- Nfdi4microbiota-announce

Invitation 3rd NFDI4Microbiota Annual Conference

by Mueller, Mattea

Dear all, We are excited to announce that registration for the 3rd NFDI4Microbiota Annual Conference is now open! The conference will cover key topics such as NFDI4Microbiota services, keynotes, and panel discussions on the cultural shift to FAIR and Open Science. Additionally, we will showcase research from our community through poster sessions and highlight our services with hands-on workshops, a software marketplace, and data steward consultations. 3rd NFDI4Microbiota Annual Conference - Services for the Community Dates: December 4-5, 2024 Location: KUBUS, Leipzig Abstract Submission is open until September 29, 2024. Registration for the conference and workshops closes on October 15, 2024. Notifications regarding abstract acceptance will be sent shortly after the submission deadline. NFDI4Microbiota Ambassadors <https://nfdi4microbiota.de/community/ambassador.html> are eligible for travel and hotel reimbursements. For the agenda and to register, please visit NFDI4Microbiota Annual Conference 2024<https://events.hifis.net/event/1756/overview><https://events.hifis.net/event/1756/timetable/#20241204> Please do not hesitate to reach out if you have any questions or need further information. We look forward to your participation and to seeing you at the conference! 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, 7 months

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Reminder: NFDI4Microbiota - 2025 Flex Funds call is open now! (closes on August 7th 2024)

by contact＠nfdi4microbiota.de

Dear NFDI4Microbiota community, This is a friendly reminder that the deadline for the Flex Fund Call for Proposals is three weeks away. The call is open from June 10th to August 7th 2024. What is the aim of the Flex Funds? The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, development of new training programs, and improvement of the ability to react to unforeseen technical challenges. Therefore, within the NFDI4Microbiota project work, flexible funding (so called 'Flex Funds') for small projects within the research community are available for the years 2023 to 2026. To implement a dynamic system that stays on track with new trends in the field, the Flex Funds will support small projects from the community and active Use Cases. What are eligible topics? Eligible topics are as follows: · Data Brokerage · Workflow development · Data storage and workflow execution · Infrastructure/Services · Training · Community engagement and outreach · Establishment of local data stewards · Use Case connection or an active Use Case · Deposition of high quality data sets in public repositories Details on the eligible topics, further information on the call and the procedure can be found on the NFDI4Microbiota web portal<https://nfdi4microbiota.de/newsroom/flexfunds.html>. While you're on the web portal, do not miss out to take a look at our newly listed services. In case you have questions, please do not hesitate to contact us via contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de>. We are looking forward to your application! Kind regards, The NFDI4Microbiota Adminsitration Unit --- 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, 9 months

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NFDI4Microbiota Newsletter 3/2024

by Aue, Stephanie

Newsletter Quarter 3 2024 [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/icon_news…] Dear Reader, With our eighth NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, cooperations and publications. 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 ________________________________ NFDI4Microbiota joined the VAAM&DGHM conference in Würzburg from June 2nd to 5th To engage and connect with the NFDI4Microbiota research community, members of our consortium attended the 7th joint Microbiology & Infection Conference of the German Society for Hygiene and Microbiology (DGHM) and the Association of General and Applied Microbiology (VAAM) in Würzburg. Our outreach team members Mattea Müller and Barbara Götz provided an informative booth at the conference on all four days. [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/vaam+dghm…] Many researchers with diverse scientific backgrounds were interested in the services provided by our consortium. Our outreach team provided answers to all the questions the community addressed them with and raffled divers merchandise articles among all booth visitors. In addition, we held the NFDI4Microbiota symposium presenting our services to making microbiology research data Open and FAIR on June 5th. NFDI4Microbiota speaker Konrad Förstner (ZB MED) introduced participants to the mission and vision of our consortium. Afterwards, a best-practice workflow development recommendation and a selection of our most interesting services was presented: * Developing and Maintaining Best-Practice Workflows and Services for Processing Microbiological Research Data by Hesham Almessady (HZI), * UseCase MetaProt: Standardization and Metadata in microbial community proteomics (Kay Schallert, ISAS), * StrainInfo: A central database for resolving microbial strain identifiers (Lorenz Reimer, DSMZ) and * VirJenDB: Toward a community-curated and open-source virus meta(data) analysis platform (Noriko Cassman, University Jena). You can find the complete presentation online.<https://zenodo.org/records/12189067> It was a great conference with inspiring encounters and exciting talks. We are already looking forward to interact with you at other upcoming conferences. For example "Gesundheit Gemeinsam", the joint conference of five different medical societies including the GDMS (German association for medical informatics, biometry and epidemiology) and the DGEpi (German society for epidemiology), which is one of our supporting societies. We will share a booth there with NFDI4Health. And of course at our annual NFDI4Microbiota conference, which will take place in December - see the text further down. HeFDI Data Week presentation of NFDI4Microbiota [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/unimr_lea…] The Hessian Federal state initiative organizes each year the HeFDI Data Week, which is aimed at researchers, educators, students and anyone interested in learning more about topics like FAIR data. On June 5th, Thomas Clavel and Shahram Saghaei presented our consortia speaking about: NFDI4Microbiota - Infrastructure, Microbiology, Databases and Interaction. The presentation started with Thomas Clavel introducing NFDI4Microbiota and detailing interaction possibilities. After that, he exemplified the Use Cases, which are research projects from the community that profit from the services of NFDI4Microibota. Sharam Saghaei who described VirJenDB - a database that aims to be the central hub to connect virus researchers with publicly available virus resources, metadata and sequences, concluded the presentation. VirJenDB is now also an active Use Case of NFDI4Microbiota. NFDI GEo-Chem-Life-Sciences-Helpdesks meeting in Bremen On May 27th and 28th 2024, representatives of NFDI4Microbiota, NFDI4Health, NFDI4Biodiversity, NFDI4Chem, NFDI4Earth, NFDI4BioImage, DataPlant und FAIRagro came together in Bremen to discuss Helpdesks and support structures. This was a great opportunity for us to meet and connect, share experiences and discuss future collaborations with consortia of closely related disciplines. Together we compiled a competence matrix and workflows for liaising on interdisciplinary questions and for the efficient transfer of tickets between consortia to ensure that inquiries can be forwarded to the most qualified Helpdesk. Our NFDI4Microbiota Helpdesk answers all kinds of questions and issues regarding data management and data analysis as well as queries about the NFDI4Microbiota consortium, services, outreach, community activities, and more. [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/helpdesk_…] You can contact the Helpdesk by filling out the contact form<https://nfdi4microbiota.de/contact-form/> or sending us an email.<mailto:helpdesk@nfdi4microbiota.de> Community Engagement Upcoming Events and Conferences ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/n4m_save-…] Save the date: NFDI4Microbiota annual conference December 3rd-4th, 2024 Please mark your calendar: we will have this year's annual conference in Leipzig, Germany on December 3rd to 4th. There will be a panel discussion, interesting keynotes, helpful workshops and more you can look forward to. More information and registration opportunity coming soon on our events page<https://nfdi4microbiota.de/newsroom/events.html>. Take part in the next NFDI4Microbiota Knowledge base sprint Are you a microbiology researcher, research data management enthusiast or developer? We need your help! Join the next NFDI4Microbiota Knowledge Base Content & Coding Sprint on September 11th. The Knowledge base offers extensive information about research data management, software development and much more. And you can help us to make this even better! Contribute to the content or improve the code. If you are interested, get more information and registration here.<https://pretix.eu/n4m/2KBsprint/> 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/eighthnewsletter/n4m_ambas…] 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 July 29th, starting at 14:30 CEST. Frank Förster of the JLU Gießen will tell us about ARUNA object storage. Did you ever wished to share your data in a domain-agnostic, fast and secure way that additionally ensures sharing accordingly to the FAIR principles? Or are you related to data management and would like to learn about ways to share data? Be sure not to miss this talk. Get more information about the program here.<https://nfdi4microbiota.de/community/ambassador.html> [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/coffee_ta…] 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 August 26th. 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 just opened! [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/megafon.p…] We are glad to inform you, that the 2025 Flex Funds call is open from June 10th to August 7th 2024. What is funded? The NFDI4Microbiota Flex Funds provide funding to perform a short one-year project from the community. The project needs to correspond to the mission of NFDI4Microbiota. A list of matching topics is provided below. What is the aim of the Flex Funds? The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, development of new training programs, and improvement of the ability to react to unforeseen technical challenges. Therefore, within the NFDI4Microbiota project work, flexible funding (so called 'Flex Funds') for small projects (12 months) within the research community are available for the years 2023 to 2026. To achieve a dynamic system that stays on track with new trends in the field, the Flex Funds support small projects from the community and active Use Cases. What are eligible topics? Eligible topics are as follows: * Data Brokerage * Workflow development * Data storage and workflow execution * Infrastructure/Services * Training * Community engagement and outreach * Establishment of local data stewards * Use Case connection or an active Use Case * Deposition of high quality data sets in public repositories Details on the eligible topics, further information on the call and the procedure can be found on the NFDI4Microbiota web portal.<https://nfdi4microbiota.de/newsroom/flexfunds.html> In case you have questions, please do not hesitate to contact us via contact(a)nfdi4microbiota.de.<mailto:contact@nfdi4microbiota.de> Training Announcements ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/Isometric…] There are several interesting training offers currently open for registration, like: * Summer-School: Trends in multiomics data analysis for Microbial Ecology and Biotechnology (July 8th-26th) * Optimizing Microbial Research Data Utilization: Integrating Electronic Lab Notebooks into your data management strategy (Aug 27th-29th) * Computational Pangenomics Workshop @ GCB (Sep 30th) * The NFDI4Microbiota and de.NBI 16S amplicon training course (Oct 8th-10th) And more courses are planned. In September you can learn about "Linux Basics for Bioinformatics" and in November about "Metagenomics". As soon as the registration opens, you will find it on the NFDI4Microbiota website.<https://nfdi4microbiota.de/services/training.html> More courses will be announced soon, so check the website regularly for training opportunities. Previous Training ________________________________ Biometadata Workshop: How to Describe Biological Data? A Primer to a FAIR Approach for Now and the Future [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/20240607_…] Did you miss the recent Biometadata workshop in Tübingen? If so, you skipped on an incredible opportunity to dive deep into the world of biological metadata with leading experts in the field. But don't worry-there's always next time! Understanding and implementing FAIR standards is crucial in modern research. Metadata provides the context necessary for data to be understood and reused, ensuring reproducibility, and facilitating further research. However, the process of thoroughly describing data with appropriate metadata can be complex and daunting. This workshop aimed to demystify the process, clearing the fog, and revealing the path forward. Designed for beginners, the workshop was perfect for those new to data submission and the collection of biological metadata in microbiome research. It focused on using terms based on existing ontologies and controlled vocabularies, crucial for enabling future machine-actionable analyses. Participants engaged with an online pad for interactive exercises and a team of helpers to support them when puzzled. All adhered to the Carpentries' code of conduct to create a safe and inclusive environment. This approach ensured that everyone felt comfortable participating and asking questions. Given the wealth of material covered in a single day, we actively monitored participants' expectations and learning goals. Here are some of the goals they shared: * Uploading metadata for metagenomics data: Participants wanted to learn how to upload data and metadata to the required online repositories and understand what these repositories are. * Organizing biological data: Many attendees sought to bring order to the chaos of their biological data. * Identifying necessary metadata: There was a strong desire to learn what metadata needs to be collected and recorded for scientific data. To address these goals, the workshop included a beginner's guide to metadata and ontologies, reviewed data repositories and metadata fields, standards, and minimal requirements. We also explored data description examples, ontologies for biological data, and introduced the DataHarmonizer tool to aid in metadata collection and validation. Interactive exercises were a core part of the workshop. Participants worked in groups to explain their own datasets and annotate them with ontology terms, turning what might have been a dry topic into a dynamic and engaging experience. This free workshop was led by two Carpentries certified NFDI4Microbiota instructors from the Functional Microbiome Research Group at the Institute of Medical Microbiology, University Hospital of RWTH in Aachen. Cooperations ________________________________ BY-COVID project is about to start A NFDI4Microbiota team consisting of Noriko Cassman and Manja Marz from FSU Jena and Konrad Foerstner from ZB MED, has secured a grant by the BeYond-COVID (BY-COVID) consortium through a successful proposal to the open call "Support for the implementation of SARS-CoV-2 data hubs at national and regional levels".<https://by-covid.org/news/support-implementation-sars-cov2/> The proposal is titled "Validation and submission tool to facilitate virus data flow into ENA via secure intermediate storage". Now, that the agreement has finally been signed, the project will extend VirJenDB, the comprehensive virus database based at FSU Jena which is currently being developed as an NFDI4Microbiota service and Use Case<https://nfdi4microbiota.de/community/usecases/virjendb> to connect researchers and virus research data and resources. The work in the proposed project has three planned parts: 1) virus pathogen metadata curation and integration, 2) validation parameter evaluation and 3) submission tool development. These will be carried out to achieve the shared goals of VirJenDB and BY-COVID projects, which are to help mobilize (German) virus sequence data to the ENA. The awarded amount is 60,000 euros over 6 months in 2024. We look forward to the results of this project! [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/social_me…] If you would like to have more information, check the following links: * BY-COVID<https://by-covid.org/> * ENA<https://www.ebi.ac.uk/ena/browser/home> * FAIR Principles<https://doi.org/10.1038/sdata.2016.18> * ELIXIR<https://elixir-europe.org/> Recent Publications ________________________________ Ten simple rules for implementing electronic lab notebooks (ELNs) NFDI4Microbiota Data Steward Justine Vandendorpe just published an excellent overview of ELNs. The paper "Ten simple rules for implementing electronic lab notebooks (ELNs)"<https://doi.org/10.1371/journal.pcbi.1012170>, published in PLOS Computational Biology, provides invaluable insight and practical steps for selecting and implementing ELNs. An ELN is a software tool for documenting laboratory experiments, research data, and processes. ELNs are poised to replace paper lab notebooks as part of the ongoing digital transformation and offer many advantages over physical lab notebooks. Dive into Justine's article to learn more about the ten rules to help you on your journey to implementing ELNs. Key highlights include an in-depth discussion of the benefits of open-source ELNs, an emphasis on the importance of standardization, and a handy questionnaire to test the usability of ELNs in the supporting information. A practical approach to using the genomic standard's consortium MIxS reporting standard for comparative genomics and metagenomics A group of scientists around NFDI4Microbiota co-speaker Alice McHardy published a protocol belonging to the book "Comperative Genomics, Methods and protocols", published by Humana, New York. The name of the protocol is: "A practical approach to using the genomic standard's consortium MIxS reporting standard for comparative genomics and metagenomics".<https://doi.org/10.1007/978-1-0716-3838-5_20> The book belongs to the book series "Methods in Molecular Biology". The protocol provides a description of the structure and terminology of the GSC's MIxS reporting standard, how to navigate ontologies for required terms in MIxS, and demonstrates practical usage through a soil metagenome example. The Genomic Standards Consortium (GSC) collaborates with the research community to develop and maintain the Minimum Information about any (x) Sequence (MIxS) reporting standard for genomic data to enable comparative analysis of (meta)genomes necessitates aggregation, integration, and synthesis of well-annotated data using standards. New video publications available 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, 9 months

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NFDI4Microbiota - 2025 Flex Funds call is open now! (closes on August 7th 2024)

by contact＠nfdi4microbiota.de

Dear NFDI4Microbiota community, We are glad to inform you, that the 2025 Flex Funds call just opened! The call will be open from June 10th to August 7th 2024. What is the aim of the Flex Funds? The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, development of new training programs, and improvement of the ability to react to unforeseen technical challenges. Therefore, within the NFDI4Microbiota project work, flexible funding (so called 'Flex Funds') for small projects within the research community are available for the years 2023 to 2026. To implement a dynamic system that stays on track with new trends in the field, the Flex Funds will support small projects from the community and active Use Cases. What are eligible topics? Eligible topics are as follows: · Data Brokerage · Workflow development · Data storage and workflow execution · Infrastructure/Services · Training · Community engagement and outreach · Establishment of local data stewards · Use Case connection or an active Use Case · Deposition of high quality data sets in public repositories Details on the eligible topics, further information on the call and the procedure can be found on the NFDI4Microbiota web portal<https://nfdi4microbiota.de/newsroom/flexfunds.html>. While you're on the web portal, do not miss out to take a look at our newly listed services. In case you have questions, please do not hesitate to contact us via contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de>. We are looking forward to your application! Kind regards, The NFDI4Microbiota Adminsitration Unit --- 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, 10 months

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NFDI4Microbiota Online Seminar on Electronic Lab Notebooks

by Vandendorpe, Justine

Dear all, We cordially invite you to our first NFDI4Microbiota Online Seminar on Electronic Lab Notebooks (ELNs) on 17 June 2024 from 13:00 to 16:00. After an introduction to the National Research Data Infrastructure for Microbiota Research (NFDI4Microbiota), we will give a general introduction to ELNs and then delve into their implementation. We will then have presentations from two eLabFTW users, Daniel Kelvin (TU Darmstadt) and Elena Bencúrová (Uni Würzburg), and from an eLabFTW developer, Nicolas Carpi (Deltablot). All presentations will be recorded and will be followed by a Q&A session. We will conclude with demo instances, the way forward and a general Q&A session. Please register here: https://us02web.zoom.us/meeting/register/tZcrdu2rrDooGdDUSZMM4VcF6l8sxYJXnh…. If you have any questions, please contact me (vandendorpe(a)zbmed.de). Yours sincerely Justine Vandendorpe -- Justine Vandendorpe, MSc. Biology of Organisms and Ecology Data Steward within NFDI4Microbiota ZB MED - Information Centre for Life Sciences Gleueler Straße 60 50931 Cologne vandendorpe(a)zbmed.de +49 (0)221/478-71 20 www.zbmed.de INFORMATION. KNOWLEDGE. LIFE.?

1 year, 11 months

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NFDI4Microbiota Coffee Talk on Electronic Lab Notebooks

by Mueller, Mattea

Dear Ambassadors, Members, Participants, and Community, We are excited to invite you to our NFDI4Microbiota Coffee Talk<https://nfdi4microbiota.de/newsroom/news/2024-02-26-coffee-talk-online> on Electronic Lab Notebooks (ELNs). Join us on Monday, 26th February, from 15:30 to 16:30 CEST, as our expert, Justine Vandendorpe, guides us through the importance of ELNs, their benefits, and key features. The event will conclude with a Q&A session, providing you with the opportunity to ask any questions you may have about ELNs. Here are the details to join the session: 📅 Date: February 26th ⏰ Time: 15:30-16:30 CEST 📍 Zoom Meeting ID: 647 3481 9818🔒 Passcode: 269915 Save the date and join us for an engaging discussion on ELNs. Best regards, The NFDI4Microbiota Outreach 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/

2 years

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NFDI4Microbiota Newsletter 2/2024

by Aue, Stephanie

[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/icon_new… Quarter 2 2024 Dear Reader, with our seventh NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, cooperations and publications. 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 ________________________________ NFDI4Microbiota joined the annual meeting of the Research Data Alliance As a part of NFDI e.V., NFDI4Microbiota is a member of the Research Data Alliance (RDA) Germany<https://www.rda-deutschland.de/>. The goals of the RDA, like to improve the social and technical requirements for an increased data exchange and an easier reuse of data, align with ours. Therefor we were happy to represent our fields of expertise at the annual meeting on February 20th and 21st. [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/rda_logo… to the recent entry of NFDI e.V. into the RDA, the presence of NFDI consortia was significantly increased compared to previous years. Alongside NFDI and NFDI4Microbiota, other consortia like NFDI4Earth also showcased their work. In total, there were approximately six posters related to NFDI, our NFDI4Microbiota Poster included. The meeting proved to be insightful, offering a different perspective on research data management than usual. Notably, several talks delved into the political aspects of research data management. One such talk was delivered by Renate Nikolay, the Deputy Director General for Communications Networks, Content, and Technology at the EU Commission, focusing on “The Cornerstones of the European Data Strategy.” Successful NFDI4Microbiota Knowledge Base Content and Coding Sprint The NFDI4Microbiota Knowledge Base<https://knowledgebase.nfdi4microbiota.de/> is a collection of information and references with relevance for the microbiology community in terms of Research Data Management, Data Analysis, FAIR principles, standards, and much more. Furthermore, information about the NFDI4Microbiota consortium are collected. To raise awareness of this resource and to further improve it, we planned a comprehensive Knowledge Base Content and Coding Sprint. After having to reschedule the event multiple times, we finally found a time slot in February 2024 to hold the NFDI4Microbiota Knowledge Base Content and Coding Sprint in Cologne. Roughly 20 participants, mostly, but not exclusively, from NFDI4Microbiota, came together in a 2-day concentrated effort to push the NFDI4Microbiota Knowledge Base forward. Some joined us online, while others met at ZB MED in Cologne. A lot of content was added by individuals and groups focusing on specific topics. Perhaps more importantly, getting so many interested people together has allowed us to have in-depth discussions about issues and strategies related to the Knowledge Base that might not have happened otherwise. [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/knowledg…] We consider the NFDI4Microbiota Knowledge Base Content and Coding Sprint an overall success. This is not just limited to the two days dedicated to the Sprint. Having people interested in the Knowledge Base and learning about it in preparation for the Sprint already had an impact. Leading up to the Sprint, and especially in the weeks following the Sprint, the Knowledge Base Git repository showed a much higher level of activity than usual. Given the reception and success of the sprint, we are aiming to have this as a regular recurring event. Specifically, we, and you, can look forward to the next instance of the NFDI4Microbiota Knowledge Base Content and Coding Sprint, planned to be hosted in Marburg on September 11th - 13th, 2024. Community Engagement - Upcoming Events and Conferences ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/DGHM_VAA…] Meet us in Würzburg on June 2-5, 2024 NFDI4Microbiota is attending the VAAM&DGHM Microbiology & Infection Conference<https://dghm-vaam.de/> in Würzburg. The conference takes place on June 2-5, 2024. We look forward to meet you in person, so feel free to step by, if you are attending and learn more about us. [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/n4m_amba… ambassador meetings On January 29th we restarted the NFDI4Microbiota Ambassador program. During the first meeting, we provided an overview of NFDI4Microbiota in general and discussed the ambassador program. On March 25th, Sarah Schulz from EMBL delivered a talk on “Standards and Policies” related to NFDI4Microbiota. In July (29th) we will delve into ARUNA Object storage<https://aruna-storage.org/>) with detailed insights shared by Frank Förstner. November (25th) Kassian Korbert (BiBI) will tell us about the NFDI4Microbiota Knowledge Base<https://knowledgebase.nfdi4microbiota.de/>. The topic for September is still to be determined. Are you a postdoc or a PhD student in the field of microbiology, or are you interested in data management? Or perhaps you know someone who might be interested? We warmly welcome new participants and invite you to join our bimonthly meetings, which are held on the last Monday of each month at 3:30 PM. Learn more about the program and register here.<https://nfdi4microbiota.de/community/ambassador.html> Services ________________________________ Involving our community through new Use Cases Three new Use Cases have been accepted recently and will expand NFDI4Microbiota’s pool of services to create targeted solutions for you and us. Our Use Cases are your explicit invitation to get involved as they offer possibilities to engage with the research community, so take a look at the new Use Cases to see what the future holds: 1. MicroBioKG will be explore and serve as a blueprint for how knowledge graphs can make microbiological data FAIR, open and sustainably accessible, and how this enables connectivity between resources. This Use Case will follow three real projects with real data. Follow them and you will soon be able to apply the guidelines developed by Vanessa Scharf and Konrad Förstner to your own data. 2. LichenMetaImage will explore the best of many worlds – namely lichen (fungus and bacterial photosymbiont) and its unique interaction with its microbiome – using a multi-omics (imaging, metagenomics, transcriptomics) approach. This Use Case will also bridge existing imaging metadata collection efforts developed by DataPLANT<https://www.nfdi4plants.de/> and NFDI4BIOIMAGE<https://nfdi4bioimage.de/home/>. We are excited to see what Björn Usadel and Stefanie Weidtkamp-Peters’ big picture will look like. 3. VirJenDB is now also a Use Case as future plans to expand the platform include adding automated and community curated analysis workflows, data, metadata and more (see above). By interacting with this Use Case, e.g. as an interested virologist with data published in ENA, you could be trained in RDM topics and contribute to community curation of the platform and datasets. These and many more interaction opportunities will be offered soon. The faces behind this Use Case are Noriko Cassmann, Manja Marz and Shahram Saghaei. Collecting publicly available virus resources, metadata and sequences: VirJenDB [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/virjendb… are pleased to announce the beta release of the VirJenDB version 0.1 which is available here.<https://virjendb.uni-jena.de/> VirJenDB is a comprehensive virus database based in Jena providing user-friendly access to community-curated virus sequences, metadata, visualizations and tools. If you are interested in becoming a beta user, joining the curation community, or helping us to improve the database, please email the VirJenDB team<mailto:virjendb@uni-jena.de>. Training Announcements ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/Isometri…] There are several interesting training offers currently open for registration, like: · the NFDI4Microbiota and de.NBI 16S amplicon training course (Oct 8th-10th 2024) · Microbiota profiling by 16S rRNA gene amplicon sequencing: Data analysis Workshop And more courses are planned. For example, there will be an “Introduction to R course” in early May, and “Basic statistic with R” at the end of May. In September you can learn about “Linux Basics for Bioinformatics” and in November about “Metagenomics”. As soon as the registration opens, you will find it on the NFDI4Microbiota website<https://nfdi4microbiota.de/services/training.html>. More courses will be announced soon, so check the website regularly for training opportunities. Join us for our next Electronic Lab Notebook (ELN) event on June 17, 2024 Our successful ELN events are going into the next round! Join the online seminar on June 17, 2024 from 13:00 - 16:00 CET. The seminar will provide you with an overview of NFDI4Microbiota and ELNs in general, followed by in-depth presentations and discussions on eLabFTW from different perspectives (experienced and new users, developers). Save the date if you are interested! Registration will start soon and will be announced here.<https://nfdi4microbiota.de/services/training.html> Previous Training ________________________________ Joint NFDI & de.NBI Metagenomic Training Course 2023 In early February, de.NBI and NFDI4Microbiota collaborated to host a comprehensive training course on metagenomic data at the University Bielefeld. With that the Task Area 1 of NFDI4Microbiota<https://nfdi4microbiota.de/aboutus/work-programme/ta1-community-network-tra…> completed one of its milestones. [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/metageno…] The participants, representing over 10 different research institutes from across Germany, were primarily at early to mid-career stages. Spanning three days, the course provided an extensive overview of tools and bioinformatics techniques essential for analyzing next-generation sequence (NGS) data from microbial communities, with ample hands-on training opportunities. The first two days focused on preprocessing, quality assessment, error management, and various genome-related tasks such as assembly, binning, and taxonomic and functional analysis. On the final day, participants learned from experts of the Helmholtz Centre of Infection Research (HZI) how to incoporate metagenomics worklflow in nf-core workflows using Nextflow for automated and reproducible analysis. [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/metageno…] In summary, the workshop proved to be both intense and engaging with lots of opportunity to ask questions and network with peers. Special thanks to all the organizers for their efforts in making this event a success! Cooperations ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/Isometri… joined JourFixe of the FDM initiatives Most of the German federal states have set up initiatives for research data management (RDM), which network with each other in a regular JourFixe, the Forum of Digital Methods (FDM) initiatives. The aim of these initiatives is to establish recommendations and solutions for RDM processes in the respective federal states and to incorporate these into an overall national strategy as part of the joint JourFixe. To support those initiatives with their profound knowledge and expertise, the NFDI consortia joined the JourFixe on February 21, 2024. The NFDI consortia were specifically invited to increase their presence and contribute to the discussions. The main topic of the meeting was “International Outreach and Exchange.” There were 25 attendees, with the majority not from NFDI4-related initiatives. Represented at the meeting were NFDI e.V, NFDI4Objects, NFDI4Ing, Base4NFDI, NFDI4Ing, and NFDI4Microbiota. The JourFixe provided an opportunity for the exchange of ideas and to plan cooperation on several projects. One of these projects is to write a paper or an abstract about the structures and diversity of Research Data Management (RDM) initiatives and actors in Germany and explain the complexity of the field. 2024 Flex Funds projects The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, development of new training programs, etc. Therefore, within the NFDI4Microbiota project work, flexible funding (so called ‘Flex Funds’) for small projects within the research community are available for the years 2023 to 2026. To implement a dynamic system that stays on track with new trends in the field, the Flex Funds will support small projects and active Use Cases from the community as they arise over time. The 2024 Flex Funds call resulted in the approval of four new Flex Funds projects funded with an overall budget of approx. 300,000 €. Short abstracts of them will be published on the web portal in the near future. The project titles are listed below. * Piloting the integration of national sequencing centers with NFDI4Microbiota through metadata capture and data submission workflows * Prediction of novel gut biotransformation pathways * Establishment of guidelines for metaproteomics research data management and quality control * Empowering All Microbiome Scientists: Building Bioinformatic Proficiency for Advancing Microbiome Science Worldwide The projects are funded on an annual basis. The 2025 Flex Funds call will be most likely opened in the mid of June 2024 and can be found on the web portal<https://nfdi4microbiota.de/newsroom/flexfunds.html>. Recent Publications ________________________________ Best practices on how to share microbiome data Microbiome data, metadata and analytical workflows have become ‘big’ in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary and multi-omic nature of the field can make resources difficult to identify and use. Do you want to learn more about sharing of microbiome data and the way it is analyzed? If this is the case, you should check the article “Challenges and opportunities in sharing microbiome data and analyses”<https://www.nature.com/articles/s41564-023-01484-x>, published 2023 in Nature Microbiology. NFDI4Microbiota co-speaker Alice McHardy, together with Curtis Huttenhower and Robert D. Finn, outlines in this article best practices, challenges and opportunities in sharing microbiome data. They are also calling out successful examples to date and suggest steps for future improvements. NFDI4Microbiota – national research data infrastructure for microbiota research Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. Learn more about NFDI4Microbiota and its way to achieve its goal in the article “NFDI4Microbiota – national research data infrastructure for microbiota research”<https://doi.org/10.3897/rio.9.e110501> by Konrad U. Förstner et.al., published 2023 in Research Ideas and Outcomes. Social Links and Contact ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/Bluesky_… is now part of the BlueSky network To replace our now deprecated X-account, NFDI4Microbiota started a Bluesky account. Follow us on BlueSky<https://bsky.app/profile/nfdi4microbiota.bsky.social>. We are looking forward to get in touch with you there. ________________________________ 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/

2 years

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[NFDI4Microbiota] New Use Cases presentations Tuesday 26th 13-14:30

by Magel, Maja

Dear NFDI4Microbiota enthusiasts, Get to know the three new Use Cases that will work on helping us and YOU to 1. create knowledge graphs for linked microbial data - MicroBioKG by Vanessa Scharf and Konrad Förstner 2. solve collection of image metadata - LichenMetaImage by Stephanie Weidtkamp-Peters and Björn Usadel 3. use & contribute to a curated database for viral sequences - VirJenDB by Noriko Cassmann and Manja Marz Meeting details: Tuesday, 26th March from 13:00 - 14:30 CET https://rwth.zoom-x.de/j/63077798681?pwd=dkZYWHRMYVZ5NmhWRjJZVTJCMW5yQT09 Meeting-ID: 630 7779 8681 Kenncode: 973383 Please feel welcome to forward this invitation to your colleagues and collaborators. Best Maja Magel Projektkoordination NFDI4Microbiota Institut für Medizinische Mikrobiologie Research Group Functional Microbiome [cid:image001.png@01DA761B.EFFCAF00] ________________________________________ Tel.: +49 (0) 241 80-38117 E-Mail: mmagel(a)ukaachen.de<mailto:mmagel@ukaachen.de> Aufzug D4, Etage 5, Raum 34 Universitätsklinikum Aachen Pauwelsstraße 30 52074 Aachen

2 years, 1 month

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NFDI4Microbiota: Newsletter and community workshop (today 10:00-12:00)

by Hege, Cordula Almut Selma

Dear Reader, With our sixth NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, ELN (Electronic Lab Notebooks), grants and new cooperations. And as this is the first newsletter of the year, there will also be a short review of 2023. 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! In case you have problems with reading the pdf, tomorrow you will be able to read it on our homepage: https://nfdi4microbiota.de/latest/newsletter Don't forgot our community workshop starting soon: NFDI4Microbiota Community Workshop (February 5th, 10-12:00 CEST, online) There are new NFDI4Microbiota<https://nfdi4microbiota.de/> services online! We will introduce them in our online community workshop on February 5, 2024, 10-12 CEST. We will talk about the NFDI4Microbiota Knowledge Base<https://knowledgebase.nfdi4microbiota.de/> which provides information about research data management, software development and much more. You will get insights how to use the ARUNA<https://aruna-storage.org/)> Object storage to store your (meta-)data according to FAIR<https://www.nature.com/articles/sdata201618> principles. A live demo of StrainInfo<https://straininfo.dsmz.de/> will introduce you to our service that is providing microbial strain identifiers. Finally, the new virus database VirJen<https://virjendb.uni-jena.de/> will be presented. Join us and log in via Zoom: https://th-koeln.zoom-x.de/j/68754647684?pwd=dXN2R0R6OGNpQ2V3VUEzUE5ZbVdsZz… Meeting ID 687 5464 7684 Passcode: 363736 Best wishes, Mattea, Barbara and Cordula Dr. Cordula Hege 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/

2 years, 2 months

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NFDI4Microbiota: Community workshop (05. February), Knowledge sprint 15-16. February

by Hege, Cordula Almut Selma

Dear NFDI4Microbiota community, There are two exciting events coming up: the 6th NFDI4Microbiota community workshop, followed two weeks later by the NFDI4Microbiota Knowledge Base sprint. In the online community workshop, we will present some of the services that NFDI4Microbiota and their partners offer. Learn how you can use the ARUNA Object Storage<https://aruna-storage.org/> to store your (meta-)data according to FAIR principles. In addition, you will get to know StrainInfo<https://straininfo.dsmz.de/>, providing microbial strain identifiers, and get insides into the new virus database VirJen<https://virjendb.uni-jena.de/>. The community workshop will take place on February 5, 2024 from 10-12 AM CEST. Join us and log in to Zoom with: Meeting ID 687 5464 7684, Passcode: 363736 After gaining insights in our services, you can actively participate in the work of NFDI4Microbiota by contributing to the Knowledge Base<https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/> Join us at the Knowledge Base sprint. The Knowledge Base<https://mail.helmholtz-hzi.de/owa/#x__msocom_1> is a collection of information and references relevant to the microbiota research community, such as research data management and data analysis. It also contains information about the inner workings of the consortium. The sprint is aimed at microbiology researchers, research data management experts and developers who are interested in contributing to the Knowledge Base, either by adding content or improving the code. If you would like to join us, please register by January 31st here<https://cryptpad.fr/form/#/2/form/view/sKOITY2GK+GGBgIBMln1UPduvIC3xbDu2CvH….>. Practical details can be found on the registration form and will be sent out again after registration. Looking forward to seeing you at one or both of the events, Barbara, Stephanie, Mattea, Justine and Cordula Dr. Cordula Hege 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/

2 years, 3 months

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