign Memorandum of Understanding | EuroScienceGateway and OpenAIRE team up to enhance accessibility and FAIRness of scientific data from the Galaxy project. |
| 21 April 2023 | You understand the data? Call for action! | Civil disobedience by climate activists is neither futile nor a criminal act statement of scientists says |
| 31 March 2023 | Using Galaxy & TIaaS to teach hands-on genome assembly and annotation | On Feb. 27 to Mar. 3, we (several VGP-associated instructors) used the UseGalaxy EU infrastructure to aid in teaching an online Physalia course of 40+ students how to assemble and annotate their own genome from their browser. |
| 21 March 2023 | Evaluation of the current usage and future needs of Galaxy for microbial data analysis - We Need Your Help! | The microGalaxy community of practice would like to learn more about use-cases where Galaxy was beneficial, and also the barriers that prevent researchers from using Galaxy. The aim is to collectively find solutions to improve user experience and reduce barriers. To this end, we are launching a survey to reach out to, and learn from, the microbial research community. |
| 16 March 2023 | New Paper "Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart" | Siatra et al. have used the European Galaxy server to identify cell populations capable of cardiac regeneration that we will be able to trace and monitor |
| 15 March 2023 | Effortlessly navigate your Galaxy history with enhanced search options | Data searchability in the Galaxy History panel has been taken to new levels with the advanced search options that allow users to not only find items with more ease, but also find relations within items in their history. |
| 14 March 2023 | Enjoy a much faster user interface | Following up on our modernization efforts, we now introduce a single top-router written in Vue, which brings all our Vue components together in a seamless user experience, dramatically reducing the number of required page reloads when navigating the Galaxy user interface. |
| 8 March 2023 | Galaxy Mentor Network: Reset | We launched the [Galaxy Mentor Network](https://galaxy-mentor-network.netlify.app/) one year ago with the idea to onboard new members in the community. Now, one year later, we realize that we failed. We still believe in the power that the Galaxy Mentor Network, and, in that spirit, we would like to relaunch the Galaxy Mentor Network with a new matching process. |
| 5 March 2023 | New Paper "Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness" | Khan et al. present a comparative genome-wide analysis and mode of evolution of Ketoacyl-CoA synthase (KCS) and Elongation Defective Elongase (ELO) gene families |
| 28 February 2023 | New Paper "Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera" | Moris et al. have used the European Galaxy server to exploit the intrasexual CHC dimorphism in a mason wasp, Odynerus spinipes |
| 27 February 2023 | We are striking! | usegalaxy.eu closes job-queue on March 3 to support climate strike |
| 24 February 2023 | New Paper "The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond" | Bray *et al.* outline the implementation and broad range of functionality of Planemo, a software development kit for designing, testing, and executing Galaxy tools, workflows, and training materials. |
| 23 February 2023 | Exporting structured data like RO-Crate or BioComputeObjects | Galaxy has a very powerful and extensible exporting framework that now can export RO-Crate and BioComputeObjects |
| 20 February 2023 | New Paper "Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression" | Broche and colleagues have used the European Galaxy server to analyse the role of m6dA in human DNA |
| 20 February 2023 | TIaaS allows trainees’ jobs to be run preferentially and avoids long execution times, depending on the server load. By providing access to this service, the Galaxy Training Network ensured that TIaaS would be freely available to anyone and facilitated access to an extensive catalogue of FAIR training materials. | |
| 9 February 2023 | New Paper "Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil" | Bertani et al. have used the European Galaxy server to analyse the whole genome sequence of Salmonella Agona carrying blaCTX-M-55 gene |
| 7 February 2023 | Two Horizon Europe projects directed toward the development and deployment of the European Open Science Cloud (EOSC)—FAIR-EASE and EuroScienceGateway (ESG)—have agreed to closely cooperate over the next three years. | |
| 5 February 2023 | How tools are created and maintained in Galaxy | A short summary about Galaxy tools development, maintenance and deployment. |
| 24 January 2023 | GPU-enabled JupyterLab enables interactive AI use-cases in Galaxy | Democratising GPU infrastructures by providing accelerated JuypterLab instances via Galaxy and combining them with HPC workflows |
| 24 January 2023 | Simple and data privacy-aware publishing of genomic variance data from Galaxy to the Beacon project | Galaxy has gained a Beacon integration that enables users to publish genetic variance data conveniently via Beacon project |
| 20 January 2023 | Accessibility in Galaxy 23.0 and beyond | Accessibility improvement Highlights for the upcoming 23.0 release, and a few words on accessibility in general |
| 19 January 2023 | Building a distributed compute network across Europe | The Work Package 3 of the EuroScienceGateway project |
| 12 January 2023 | The Climate community within the EuroScienceGateway project | Climate Community Strategy for Work Package 5 |
| 12 January 2023 | Stimulate FAIR and reusable research with computational workflows | The Work Package 2 of the EuroScienceGateway project |
| 9 January 2023 | The Materials Science community within the EuroScienceGateway project | One of the most recent adopters of the Galaxy platfrom |
| 4 January 2023 | New Paper "Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome" | Akol *et al.* analyzed mouse FOXG1 functions on the chromatin level, having processed the multiomics data set on the European Galaxy server. |
| 3 January 2023 | Galaxy is part of NFDI4Bioimage | |
| 3 January 2023 | New Paper "STAT3 signaling induced by the IL-6 family of cytokines modulates angiogenesis" | Rapp *et al.* investigated on IL-6 cytokines effects on angiogenesis invoking STAT3 signaling pathway, relying on the European Galaxy server |
| 20 December 2022 | New Paper "A panel of blood-derived miRNAs with a stable expression pattern as a potential pan-cancer detection signature" | Sabbaghian et al. used the European Galaxy server to identify the roles of miRNAs in cancer |
| 12 December 2022 | The Astronomy community and the EuroScienceGateway project | Towards harmonizing Open Data Practices in Astronomy with EuroScienceGateway community |
| 8 December 2022 | Building blocks for a sustainable operating model of the EuroScienceGateway | Work Package 4 of the EuroScienceGateway project |
| 8 December 2022 | The Biodiversity community and the EuroScienceGateway project | One of the early adopters to embrace Open Science best practices |
| 30 November 2022 | Slow Storage on EU | Storage bottleneck on usegalaxy.eu results in slow queueing times |
| 24 November 2022 | Introduction to the EuroScienceGateway project administration and project management | Work Package 1 of the EuroScienceGateway project |
| 24 November 2022 | Use-cases from early adopters to embrace Open Science best practices | Work Package 5 of the EuroScienceGateway project |
| 14 November 2022 | BGE - Kickoff meeting | The BGE project kick-off meeting was celebrated between November 14th and November 18th in Leiden. |
| 12 November 2022 | Amazing Twitter Post on Cake-based explanation of single cell RNA sequencing | Combining baking and research |
| 6 November 2022 | EuroScienceGateway - Kickoff meeting | The EuroScienceGateway project started officially with a 2 days kickoff meeting with all 17 partners |
| 5 November 2022 | The start of the EuroScienceGateway - an EOSC project | EuroScienceGateway will deliver a robust, scalable, seamlessly integrated open infrastructure for data-driven research |
| 4 November 2022 | Are you passionate about training in life sciences? The Freiburg Galaxy Team is looking for a team member who will develop, coordinate and implement training programs within international communities, especially via BioNT, a new multi-organization project funded by the European Commission, and via the Galaxy Training Network (GTN). | |
| 1 November 2022 | Impact on Galaxy of OpenSSL 3.0.x Vulnerabilities CVE-2022-3602 and CVE-2022-3786 ("Spooky SSL") | Official severity downgraded to HIGH, exploitability and impact to Galaxy is very low |
| 30 October 2022 | New Paper "Semi-automated assembly of high-quality diploid human reference genomes" | Jarvis et al. determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation |
| 19 October 2022 | Research Data Management in Galaxy | How Galaxy manages your (meta)data |
| 17 October 2022 | Galaxy as a cross-EOSC platform | New scientific collaboration agreement between EOSC-Life and EOSC-Pillar |
| 14 October 2022 | Well-being and Mental Health Guideline | Publication of the Guideline |
| 12 October 2022 | Outcomes of the European Galaxy Days | The European Galaxy Community gathered in Freiburg to discuss recent and future Galaxy developments |
| 30 September 2022 | EOSC4Cancer Kick-off Meeting" | EOSC4Cancer has been launched |
| 28 September 2022 | Introducing the Galaxy Global Hub | Find all your Galaxy info in one website |
| 10 August 2022 | The European Galaxy Team is hiring! | The Freiburg Galaxy Team is looking for a Systems Engineer/DevOps Engineer! |
| 6 July 2022 | New Paper "Creating a good learning and sharing environment for bioinformatics" | Tomas Klingström and J.I. Ohlsson have published a paper about the use of BioContainers, Galaxy, and the GTN for bioinformatics researchers. |
| 27 June 2022 | GCC2022: Registration open for Webinar mode | For those that won't attend in person, the GCC Organizing Committee is happy to announce a virtual webinar-like option |
| 23 June 2022 | Usegalaxy.eu has reached 50,000 registered users | Big thanks to everybody that has contributed to the success of UseGalaxy.eu and to each of the 50K users for using Galaxy! Next stop: 100K! |
| 21 June 2022 | Galaxy taking part @ Elixir All Hands 2022 | During 6-9th of June, members of the European Galaxy team travelled to Amsterdam to join the ELIXIR All Hands meeting 2022 where we joined other colleagues from ELIXIR-DE. |
| 28 April 2022 | Training Infrastructure Feedback from Hans-Rudolf Hotz and Lucille Delisle | After 2 years running the SIB "Galaxy Introduction for Life Scientists" course only online, we were super happy to stand in front of a crowd and meet again the students in person. |
| 20 April 2022 | Towards a sustainable storage, enabling co-financing of public infrastructure | Research groups and networks can include their own storage into the European Galaxy server and decide about quota and data policies. |
| 10 November 2021 | Access data from the GTN in a more accessible, API based way. | |
| 1 October 2021 | Teaching bioinformatics through blood, mucus and tears | Watch out for that My Little Pony baby stroller. |
| 10 September 2021 | Annual reports 2020: ELIXIR and IFB | The ELIXIR and IFB annual reports for 2020 are out, and they highlight Galaxy work throughout. |
| 24 August 2021 | Updates from the ELIXIR Galaxy Community | An updated ELIXIR Galaxy website includes our goals, with a special emphasis on interactions with the local, domain-specific and global communities; plus much more |
| 24 August 2021 | Training Infrastructure as a Service (TIaaS) is sponsored by EOSC-Life | Anyone providing training is eligible to request the use of this service. |
| 13 July 2021 | Highlights from the Galaxy Community Conference 2021 | 399 participants from 55 countries |
| 28 June 2021 | Open Life Science program & the Galaxy community: involvement in OLS-3 and invitation to apply to the next cohort | Open Life Science (OLS) is an online mentoring & training program |
| 28 May 2021 | Webinars: Galaxy Resources for ... | Watch them now. |
| 20 May 2021 | The first Spanish tutorial is live! Galaxy has always had google-translated tutorials, but we are now embarking on a project to assess the learning experience with human-translated, vs google-translated, bioinformatics tutorials. | |
| 14 May 2021 | Two New Teaching Papers using Galaxy | Two hand-in-hand teaching papers have been published this week using Galaxy as a teaching platform. |
| 4 May 2021 | May 2021 Galactic News | GCC2021 and James Taylor Video Deadlines Extended, plus a whole lot more. |
| 4 May 2021 | GCC2021 Abstract and Fellowship Submission, and Early Registration Deadlines Extended | Talks & Fellowships due 17 May; Poster/Demos due 14 June |
| 30 April 2021 | Outcomes of the workshop 'SARS-CoV-2 Data Analysis and Monitoring with Galaxy' | Building capacity, both in the analysis and data management sides of SARS-CoV-2 |
| 19 April 2021 | The Galaxy community involved in several ELIXIR Implementation Studies | |
| 14 April 2021 | GCC2021 Abstract Submission are Open | Abstracts are due May 17 |
| 14 April 2021 | GCC2021 Conference Fellowships | Apply by May 17 |
| 14 April 2021 | GCC2021 Registration is Open | Please join us at Galaxy's annual community gathering |
| 12 April 2021 | April 2021 Galactic News | GCC2021 Abstracts and Registration are open, plus lots more. |
| 17 March 2021 | March 2021 Galactic News | New Featured and Community News sections; new events, releases, training, and lots of videos |
| 16 March 2021 | 2021 Google Summer of Code | Galaxy is participating |
| 10 March 2021 | Successful use cases from EOSC-Life using Galaxy | The first round of EOSC-Life demonstrators has driven eight successful use cases, three of them using Galaxy. |
| 14 February 2021 | Massive open online education party: GTN Smörgåsbord | Starting Monday the 15th of February, the Galaxy Training Network (GTN) is running a global Galaxy online course |
| 8 February 2021 | February 2021 Galactic News | Events, platform news, blog posts, videos, pubs, jobs and releases |
| 4 February 2021 | 2021 Galaxy Community Conference will be virtual, global, and affordable | And globally accessible |
| 30 January 2021 | New and updated CNV and Variant Calling tools | on UseGalaxy.eu and in the Toolshed |
| 22 January 2021 | Variant Analysis of SARS-CoV-2 Sequencing Data (Jan 2021 update) | January 2021 update |
| 18 January 2021 | UseGalaxy.fr is hiring | |
| 7 January 2021 | January 2021 Galactic News | Events, platform news, blog posts, videos, pubs, jobs and releases |
| 22 December 2020 | Open Life Science program & the Galaxy community: involvement in OLS-2 and invitation to apply to the next cohort | involvement in OLS-2 and invitation to apply to the next cohort |
| 8 December 2020 | December 2020 Galactic News | And what a month it is |
| 16 November 2020 | Biohackathon Europe 2020 | The Galaxy community has participated in several projects |
| 3 November 2020 | November 2020 Galactic News | JXTX Foundation, Events, Platforms, Jobs, Pubs, ... |
| 29 October 2020 | The first Paper Cuts Community Fest was a success! | So we will do this again in November! |
| 22 October 2020 | More than 8000 packages/containers in Bioconda/BioContainers from more than 1000 contributors | from 1000+ contributors |
| 22 October 2020 | The EOSC-Life newsletter is out! | Galaxy training, CellProfiler, and more |
| 14 October 2020 | Training Infrastructure Feedback from Leighton Pritchard | Addressing challenges the global coronavirus pandemic |
| 7 October 2020 | October 2020 Galactic News | Events & JTech, platforms, blog posts, tutorials, pubs, releases, ... |
| 23 September 2020 | EOSC-Life Open Calls | Two funding opportunities are now open in EOSC-Life. |
| 1 September 2020 | September 2020 Galactic News | BCC2020 & GCC2021, events, platforms, blog posts, tutorials, pubs, releases, obs ... |
| 22 August 2020 | 3 steps to get your tool into Galaxy - A real-world example | A real-world example |
| 1 July 2020 | July 2020 Galactic News | BCC2020, SRA, Events, Platforms, Training, Jobs, ... |
| 11 June 2020 | June 2020 Galactic News | James Taylor Foundation, BCC2020, Galaxy+SRA, Events, Platforms, ... |
| 4 May 2020 | May 2020 Galactic News | James Taylor, BCC2020, COVID-19 Response, and more |
| 3 April 2020 | James Taylor | 1979 - 2020 |
| 6 March 2020 | de.NBI Training Infrastructure Feedback from Helena Rasche | and was wildly successful |
| 27 February 2020 | TIaaS Calendar and Stats site | Training Infrastructure as a Service |
| 11 February 2020 | Towards a European network of Galaxy resources | |
| 8 January 2020 | January 2020 Galactic News | Events, Pubs, Blogs, Platforms, Tutorials, Doc, and Happy New Year too |
| 8 January 2020 | Galaxy Training Survey | We need your input on preparing and giving Galaxy Trainings |
| 9 December 2019 | December 2019 Galactic News | Events, Pubs, Blogs, Platforms, Tutorials, Doc, Jobs, Releases, and Platypi too. |
| 2 December 2019 | 10,000 users, 6,370,000 jobs and 11,900,000 datasets | A big thank you to all our users and people that have contributed to this project! |
| 12 November 2019 | November 2019 Galactic News | Events! Pubs! Platforms! Jobs! Releases! |
| 2 November 2019 | Training update from Tomas Klingström | Agricultural Sciences collaboration between Swedish University of Agricultural sciences researchers and the Agricultural Research Council in South Africa |
| 2 October 2019 | October 2019 Galactic News | Events! Pubs! Platforms! Jobs! Doc! Tutorials! And some other news too. |
| 30 August 2019 | September 2019 Galactic News | Events! Pubs! Platforms! Jobs! Doc! Tutorials! Releases! And some other news too. |
| 6 August 2019 | Galaxy Community Conference - a brief summary! | A brief summary |
| 1 August 2019 | August 2019 Galactic News | GCC2019 is done; BCC2020 is coming |
| 28 June 2019 | July 2019 Galactic News | GCC2019 is here! (And other new stuff too) |
| 17 June 2019 | TIaaS Queue Status | using UseGalaxy.eu’s Training infrastructure as a Service (TIaaS). |
| 13 June 2019 | Native support for Elixir-AAI in Galaxy v.19.05 | the European Galaxy Server hosted by Elixir Germany is now ready to accept logins from users using their Elixir AAI identity for authentication.. |
| 3 June 2019 | June 2019 Galactic News | GCC2019 registration / Poster/Demo abstracts / sponsors, GTN CoFest, Platforms, Pubs, Jobs, Blog!, Training, Tools, Releases and more! |
| 6 May 2019 | May 2019 Galactic News | GCC2019 registration / Poster/Demo abstracts / sponsors, GTN CoFest, Platforms, Pubs, Jobs, Blog!, Training, Tools, Releases and more! |
| 3 April 2019 | April 2019 Galactic News | GCC2019 registration and abstract submission, Platforms, Pubs, Jobs, Blog!, Training, Tools, Releases and more! |
| 4 March 2019 | March 2019 Galactic News | GalaxyAdmins, GCC2019 Childcare sponsors, Platforms, Pubs, Jobs, Blog!, Training, Tools, Releases and more! |