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The ERGA Knowledge Hub  is live! The main goal of this new portal is to gather and share educational materials on genomics and related topics, lowering access barriers and promoting knowledge exchange across Europe and beyond. Links to various types of training materials are available in the Hub, including lectures PDFs, videos, GitHub pages, interactive content. The Hub will collect content covering all steps relevant to production and application of reference genomes and genomic data  - from data generation and analysis to the ethical and social aspects that the workflow entails. This collection of educational materials is built based on the community’s input and everyone is welcome to submit their own educational materials or those from others - as long as a licence that allows free distribution and sharing with or without accreditation is provided. All the material available in the Hub is curated by a team of ERGA committee coordinators, ensuring the high quality of the content.  The ERGA Knowledge Hub was made possible thanks to Biodiversity Genomics Europe  (BGE) funded by the European Union under the Horizon Europe research and innovation program, co-funded by the Swiss and British governments. The portal was developed by the ERGA Training & Knowledge transfer Committee  in collaboration with the Swiss Institute for Bioinformatics.  Contribute! To submit a link to the collection, you just need to click on “ Contribute !” on the upper right corner of the Knowledge Hub.  You’ll need to select the type of license associated with this resource - if no licensing information is available on the page, you can try contacting the authors and ask if they agree to have their materials linked in the Hub. ⏯️ To learn more about the ERGA Knowledge Hub watch the Camila Mazzoni's presentation introducing the Hub to the Earth Biogenome Community: -- If you have any questions or suggestions related to the ERGA Knowledge Hub, please contact us at training@erga-biodiversity.eu.

June saw the annual meeting of Galaxy  developers and users at the Galaxy Community Conference 2024  in Brno, Czechia. This year over 150 participants came together to share updates to the Galaxy platform and present use-cases showing how Galaxy has enabled high-quality science through providing computational infrastructure and software support. Galaxy has established open computational servers in the United States , Europe  and Australia  alongside a suite of tools to give scientists the opportunity to process and analyse data of any size without the need to establish or use a local High Performance Computing service.  During the 4-day conference ERGA, the Vertebrate Genomes Project  and the wider Earth BioGenome Project  were well-represented, demonstrating how Galaxy fits into a distributed model of reference genome generation. Updates to the VGP pipeline were presented by Delphine Lariviere and Linelle Abueg, showcasing how they have used a Galaxy server at the Vertebrate Genomes Lab to assemble over 150 species. They also introduced the efforts made to assist manual curation of the assemblies.  The VGP uses their published pipelines and training material to give instructional workshops on how anyone can use Galaxy to assemble a genome without access to an HPC or even needing to install any software. Within the ERGA framework, Tom Brown presented how collaborators from Galaxy EU are helping ERGA to establish a review system for genome assembly via the ERGA Assembly Report ( EAR ) and assist the genome annotation community in installing necessary tools and developing workflows that enable researchers to annotate their favourite genome using best-practice tools and pipelines. You can learn more about the VGP’s efforts to assemble vertebrate genomes in their paper published in Nature Biotechnology  and read about ERGA’s efforts to benchmark annotation tools and workflows on a diverse range of organisms in their report from last year’s BioHackathon Europe . Click to check the poster and slides presented at the conference: The Galaxy Community Conference 2024 presented a fantastic opportunity for developers, systems administrators and researchers from the genomics, astronomy and material science communities to come together and hear about the latest advancements in Galaxy and its uses. Many thanks to the organisers and especially Björn Grüning and Anton Nekrutenko for their support given to the biodiversity genomics community. About the Author Tom Brown is the coordinator of the ERGA IT & Infrastructure Committee and also participates in the ERGA Sequencing & Assembly and Annotation Committees .

Dozens of scientific institutions and laboratories open their doors and invite visitors to discover their current research by interacting with scientists in an informal, playful atmosphere - that’s the spirit of the Lange Nacht der Wissenschaften  (“Long Night of Science”) which happens every summer in Berlin. On Saturday, June 22nd, 2024, Biodiversity Genomics Europe and ERGA participated in the event for the first time with a stand organised by the BGE team from the Leibniz Institute for Zoo and Wildlife Research  at Haus der Leibniz-Gemeinschaft in the heart of the German capital. Our main goal was to spread information about BGE and the European Reference Genome Atlas  (ERGA), highlighting the urgent need for conservation efforts for European species and discussing how state-of-the-art genomic technologies are helping to improve our understanding of biodiversity and advance its protection. We developed an interactive guessing game that allowed visitors to test their knowledge about some of the species that are having their genomes sequenced by BGE - with a particular focus on those of conservation concern.  Some snapshots of a very busy evening at the Haus der Leibniz-Gemeinschaft. You can find more photos of other activities here . Photos: Donat Agosti and Diego de Panis The board game attracted visitors of all ages - including families with children, young adults, and senior citizens - through the duration of the event and promoted an exciting dialogue with this varied audience. “When I think of corals, I immediately picture Australia. I had no idea such beautiful species were also present here in Europe!” - said one of the visitors, referring to the Yellow Gorgonian ( Eunicella cavolini), a common species in the Mediterranean Sea classified as “Near Threatened” by the International Union for Conservation of Nature (IUCN).   Another case that surprised the visitors was the charismatic and critically endangered European mink ( Mustela lutreola ). Once widespread in Europe, its range has suffered a drastic reduction by over 85% since the mid-19th century due to habitat loss and illegal hunting. Only a few fragmented populations still exist and its genome, sequenced as part of the ERGA Pilot project, will bring insights that can support and guide management and conservation actions. The Yellow Gorgonian coral, the Spanish moon moth and European White Elm illustrate the broad diversity of species sequenced by BGE and ERGA.  Photos: albert kok, CC BY-SA 3.0 , via Wikimedia Commons ;  Banco de imágenes del CNICE - MEC, CC BY-SA 2.5 ES, via Wikimedia Commons; Christian Fischer, CC BY-SA 4.0 , via Wikimedia Commons. Many other fascinating species captivated the audience, such as the smallest bat species found in Europe ( Pipistrellus hanaki), the beautiful Spanish Moon moth ( Graellsia isabellae ), and the gigantic European White Elm . The   Long Night of Science offered a great opportunity to reach out to citizens and tell them a bit about what we do at BGE and ERGA and why. Science communication events like this one are a rewarding two-way street, allowing us to learn from each other and gather diverse perspectives that guide us forward as a community of researchers, advancing and advocating for the development of biodiversity genomics in Europe. We thank everyone who stopped by our stand and the organisers of this year’s Long Night of Science and look forward to participating again next year! — About I’m Luísa Marins, and I coordinate communication actions for the European Reference Genome Atlas. If you want to know more about this event or the game, or if you would like help organizing a similar stand or any ERGA/BGE outreach activity across Europe, please reach out to media@erga-biodiversity.eu . References https://www.iucnredlist.org/species/50012182/50606230 https://www.berlin.de/en/events/2096550-2842498-long-night-of-the-sciences.en.html https://globalconservation.org/endangered-species/european-mink

ERGA, in collaboration with the Global Genome Biodiversity Network (GGBN) and the Earth Biogenome Project (EBP), held a webinar on Access and Benefit Sharing (ABS) with a special focus on the Nagoya Protocol on April 8th, 2024. We organized this seminar in response to frequent questions from the ERGA community regarding this topic, which highlights its complexity and relevance. ERGA’s goal for this seminar was to enhance understanding and provide clarity on ABS regulations, especially in relation to the Nagoya Protocol, an agreement that governs the fair and equitable distribution of profits arising from the utilization of genetic resources. The main speaker, Scarlett Sett (CSIRO ACDP), delivered an outstanding presentation, shedding light on the complexities and necessities of ABS in biodiversity research. The event was a success with over 90 participants from 29 countries around the world. Participating researchers from a few countries were working with genetic samples originating from over 50 different countries. This underscores the global nature of biodiversity research and highlights the critical need for clear and effective ABS regulations. However, the seminar also revealed that the bureaucracy associated with these regulations can significantly slow down research projects. This is particularly concerning during this period of the sixth mass extinction when swift scientific progress is essential. While the seminar focused on raising these challenges, it set the stage for future discussions on how to streamline bureaucratic processes without compromising the Nagoya Protocol goals. We recognised the necessity of highlighting the concrete benefits of the Nagoya Protocol for researchers, local communities, indigenous people, and stakeholders. Europe lacks comprehensive information on these benefits. We encourage the community to share their insights and experiences regarding the positive impacts of the Nagoya Protocol: How has it benefited your research, local communities, or indigenous groups in Europe? What successes or improvements have you witnessed? If you have insights or data on these benefits, please contact us at elsi@erga-biodiversity.eu . Your contributions can help demonstrate the value of ABS regulations and support ongoing research and conservation efforts globally. The benefit should outweigh the bureaucratic burden, which has been highlighted by Italian researchers' negative experiences: “Italy adhered to the Nagoya Protocol on June 23, 2011, at the same time as the European Union and 11 of its member states. Although the Nagoya Protocol entered into force on October 12, 2014, coinciding with the holding of COP 12 of the Convention of Biological Diversity (CBD), Italy has not yet ratified the Protocol. As a result, as of today, access to all genetic resources present on Italian soil is not regulated, meaning that any violation of the Nagoya Protocol does not result in any legal prosecution. As the Nagoya Protocol has not yet been ratified, researchers are facing challenges in complying with the principles of Access and Benefit Sharing (ABS), challenges that are further exacerbated by the absence of an authority to consult either at the university level, regional level, or national level. This has led to very unclear and opaque guidelines, that are often unclear to the experts themselves, who are often unwilling to answer clarification requests, as they do not want to take responsibility for misleading or misguiding researchers. As researchers are in dire need of clarification and guidelines, a “do-it-yourself” approach has started to be applied for the most studied species. Although this approach should be discouraged, it seems researchers must go with it while waiting for the establishment of a centralised authority for the regulation of the Nagoya Protocol. The lack of abundant resources in academia has also led researchers to be protective over the data collected or generated throughout the research, hampering the full compliance of ABS. Research findings are also not often communicated to the lay public and local communities as this step in the research process is not considered a priority. Early signs of improvement have emerged since the implementation of the National Recovery and Resilience Plan (PNRR), but only the coming years will tell whether these improvements have been successful or not.“ The seminar on ABS and the Nagoya Protocol was a productive event, providing a deeper understanding among participants and emphasizing the importance of efficient and fair access to genetic resources. We extend our gratitude to Scarlett Sett for her fantastic presentation, to GGBN for their collaboration in organizing this seminar, and to Amber Scholz (DSMZ) who made this webinar possible. For those who missed the event, the slides are available here and a recording of the presentation is available on YouTube. About the Authors The Ethical, Legal, and Social Implications Committee of ERGA. Social Media Dissemination Follow us for more updates: ERGA Twitter, ERGA LinkedIn, ERGA Mastodon For any questions, feel free to reach out to us at elsi@erga-biodiversity.eu or through our #ELSI channel in Keybase.

This month's session of the ERGA BioGenome Analysis & Applications Seminars will focus on phylogenomics, with talks by Iker Irisarri and Maaike Bierenbroodspot. Don't miss it! 🕚 Monday, May 27th 2024 - 12:00 CEST (Add the seminar to your calendar) Join us live on YouTube: Abstracts About the speakers Iker Irisarri Iker did his PhD at the Museo Nacional de Ciencias Naturales in Madrid. He was a postdoc at the Universities of Konstanz (Germany), Uppsala (Sweden), and Göttingen (Germany), and at the Museo Nacional de Ciencias Naturales (Spain). Since 2022, he is a group leader at the Leibniz Institute for the Analysis of Biodiversity Analysis and the Museum of Nature, Hamburg. He will soon join the Museo Nacional de Ciencias Naturales as a Ramon y Cajal fellow. Iker is passionate about phylogenomics and major evolutionary transitions, particularly the conquest of terrestrial environments, which he has studied in both vertebrate animals and plants. Maaike Bierenbroodspot Maaike studied life sciences at Utrecht University. She pursued her master's degree in Molecular Life Sciences at the University of Göttingen, where her interests shifted from wet lab work to computational analyses. Currently, she is pursuing her PhD in the group of Prof. Jan de Vries in Göttingen, whose primary focus is to understand the molecular adaptation to land in plants. Here, she helped establish a phylogenomic pipeline using genomic and phylotranscriptomic data.

We're happy to announce that the Global Genome Biodiversity Network (GGBN) and ERGA with the support of Digital Sequence Information (DSI) network are organizing a two-part webinar series focused on ABS (Access and Benefit Sharing), the Nagoya Protocol and DSI this April. Join us by filling the registration form below! Spots are limited. First Session (April 8th 2024, 09:00 - 11:00 CET) An introduction to Access and Benefit Sharing (registrations closed) This session will concentrate on the Nagoya Protocol, intended as an introductory guide tailored to our communities. It will be structured in two parts: a theoretical segment, which will be recorded, followed by an interactive Q&A segment, which will not be recorded. We invite members from EBP, GGBN, ERGA, and Africa BP to join this enlightening discussion. Speaker: Scarlett Sett (CSIRO-ACDP) Second Session (April 24th 2024, 17:00 - 19:00 CET) Digital Sequence Information (DSI) & the Convention on Biological Diversity This session will dig deeper into Access and Benefit-Sharing (ABS), Digital Sequence Information (DSI), and the Convention on Biological Diversity. It is designed to build on the foundational knowledge from the first session and provide deeper insights into DSI-related topics. Speaker: Amber Scholz (Leibniz Institute DSMZ) Further details: Each webinar is designed to accommodate up to 300 participants. Registration for each session will close two days prior to the first seminar. Access to the webinar, including the Zoom link, will be exclusively provided to those who have registered. In collaboration with the ERGA ELSI committee, we've decided to offer a certificate of attendance. Recorded talks are now available on the ERGA Youtube channel: Slides for download:

At this month's ERGA Plenary meeting (Monday, May 27 at 15:00 CEST) Vice-chair Olga Vinnere Pettersson gave an interesting talk about her experience at a sequencing facility producing reference genomes for non-model organisms. Find details and the recorded talk below: Abstract Since 2013, the Genomics Platform at SciLifeLab has been operating PacBio and ONT instruments. However, there still were many challenges of applying these technologies to non-model genomes. Our team spends lots of effort to understand and mitigate some of these challenges. In this talk, I will present the layout of a reference genome generation process from sampling to sequencing and introduce the auditorium to the main challenges of long-read sequencing of non-model species. Sequencing procedure and chemistry will be explained and some real-life examples will be presented. Speaker's Bio - Olga Vinnere Pettersson Mycologist, PhD in Molecular Evolution. Sequenced my first reference genome in 2009. Since 2012 - sequencing technology consultant / project coordinator at the National Genomics Infrastructure, a part of Genomics Platform of SciLifeLab: the center of excellence in molecular biosciences in Sweden. Currently, I am leading the SciLifeLab – Uppsala University involvement in the Biodiversity Genomics Europe (BGE) consortium, an initiative founded by the EU Horizon Europe program. Together with the Sanger institute, we are leading the effort of sequencing reference genomes of the European eukaryotic biodiversity and creating a de-centralized infrastructure to carry out this work on our continent. Vice-chair of ERGA, member of ERGA SSP and EBP Sampling Committee. To receive the Zoom link and join this and our upcoming plenary meetings, register as an ERGA member.

On the 18th of June, Biodiversity Genomics Europe will organise a panel discussion at the World Biodiversity Forum 2024 that will take place next 16-21 June in Davos. 👉 The topic of the panel will be ‘Unleashing biodiversity's secrets through integrated and scaled genomic science solutions’. The panel discussion aims to bring together experts from both the DNA barcoding (iBOL Europe) and full-genome sequencing (ERGA) stream in an open forum to: Introduce the current state-of-the-art to the wider community of stakeholders in biodiversity research and policy; Debate the priorities for addressing challenges and seizing opportunities needed to accelerate and integrate genomic science solutions into practices. Interested in participating? 📩 Registration is open until June 7: https://worldbiodiversityforum2024.org/registration/ Please note that the event is in-person only. — More information about BGE’s panel discussion (look for PD-2): https://worldbiodiversityforum2024.org/workshops-and-panel-debates/ More information about the programme: https://worldbiodiversityforum2024.org/session-program/

Read the full interview with Alice Mouton below: 1. Can you introduce yourself and how you got involved with ERGA and the Training and Knowledge Transfer Committee? My name is Alice Mouton and I’m a researcher based in Belgium. I got actively involved in the early stages of building the European Reference Genome Atlas (ERGA). Early on, I was actually engaging with the Belgian representative of the Cluster 6 of the Horizon Europe Work Program to make some modifications on the draft of the call for the future Horizon Europe project that would better fit ERGA and is now currently underway (BGE). I got naturally involved as well in the early stages of ERGA by being elected as one of the Belgian representatives in the ERGA Council. Back in 2021 I was mostly involved with the SSP (Sampling & Sample Processing) Committee and I started to supervise and coordinate the ERGA Pilot project with Ann Mc Cartney and Giulio Formenti. Because I was starting to have a heavy workload with the ERGA Pilot project on a voluntary basis while working on my postdoc project, I had to slow down my different activities in the other committees. I actually got involved in the TKT committee more recently around 2022. I helped with the submission and the organization of the EMBO course that was held in Belgium by another TKT member. That's how I put my foot into the TKT committee. I got hired through the Biodiversity Genomics Europe projects as a training and knowledge transfer officer. It  was quite evident that I would lead the TKT committee due to my position. 2. What are the main activities of the ERGA Training & Knowledge Transfer Committee? Our committee has several types of actions. We support the design and the implementation of learning and skill sharing activities. We also have the goal of collecting, promoting and developing training materials in biodiversity genomics - like webinars, workshops and other activities. We also receive more direct support requests from members who want to organize a workshop. We offer help promoting and organizing these community workshop. We have the goal of connecting and supporting members to develop proposals for financing activity related to Training and Knowledge Transfer. We have gained experience by submitting a few of those applications in the last few years. We are also building a knowledge hub where everyone will be able to find educational/learning materials, such as tutorials related to every step of the genome generation workflow: from genome assembly to how to request a permit and downstream analysis or how to involve stakeholders in the project. Right now, we are working on a guide with some tips and practical advice on how to organize events such as workshops, conferences, webinars, which will be openly available to everyone. 3. What are the most interesting and the most challenging aspects of chairing TKT? The most interesting part is actually seeing that we can make a difference. When we organize workshops they are free of charge and we have high attendance. So I think it's really exciting because it shows that there is a lot of interest in training activity around biodiversity genomics. Perhaps one of the challenges within ERGA is to make connections with the other committees. When other committees need help organizing workshops or webinars, TKT is here to offer support but sometimes there is a lack of communication. One of the challenges is making TKT visible to the other committees. 4. In your experience, what do you see as the most effective strategies to promote effective biodiversity genomics training and capacity building across Europe, considering the complexity of the task and great heterogeneity between countries? It really is a challenging task to promote training in biodiversity genomics across Europe. Mostly because genomic knowledge is not equally distributed across the continent, we have a strong bias: Western European countries generally having more experienced researchers in the field while Eastern European countries tend to have less people with training in genomics. So there is a bias that we should somehow address. There is also a strong financial barrier to access to knowledge and training because of access to funding. Access to adequate computational infrastructure is another challenge. When we offer free genomics workshops, they are often too short for the participants to fully grasp the complexity of a certain type of genomic analysis. Online workshops also require a stable internet connection and we have high demand and not that many spots can be offered. So I think maybe the most effective strategy to promote biologist genomics training would be first to have an European computer infrastructure that would be available to all researchers in the continent. This would solve a critical issue: when we organize a workshop we offer access to a high performance computer and then when the workshop ends the participant might not have access to this kind of resource. So they might learn how to do the analysis but they don't have access to the resources needed to perform this analysis with their own data. That’s why I think that one of the best strategies to really boost training in genomics in Europe would be to invest in infrastructure development. Another effective strategy to promote genomics training is to provide all of these tutorials and step by step tutorials free of charge. Currently a lot of knowledge and resources are kept private or within individual research groups. 5. What do you see as the next steps for the ERGA TKT Committee? I think the most important step right now for the TKT committee is to finalize the ERGA Knowledge Hub. This will be a really important resource for the biodiversity genomics community from Europe and beyond to have easy access to many step by step tutorials and other training materials. Send an email to the Training & Knowledge Transfer Committee and learn more about how you can participate!