- Nfdi4microbiota-announce

NFDI4Microbiota - Invitation: Community Workshop on 15 May 2025, 1:00 - 3:00 pm, online

by Paulmann, Carmen

Dear microbiome research enthusiasts, In the past year, you have seen more and more of NFDI4Microbiota’s technical solutions and trainings for the microbiology community in action. Now we need you! Since the successful launch of NFDI4Microbiota in October 2021, we were able to welcome many new participants, we have seen our selection of services and tools grow and become more refined. Now after 3 years and 7 months, it is time to look back at what we have achieved and where our next steps are leading us. We warmly invite you to the 7th edition of our Community workshop to join us and share your ideas, wishes and tools with us. Let's shape the future of the microbiome research landscape together! Feel free to forward the meeting invite to your colleagues. 📝 Agenda: https://nextcloud.nfdi4microbiota.de/s/9Y6NH7JmCA4dy32 📅 Date: 15 May 2025 🕝 Time: 1:00 - 3:00 pm CEST (Berlin time) 🔗 Zoom Link: https://rwth.zoom-x.de/j/69264435862?pwd=7IbTbahRW8dJBC8pAwvRjdU33GrtXJ.1 Meeting ID: 692 6443 5862 Passcode: 604995 Best wishes from Konrad Förstner and Alice McHardy, on behalf of the NFDI4Microbiota consortium. --- Dr. Carmen Paulmann Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

1 year

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TODAY: ISCBacademy Webinar today with Nico Pfeifer on HIV

by Mueller, Mattea

ISCBacademy<https://www.iscb.org/iscbacademy> Modeling Microbe Evolution Due to Immune System Pressure by Nico Pfeifer (University of Tübingen) Today - February 25, 2025, at 3:00 PM CET Microbes are under constant evolutionary pressure from their environment, with the immune system playing a significant role in shaping their adaptation strategies. Viruses, in particular, must evolve to evade immune responses, enabling them to establish persistent infections. A well-studied example is HIV, where viral adaptation to the host's immune system has been extensively modeled using computational methods. In this talk, Nico Pfeifer will explore the computational approaches developed to model viral adaptation and their implications for understanding microbe evolution under immune pressure. The session will cover: * Early computational models of HIV immune adaptation [1] * Recent advances in Bayesian modeling for predicting viral evolution [2] * The impact of founder effects on adaptation predictions * Applications beyond viruses, including resistance prediction for Mycobacterium tuberculosis These insights not only enhance our understanding of viral evolution but also inform strategies for tackling antimicrobial resistance and improving predictive models for microbial adaptation. [1] Carlson, J., Du, V., Pfeifer, N. et al. Impact of pre-adapted HIV transmission. Nat Med 22, 606–613 (2016). [2] Hake, A., Germann, A., de Beer, C. et al. Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models, PLOS Computational Biology, 19(12): e1010355 (2023). Join the Webinar by logging in to ISCB Nucleus<https://iscb.junolive.co/> ________________________________ Dr. Mattea Müller Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

1 year, 1 month

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NFDI4Microbiota Coffee Talk on February 24 on Microbial Protein Prediction

by Mueller, Mattea

Dear Ambassadors, Members, Participants, and Community, We are excited to invite you to our next NFDI4Microbiota Coffee Talk on February 24 at 2:30 PM CET! This session will host Dr. Thomas Hitch (RWTH Aachen University), who will present: Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut Microbes use a range of genetic codes and gene structures, yet these are ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment and limiting our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on taxonomic assignment, removes partial predictions, and optimizes the prediction of small proteins. Applied to 9,634 metagenomes and 3,594 genomes from the human gut, this approach increased the captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimized small protein prediction captured 3,772,658 small protein clusters, many with antimicrobial activity. Integration of these protein sequences and sample metadata into a tool, InvestiGUT, enables the association of protein prevalence with host parameters. Accurate prediction of proteins is critical for understanding microbiome functionality, and this work enhances our mechanistic understanding of microbe-host interactions. When? 📅 Date: Monday, February 24 🕝 Time: 2:30 PM CET Where? 💻 Online on Zoom 🔗 Join the Meeting https://helmholtz-hzi-de.zoom-x.de/j/68764089023?pwd=cvlqk3FLgKyIyK3xkUy2Lh… We look forward to seeing you online for an engaging discussion! Please feel free to share this invitation with colleagues who may be interested. Best regards, Mattea Müller NFDI4Microbiota Team ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

1 year, 2 months

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NFDI4Microbiota Newsletter 1/2025

by Mueller, Mattea

Newsletter Quarter 1 2025 [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/icon_news…] Dear Readers, With our tenth NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, services and cooperations. If you can think of other topics that we should cover, please let us know. We are happy to hear from you!<https://nfdi4microbiota.de/contact-form/> And now: Enjoy reading the newsletter! [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/new_yea…] We wish you all a great and healthy start into 2025. Community Engagement Events and Conferences ________________________________ Great experiences at our 3rd Annual Conference [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/annual_…] The NFDI4Microbiota conference was a fantastic opportunity for the NFDI4Microbiota community to meet in person. We presented current development of our services and future plans during the public conference. .It was great to have several representatives from other NFDI consortia and Base4NFDI attend the event, as it provided the chance to exchange updates, discuss upcoming events, and align on shared goals. The keynote and panel talks inspired discussion of the policy, infrastructure, training and support needs of our various user communities. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/panel_a…] The Hands-on Workshops covered a variety of topics and were set in different styles, according to the topics. The Use Case workshop for example was a discussion-style workshop, were the Use Cases VirJenDB and MetaProt were presented and discussed with the participants. The workshop on Research Data Management on the other hand used a LEGO activity that highlighted the importance of metadata in experimental reproducibility. The game was based on a similar exercise by University of Glasgow. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/collage…] The workshop participants were divided into small groups of 2-3 people, each tasked with building a vehicle using at least 10 LEGO pieces within a limited timeframe of 15 minutes. Once the vehicles were built, each group documented their construction process by creating Standard Operating Procedures (SOPs). This documentation was crucial, as it provided detailed instructions on how to reconstruct their creations accurately. The emphasis on thorough SOPs mirrored the nature of scientific documentation, reinforcing its significance in ensuring reproducibility. After the initial LEGO creation and documentation of SOPs, groups switched tables with another team. They then had 15 minutes to rebuild the vehicles based solely on the provided instructions. This phase was not only a test of clarity and precision in documentation but also an opportunity for participants to appreciate how well-structured metadata can aid in replicating complex experiments. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/first_b…] [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/second_…] The LEGO activity served as a playful yet impactful reminder of the vital role that metadata plays in research. Just as accurate instructions can lead to successful LEGO constructions, comprehensive data management is essential for fostering reproducibility and reliability in scientific endeavors. Participants left with a renewed understanding of collaboration and communication's importance in both science and play. Successful first NFDI BioMed Workshop [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/BioMed_…] Several NFDI consortia supporting the work with biomedical and health data came together for a cross-consortium workshop on biomedical research data management (RDM). The event, jointly organized by NFDI4Bioimage, NFDI4Health, NFDI4Immuno, NFDI4Microbiota, and GHGA, successfully brought together experts from different NFDI consortia to share knowledge, discuss challenges, and identify opportunities for collaboration. The workshop provided a unique opportunity for exchange within the NFDI. Participants discussed potential joint use cases , explored areas of synergy for collaborative efforts, and developed pathways for further collaboration in biomedical RDM. This event was an important step in fostering collaboration and advancing research data management to generate solutions for the Germany biomedical research community. Community Engagement Upcoming Events and Conferences ________________________________ Next Community Workshop coming soon! [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/communi…] The upcoming Community Workshop will be held online in spring. We want to get YOUR feedback - straight out of the community. We will discuss how we further can support your microbiological research by providing data management infrastructure. The exact date will be announced soon in the Event section of our website<https://nfdi4microbiota.de/newsroom/events.html>. Stay tuned! Use Case Conference in May 2025 Join the experts and learn more about the NFDI4Microbiota Use Cases at the Use Case Conference on May 19. More information coming soon in the Event section of our website<https://nfdi4microbiota.de/newsroom/events.html>. See you in person! [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/coffee-…] We will attend different events over the next year - find some of them below - and are looking forward to meet you there: * GfV 2025, March 4-7<https://virology-meeting.de/> * VAAM 2025, March 23-26<https://vaam-kongress.de/> * EVC 2025, April 27-30<https://eusv-congress.eu/> * ViBiom 2025, May 13-15<https://evbc.uni-jena.de/events/vibiom2025/> Announcing the next Knowledge Base Sprint [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/KB-spri…] Join the ambassador meetings Do you know our Ambassador Program? The mission of the NFDI4Microbiota consortium is to serve as the central hub in Germany, providing essential support to the microbiology community by facilitating access to data, analysis services, data/meta-data standards, and training. To fulfill this mission, we are running the NFDI4Microbiota Ambassador Program, dedicated to connecting and training (early career) researchers within the microbiology community. [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/n4m_ambass…] As part of our commitment, we aim to assist young scientists in expanding their research networks and disseminating knowledge on data handling, metadata standards, standardized bioinformatic workflows and further related topics. Join us in our ambassador program for networking and spreading FAIR principles and openness in microbiome research! For our Ambassadors, we host bimonthly ambassador meetings with interesting topics. The next meeting will be announced soon! Get your updates and more information on the program here.<https://nfdi4microbiota.de/community/ambassador.html> Take a break and join our Coffee Talks The Coffee Talk meetings provide an opportunity to learn more about NFDI4Microbiota's services and mission from within and around the NFD4Microbiota community. These bimonthly meetings take place online and are open to all who are interested in staying informed about current developments and topics related to data in microbiology research. We will continue our Coffee Talks this year, too. Get your updates and more information on the schedule and registration information here.<https://nfdi4microbiota.de/newsroom/news/2024-04-26-nfdi4microbiota-coffee-…> [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/coffee_…] Services ________________________________ Foundational Guidelines published To support our community we published NFDI4Microbiota Foundational Guidelines<https://zenodo.org/records/13628175> on Zenodo. The Guidelines shall act as basis for specific policies of all NFDI4Microbiota projects and services and are supposed to help researchers to offer data handling and storage, bioinformatic tools and services as well as training within the scope of a centralized infrastructure to a broad scientific audience. Training Announcements ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/Isometric_…] We updated the Training section on our website! Now you get a more comfortable view on the interesting trainings, courses and workshops to come. Check it out!<https://nfdi4microbiota.de/services/trainings.html> More courses will be announced soon, e.g. the "Joint NFDI4Microbiota, de.NBI & DZIF Nextflow Metagenomic Training Course 2025", which will take place in person in Brunswick in April, so make sure to check the section regularly. Previous Training ________________________________ Intense 3-day-workshop on 16S Amplicon microbiome experiments [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/group_p…] Evaluating the mountain of 16S rRNA amplicon sequencing data after a successful microbiome experiment can be daunting, especially if you do not know where to start. That is why, as part of an on-going collaboration, de.NBI and NFDI4Microbiota hosted a course on Microbiome Analyses at Justus Liebig University in Gießen at the beginning of October. The aim was to encourage fellow scientists to feel confident enough in their skills to kickstart the analyses of their own data. Over the span of three days, the 17 participants, from PhD student to PI, were first introduced to the basic steps for running amplicon experiment analyses, including the pitfalls and best practices connected to high-throughput computations. The main part of the course was spent with hands-on sessions, assessing the quality of reads, using the tools Qiita and QIIME2 to preprocess the data, and subsequently analysing it. Cooperations ________________________________ Presentation at BY-COVID consortium meeting The final BY-COVID consortium meeting took place in Brussels on September 10 and 11. Noriko Cassman and Kilian Ossetek from VirJenDB attended and Kilian presented his project, which was funded by the open call that VirJenDB was awarded. His project is a submission web tool for the upload of virus sequences to ENA via the VirJenDB as a data broker. The pilot tool is available here<hxxps://www[.]virjendb[.]org/submission>. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/BY-COVI…] Recent Publications ________________________________ Memorandum of Understanding on Biodata Interest Group published We intensify the collaboration with the consortia DataPLANT and NFDI4Biodiversity as the Biodata Interest Group. Therefore, our consortia signed a Memorandum of Understanding (MoU) which is now published here<https://zenodo.org/records/13880944>. Our three NFDI-consortia will pool expertise, energies and technologies in order to provide the scientific community with even better support in managing and processing their biological data. The focus of the MoU is on the cross-consortium harmonization of research data management strategies. Lesson plan on data organization Data Steward Justine Vandendorpe and Sophie Boße from ZB MED created a lessons plan and slides on data organization<https://zenodo.org/records/14234219> for an interactive workshop on the same topic. The lessons plan covers topics such as the motivation behind good data organization, file naming, versioning, folder structure and tidy data. Video publications on TIB AV-Portal In addition to the written publications we provide on our website, we proudly present our very own NFDI4Microbiota channel on the TIB AV-Portal.<https://av.tib.eu/publisher/NFDI4Microbiota> There you can find recordings of talks given within the consortium, for example on topics like ELNs, workflows, our Use Cases and, of course, an introduction to NFDI4Microbiota. Some selected video publications you can also find directly in the new media center on our website.<https://nfdi4microbiota.de/newsroom/mediacenter.html> Social Links and Contact ________________________________ This newsletter is brought to you by NFDI4Microbiota Mail: contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> Web: www.nfdi4microbiota.de<https://www.nfdi4microbiota.de/> If you no longer wish to receive this newsletter, click here to unsubscribe.<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…> Follow us Mastodon<https://nfdi.social/@NFDI4Microbiota> LinkedIn<https://www.linkedin.com/company/98488870/admin/feed/posts/> BlueSky<https://bsky.app/profile/nfdi4microbiota.bsky.social> GitHub<https://github.com/NFDI4Microbiota> ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

1 year, 3 months

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NFDI4Microbiota - Happy holidays and a happy new year!

by contact＠nfdi4microbiota.de

Dear NFDI4Microbiota community, We are looking back on a very successful year 2024. You have parts in the success of the consortium in 2024, e.g. as participants in our trainings and events in 2024. Some of you we have met during these events and our NFDI4Microbiota conference two weeks ago. It was a pleasure to work with you in 2024 and we hope to work even closer with you in 2025. In the beginning of 2025 we will announce our big events and new training dates planned for 2025. Until then, we wish you happy holidays and a happy new year 2025! [cid:image002.jpg@01DB51FE.FFF04100] Kind regards, Barbara Götz --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota E-Mail: goetz(a)zbmed.de<mailto:goetz@zbmed.de> Tel.: +49 0221 999 892 513 Webportal: www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Mastodon: nfdi.social/@NFDI4Microbiota<https://nfdi.social/@NFDI4Microbiota> LinkedIn: linkedin.com/company/nfdi4microbiota/<https://www.linkedin.com/company/nfdi4microbiota/> ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

1 year, 4 months

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Join Us for the Last NFDI4Microbiota Coffee Talk of the Year!

by Mueller, Mattea

Dear all, We are excited to invite you to the final NFDI4Microbiota Coffee Talk of 2024! Metadata and Research Data Management for Metaproteomics Speaker: Kay Schallert (ISAS) Metaproteomics uses LC-MS/MS to investigate microbial communities, producing large and complex data sets, where recording of important metadata - as so often - is neglected. This presentation will detail efforts to improve metadata acquisition using research data management for improved collection of metadata and the tool MetaForge<https://mdoa-tools.bi.denbi.de/metaforge_test/home> for streamlined metadata annotation of whole projects. 📅 Date: 16 December 2024 ⏰ Time: 14:30 – 15:30 CET 💻 Location: https://helmholtz-hzi-de.zoom-x.de/j/63366496382?pwd=Q2J2SHcyNEFLT05hQS81UU… Meeting ID: 633 6649 6382 Passcode: 203545 Should you have any questions or suggestions, please don’t hesitate to reach out. Best regards, Mattea Müller Dr. Mattea Müller Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

1 year, 4 months

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Reminder: Registration for 3rd NFDI4Microbiota Annual Conference

by Mueller, Mattea

Dear all, This is a friendly reminder that registration for the 3rd NFDI4Microbiota Annual Conference is still open, and it’s free of charge! Don’t miss this opportunity to join us for an exciting program featuring NFDI4Microbiota services, keynotes, and panel discussions on the cultural shift to FAIR and Open Science. We will also highlight research from our community through poster sessions and provide hands-on workshops, a software marketplace, and data steward consultations. Event Details: 3rd NFDI4Microbiota Annual Conference - Services for the Community Dates: December 4-5, 2024 Location: KUBUS, Leipzig Important Deadline: * Registration and Abstract Submission: Closes on October 31, 2024 Note: NFDI4Microbiota Ambassadors and Participants are eligible for travel and hotel reimbursements. For more information on the agenda and to register, please visit: https://events.hifis.net/e/NFDI4Microbiota-conference2024 If you have any questions, feel free to reach out. We look forward to your participation and hope to see you in Leipzig! Best regards, The NFDI4Microbiota Conference Team Mattea Müller, Barbara Goetz, Cordula Hege, and Stephanie Aue Dr. Mattea Müller Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

1 year, 6 months

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NFDI4Microbiota Coffee Talk on October 28th: Microbe Data Drama: Share and Standardize, or Stagnate!

by Mueller, Mattea

Dear Ambassadors, Members, Participants, and Community, We are excited to invite you to our next NFDI4Microbiota Coffee Talk on 28 October! This session will host Ulisses da Rocha, Junior Group Leader at the Helmholtz Centre for Environmental Research (UFZ, Leipzig, Germany). Talk Title: Microbe Data Drama: Share and Standardize, or Stagnate! Ulisses leads the Microbial Data Science group at UFZ, where they explore the intersection of Microbial Ecology, Modeling, Microbial Physiology, and Bioinformatics through a Systems Biology approach. Join us to hear his insights on the challenges and opportunities in microbial data sharing and standardization. When? Date: Monday, 28 October Time: 2:30 PM - 3:30 PM CEST. Where? Online on Zoom https://helmholtz-hzi-de.zoom-x.de/j/63366496382?pwd=Q2J2SHcyNEFLT05hQS81UU… Meeting ID: 633 6649 6382 Password: 490003 We look forward to seeing you online for an engaging discussion! Please feel free to share this invitation with colleagues who may be interested. Best regards, Mattea Müller NFDI4Microbiota Team Dr. Mattea Müller Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

1 year, 6 months

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NFDI4Microbiota Newsletter 4/2024

by Aue, Stephanie

Newsletter Quarter 4 2024 [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/icon_news…] Dear Reader, With our ninth NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, services and cooperations. If you can think of other topics that we should cover, please let us know. We are happy to hear from you!<https://nfdi4microbiota.de/contact-form/> And now: Enjoy reading the newsletter! Community Engagement Events and Conferences ________________________________ Performing ancient metagenomics at SPAAM summer school [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/Spaam_800p…] The online SPAAM summer school (August 5-9) introduced essential steps to perform ancient metagenomics, including how to process next-generation assembly and how to perform de novo metagenomic assembly. The online event had a lovely design like a little RPG, in which you actual had to walk to the seminar rooms with your avatar, as shown in the picture above. Integrated into the summer school Konrad Förstner, Hesham Almessady and Justine Vandendorpe each delivered a 15 minute talk on August 8. First, Konrad Förstner introduced NFDI4Microbiota. Subsequently, Hesham presented relevant workflows and services such as CAMI (critical assessment of metagenome interpretation) benchmarking and CloWM (Cloud online workflow manager). Lastly, Justine introduced electronic lab notebooks (ELN), including the advantages of ELN and examples. The talks were well received, attracted over 45 attendees, and generated significant interest. Successful Knwoledge Base Coding Sprint on September 11-13, 2024 In our recent three-day coding sprint we continued to develop the NFDI4Microbiota knowledge base. New and experienced contributors collaborated to improve the platform, demonstrating the power of open collaboration. [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/sprint_800…] There were 23 active pull requests, as the Sprint started, and seven contributors merged 21 of them. From 38 issues we closed 28, including fixes for broken links, formatting, and tracking key performance and nine authors made 264 commits. Finally yet importantly, we updated 55 files and 1,928 lines of code, which added notable improvements including better documentation, enhanced internal linking, and a more user-friendly design. In addition, major updates to experimental SOPs ensure a more reliable resource for researchers. The sprint strengthened both the platform and community, setting the stage for future progress. Thanks to all that contributed during the four sessions. Community Engagement Upcoming Events and Conferences ________________________________ Join us at the 3rd NFDI4Microbiota annual conference in Leipzig on December 4-5, 2024 [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/annual_con…] Do you want to take your knowledge about FAIR and Open Data to the next level? Are you interested in learning something new in interesting Hands-on Workshops? Do you want to gain insights on the work of our consortium, NFDI4Microbiota? Yes? In this case join the NFDI4Microbiota Annual Conference! On two days, we are divníng deep into the main topics of NFDI4Microbiota: * The services we offer to support you in YOUR research cycle * How to make YOUR research data FAIR and Open The Conference will take place in the KUBUS (UFZ) Leippzig from December 4th to 5th. There will be Poster Sessions on each day with additional services, such as a software marketplace and Data Steward consultation. The days are starting with interesting keynotes, followed by a comprehensive overview on the services, we offer on day one and an exciting panel discussion about encouraging Cultural Change to FAIR and Open Data on day two. The afternoons are filled with said poster sessions and Hands-on Workshops on different related topics, such as “Basics in Research Data Management”, Workflows for Microbiological Data” and “First steps towards FAIR (meta)data descriptions, ontology terms and data deposition. You can find the complete timetable here on the registration site.<https://events.hifis.net/e/NFDI4Microbiota-conference2024> Meet your peers at the CarpentryConnect Heidelberg 2024 Following the CarpentryConnect Manchester 2019, this year’s community event takes place in Heidelberg, Germany, from November 12th-14th. The CarpentryConnect Heidelberg 2024 (CCHD2024) will feature a diverse range of sessions, such as breakouts, posters, lightning talks, workshops and curriculum co-working sessions, all centred around the Theme: “Community-led training beyond academia.” NFDI4Microbiota sponsors the event and we invite our fellow Carpentries to join: https://biont-training.eu/CarpentryConnect2024.html. Never heard about The Carpentries<https://carpentries.org/about/> communtiy? The project compromises the Software Carpentry, Data Carpentry, and Library carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researcher. It builds global capacity in essential data and computational skills for conducting efficient, open, and reproducible research. [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/n4m_ambass… the ambassador meetings Do you know our Ambassador Program? The mission of the NFDI4Microbiota consortium is to serve as the central hub in Germany, providing essential support to the microbiology community by facilitating access to data, analysis services, data/meta-data standards, and training. To fulfill this mission, we are running the NFDI4Microbiota Ambassador Program, dedicated to connecting and training (early career) researchers within the microbiology community. As part of our commitment, we aim to assist young scientists in expanding their research networks and disseminating knowledge on data handling, metadata standards, standardized bioinformatic workflows and further related topics. Join us in our ambassador program for networking and spreading FAIR principles and openness in microbiome research! For our Ambassadors, we host bimonthly ambassador meetings with interesting topics. The next meeting will take place on November 25th, starting at 14:30 CEST. Kassian Kobert of the University Bielefeld will tell us about the NFDI4Microbiota Knowledge Base and how you can contribute. Get more information about the program here.<https://nfdi4microbiota.de/community/ambassador.html> [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/coffee_tal…] Take a break and join our Coffee Talks The Coffee Talk meetings provide an opportunity to learn more about NFDI4Microbiota’s services and mission from within and around the NFD4Microbiota community. These bimonthly meetings take place online and are open to all who are interested in staying informed about current developments and topics related to data in microbiology research. The next Coffee Talk will take place on October 28th. Ulisses da Rocha from Helmholtz Centre for Environmental Research (UFZ) will talk about Metadata standards in connection with data quality. Get more information on the topics and the schedule here.<https://nfdi4microbiota.de/newsroom/news/2024-04-26-nfdi4microbiota-coffee-…> Services ________________________________ 2025 Flex Funds call closed! Thank you to all of you who participated in our 2025 Flex Funds call. We received many exciting proposals and are now busy reviewing them. We will announce the new Flex Funds projects in one of our next newsletters. [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/provenance…] Introducing the New Provenance Guidelines for Workflow Developers The Task Area 3.4 of NFDI4Microbiota is pleased to announce the release of our Provenance Guidelines for Workflow Developers.<https://zenodo.org/records/13627510> These guidelines are designed to support new and experienced developers in creating bioinformatics workflows that prioritize provenance tracking, reproducibility, and transparency. By following these standards, developers can ensure that their workflows are scientifically robust, easily reproducible, and verifiable. Why Provenance Matters In bioinformatics, the ability to trace the origin and evolution of data within a workflow—known as provenance—is crucial. Provenance tracking ensures that every step of a workflow, from data acquisition to the final output, is documented and reproducible. This level of detail not only fosters scientific transparency but also facilitates the validation and replication of results by others in the community. Key Components of the Guidelines Our guidelines cover several critical areas: * Improve Reproducibility: To enhance reproducability, we advise to pin all software versions and set random seeds. * Version Management: Proper version control is essential for tracking changes over time. The guidelines emphasize the importance of managing and reporting versions of both the workflow and any associated software tools or libraries. Examples are given how the expected provenance output can be created. * Data and Metadata Management: The guidelines outline best practices for managing inputs and outputs as well as metadata. Examples are given how the expected provenance output can be created. * Detailed Documentation: Developers are encouraged to provide comprehensive documentation for every aspect of their workflows. This includes clear descriptions of inputs, outputs, and intermediate steps, as well as the rationale behind specific choices. * Validation Practices: To guarantee that workflows produce reliable results, the guidelines recommend validation practices. These include testing workflows with different datasets and verifying that the outputs remain consistent and accurate. Introducing the Provenance Scoring System To encourage adherence to these guidelines and foster continuous improvement, we have introduced a Provenance Scoring System. This system assigns a rating to each workflow based on its compliance with the outlined standards, with the highest possible score being 100 provenance points. Benefits of the Scoring System: This scoring system should serve as a benchmark for quality, providing developers with a clear understanding of where their workflows excel and where they may need improvement. For users, the score offers a reliable measure of a workflow’s reliability and reproducibility, helping them make informed decisions about which tools to use. Get Involved We encourage all developers to review these guidelines and consider how they can be integrated into their current and future projects. We welcome your feedback on these guidelines as we aim to refine and improve them further. Please send any comments or suggestions to klemmp(a)staff.uni-marburg.de<mailto:klemmp@staff.uni-marburg.de>. New Template for your Data Management Plan published You work with microbiological data and struggle with the data management? We got your back and developed a special “NFDI4Microbiota Edition” Data Management Plan (DMP) Template. The PDF guides you with simple questions through the data management process. And once you gone through all of the questions, your DMP is finished. Check it out!<https://zenodo.org/records/13628589> You tried the template and got feedback for us? Please get in touch via contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> Training Announcements ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/Isometric_…] There are several interesting training offers currently open for registration, like: * The NFDI4Microbiota and de.NBI 16S amplicon training course (Oct 8th-10th) * Microbiota profiling by 16SrRNA gene amplicon sequencing: Data analysis Workshop (Oct 23rd) * DSMZ Digital Diversity: How to efficiently access the data of BacDive, BRENDA, LPSN, SILVA and more (Nov 11th) * Research data management: how to start and maintain a project (Nov 12th) And more courses are planned. In November you can also get an “Introduction on Python”. As soon as the registration opens, you will find it on the NFDI4Microbiota website.<https://nfdi4microbiota.de/services/trainings.html> More courses will be announced soon, so check the website regularly for training opportunities. Previous Training ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/preservati…] Exciting workshop initiated crucial dialogue On September 3rd, 2024, NFDI4Microbiota hosted a digital workshop on long-term data preservation for life sciences, with a focus on maintaining the FAIRness of valuable research data over time. The workshop convened researchers, research data management (RDM) staff, and infrastructure providers to explore key questions around data selection, safety, reusability, and institutional responsibilities. A highlight of the event was a presentation by the European Bioinformatics Institute (EBI), which outlined the massive scale of data they manage, their role in stewarding the data submission process, and ongoing challenges with metadata completeness that directly impact the long-term reusability of data. The workshop also featured two hands-on interactive sessions: · What to Preserve? The Participants discussed the criteria for selecting data to be preserved long-term. The session covered various aspects, including funder and institutional obligations, valuable data and reusability and standards. · Who Preserves How? This session focused on the roles and responsibilities of institutions in the preservation process. Key discussion points included institutional policies, challenges and gaps and collaborative preservation. In the end, the workshop initiated a crucial dialogue on aligning preservation strategies, managing institutional resources, and ensuring long-term data reusability in life sciences. Cooperations ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/MoU_800px.…] DataPLANT, NFDI4Biodiversity and NFDI4Microbiota intensify their collaboration as the Biodata Group We signed a Memorandum of Understanding (MoU) with the consortia DataPLANT and NFDI4Biodiversity. Our three NFDI-consortia will pool expertise, energies and technologies in order to provide the scientific community with even better support in managing and processing their biological data. The focus of the MoU is on the cross-consortium harmonization of research data management strategies. Learn more about this new cooperation in the news section of our website.<https://nfdi4microbiota.de/newsroom/news.html> Recent Publications ________________________________ Interesting poster on CAMI web portal available There is an interesting poster on benchmarking metagenomics software with the new CAMI web portal<https://zenodo.org/records/13136314> available on our NFDI4Microbiota Zenodo section.<https://zenodo.org/communities/nfdi4microbiota/records?q=&l=list&p=1&s=10&s…> Fernando Meyer, Gary Robertson and our co-speaker Alice McHardy created the poster and Fernando presented it at the 32nd Conference on Intelligent Systems for Molecular Biology (ISMB 2024). The poster introduces the new CAMI web portal, which allows users to assess software for common metagenome analyses using the CAMI benchmarking metrics. The community-led initiative for the Critical Assessment of Metagenome Interpretation (CAMI) promotes standards and good practices agreed upon the community. Video publications on TIB AV-Portal In addition to the written publications we provide on our website, we proudly present our very own NFDI4Microbiota channel on the TIB AV-Portal.<https://av.tib.eu/publisher/NFDI4Microbiota> There you can find recordings of talks given within the consortium, for example on topics like ELNs, workflows, our Use Cases and, of course, an introduction to NFDI4Microbiota. Some selected video publications you can also find directly in the new media center on our website.<https://nfdi4microbiota.de/newsroom/mediacenter.html> Social Links and Contact ________________________________ This newsletter is brought to you by NFDI4Microbiota Mail: contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> Web: www.nfdi4microbiota.de<https://www.nfdi4microbiota.de/> If you no longer wish to receive this newsletter, click here to unsubscribe.<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…> Follow us Mastodon<https://nfdi.social/@NFDI4Microbiota> LinkedIn<https://www.linkedin.com/company/98488870/admin/feed/posts/> BlueSky<https://bsky.app/profile/nfdi4microbiota.bsky.social> GitHub<https://github.com/NFDI4Microbiota> ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

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NFDI4Microbiota Abstract and Registration Deadline Extended to October 30

by Mueller, Mattea

Dear all, The abstract submission and registration deadlines for the 3rd NFDI4Microbiota Annual Conference have been extended to October 30, 2024. This is a great opportunity to submit your abstracts and secure your spot at the conference, which will cover key topics such as NFDI4Microbiota services, keynotes, and panel discussions on the cultural shift to FAIR and Open Science. We will also showcase research from our community through poster sessions, along with hands-on workshops, a software marketplace, and data steward consultations. Event Details: * 3rd NFDI4Microbiota Annual Conference - Services for the Community Dates: December 4-5, 2024 Location: KUBUS, Leipzig For the updated agenda and to register, please visit: NFDI4Microbiota Annual Conference. If you have any questions, feel free to contact us. We look forward to receiving your abstracts and welcoming you to the conference in December! Best regards, The NFDI4Microbiota Conference Team Mattea Müller, Barbara Goetz, Cordula Hege, and Stephanie Aue Dr. Mattea Müller Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

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