- Nfdi4microbiota-announce

NFDI4Microbiota - Save the date: Lecture talks on the 24th of April 2023 11-12:30 CEST + training announcements

by Goetz, Barbara

Dear NFDI4Microbiota community, save the date for our short lecture talks on different services NFDI4Microbiota provides for its community: training, workflows, Use Cases and the NFDI4Microbiota Knowledge Base. The lectures will be webcasted on the 24th of April 2023 11-12:30 CEST. The login details will be shared with you soon. We also would like to announce training offers by our partner: · 3-day Workshop on Nanopore Sequencing<https://bic.uni-jena.de/what-we-offer/training/>, 2023-04-26 - 2023-04-28, 09:00 - 16:00 CEST. · Introduction to R<https://docs.google.com/forms/d/e/1FAIpQLSd3U-NmjfZOIORKmhGsd__q1SwtWSvI3dY…>, 2023-05-15 - 2023-05-17, 10:00 - 13:00 CEST. Your NFDI4Microbiota Administration Unit, Barbara Götz, Carmen Paulmann and Cordula Hege --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years

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NFDI4Microbiota Newsletter 01/23

by Paulmann, Carmen

Welcome Dear Reader, With our third NFDI4Microbiota newsletter, we would like to share news about our upcoming conferences and events. In this issue, you can also read about our connecting efforts and we continue presenting recent publications, news and much more. If you are interested in other topics we should cover, please let us know. We are happy to hear from you! And now: Enjoy reading the newsletter! [cid:acbf171d-64b1-4e79-b779-c87d658e74e1] _________________________ Community engagement – events and conferences Save the date for the second NFDI4Microbiota annual conference The theme of this year's NFDI4Microbiota conference is "Community Engagement", as we want to get to know our participants and their needs, and give them an insight into our services. The conference will take place April 24-26, 2023, venue and registration information will follow shortly. On the morning of the first day, we will present our services to the community during NFDI4Microbiota lectures, which will be available online for everyone to attend. The rest of the conference will be reserved for NFDI4Microbiota participants, ambassadors, committees and the NFDI4Microbiota consortium. The first day will be a community day to connect with our participants and ambassadors. The second day will be dedicated to cross-cutting issues such as training and workflows, as well as the General Assembly. The third day will feature inspirational talks from international speakers involved in similar projects, followed by roundtable discussions about our Use Cases and a community workshop. Love is in the air! NFDI4Microbiota contributes to Love Data Week 2023 with a panel discussion on the benefits of data-driven decisions in life sciences During the Love Data Week 2023, several NFDI consortia participate in events or training regarding the topic “Data: Agent of Change”. Together with the NFDI consortia DataPLANT, NFDI4Health and NFDI4Biodiversity, we will host an in-person panel discussion on ‘Wind of change - sharing is caring! How to improve research data and its benefits in the Life Sciences’ at the University of Bremen. Data-driven decisions in the life sciences have an immense impact on human and environmental well-being, as well as on the development of research directions. Therefore, experts from different areas of the life sciences will discuss the importance of data-driven decisions using best practice examples. Expect an in-depth discussion on the challenges and benefits of cultural change related to research data governance, Open Science and FAIR principles and their impact on the daily life of each individual. * Panelists: Prof. Dr. Konrad Förstner (NFDI4Microbiota), Björn Usadel (DataPLANT), Dr. Barbara Ebert (NFDI4Biodiversity), Prof. Dr. Dagmar Waltemath (NFDI4Health) * Moderation: Dr. Kerstin Elbing (VBio) * Location: University of Bremen Bremen, Room NW2 C0290 (Hörsaal 1) * Date and time: 2023/02/16 15.00 - 17.00 PM CEST * Zoom option: Meeting-ID: 812 3227 9619, Password: 092856 [cid:967bf743-0b62-405f-9667-f0b7a6addb88] NFDI4Microbiota World Café on Electronic Lab Notebooks (ELNs) To identify the needs of the German microbiology research community on Electronic Lab Notebooks (ELNs), we will run a virtual World Café on 2023-02-24, 10:00 - 12:00. After an introduction, we will discuss topics such as General Needs, Interoperability, Ergonomics and Processes & Workflows. Ultimately, we would like to help the microbiology sub-communities to select and implement an ELN in their research group. To participate, please register here<https://us02web.zoom.us/meeting/register/tZAqceyppjwpHdRHg7uF7AqPb6Yxq4Phq3…>. NFDI4Microbiota will showcase its activities to the virology and parasitology communities In March, we will present our mission, work progress and services at the 32nd Annual Meeting of the Society for Virology <https://virology-meeting.de/> and the 30th Annual Meeting of the German Society for Parasitology<https://parasitology-meeting.de/>. The NFDI4Microbiota consortium members met at the first NFDI4Microbiota annual conference In November 2022, we met for the first time during the internal NFDI4Microbiota conference in Cologne. Presentations and fruitful discussions took place on our current work in the areas of computational infrastructure, data storage and analysis, data and metadata standards, training and outreach. In addition, our six active Use Cases<https://nfdi4microbiota.de/latest/usecase> were presented and discussed in roundtable sessions. [cid:729f6990-ab4c-44e2-8221-03696c157b63] The NFDI4Microbiota consortium met in Cologne. _________________________ Networking and Collaborations Regular exchange of NFDI4Microbiota and NMDC The National Microbiome Data Collaborative (NMDC) was initiated in July 2019 as the foundation of a community-driven US national effort aimed to develop standards, processes, and infrastructure for an integrated microbiome data ecosystem. The NMDC aims to achieve similar solutions for the US as we at NFID4Microbiota are pursuing for Germany. They are working with the community to develop and lead an integrated, open-source microbiome science gateway that leverages existing resources and enables comprehensive access to multidisciplinary microbiome data and standardized, reproducible data products. Like our NFDI4Microbiota consortium, NMDC is committed to open science and the FAIR principles. Our representatives from NFDI4Microbiota meet regularly with those from NMCD to explore synergies and to determine how best to integrate efforts in all areas, such as standards, analytical workflows, data and results sharing, and training. [cid:fb6eee7e-d580-43c5-9cc4-4fb56ca0ae39] _________________________ Publications Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities – Published in Cell Host & Microbe Microbiome research needs comprehensive repositories of cultured bacteria from the intestine of mammalian hosts. The groups of our NFDI4Microbiota partners, Prof. Thomas Clavel and Prof. Jörg Overmann, both NFDI4Microbiota partners, expanded the mouse intestinal bacterial collection to 212 strains, all publicly available and taxonomically described. This includes strain-level diversity, small-sized bacteria, and previously undescribed taxa (one family, 10 genera, and 39 species). This collection enabled metagenome-educated prediction of synthetic communities (SYNs) that capture key functional differences between microbiomes, notably identifying communities associated with either resistance or susceptibility to dextran sulphate sodium (DSS)-induced colitis. Additionally, nine species were used to amend the Oligo-Mouse Microbiota (OMM)12 model, yielding the OMM19.1 model. The added strains compensated for phenotype differences between OMM12 and specific pathogen-free mice, including body composition and immune cells in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks are available for future studies. In conclusion, this work improves the knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates. Microbiota research is hampered by the fact that approximately half of complex microbial communities is still unknown. Moreover, there is a lack of cultured isolates publicly available, which prevents functional studies. This published work addresses both issues by making cultured bacteria from the mouse intestine and their metadata available according to FAIR principles. Read more Toward FAIR Representations of Microbial Interactions – Published in mSystems Despite an ever-growing number of datasets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies. Here, Charlie Pauvert from our consortium and the other authors propose guiding principles to make microbial interaction data more findable, accessible, interoperable, and reusable (FAIR). They outline specific use cases for interaction data that span the diverse space of microbiome research, and discuss the untapped potential for new insights that can be fulfilled through broader integration of microbial interaction data. These include, among others, the design of intercompatible synthetic communities for environmental, industrial, or medical applications, and the inference of novel interactions from disparate studies. Lastly, they envision potential trajectories for the deployment of FAIR microbial interaction data based on existing resources, reporting standards, and current momentum within the community. Read more _________________________ Services and Infrastructure The BacDive database of the Leibniz Institute DSMZ has been selected as a Global Core Biodata Resource The Bacterial Diversity Metadatabase (BacDive) of the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH has been selected as a Global Core Biodata Resource by the renowned Global Biodata Coalition. This makes BacDive one of the most important global databases for bacterial research. BacDive is the world’s largest database for standardised bacterial phenotypic data, developed by one of our partners. It aims to mobilise and standardise research data to improve the accessibility and comparability of phenotypic data in microbial research. Read more [cid:7991d46f-b833-4752-b89d-ac3f61cd42b2] _________________________ Media In a recent episode of the Open Science Radio Podcast the director of the NFDI, York Sure-Vetter, gives an overview of the NFDI including the potential and challenges as well as its history and international context. Listen to it. _________________________ Social links and Contact Follow us on Twitter and GitHub! Questions or suggestions? Learn more about NFDI4Microbiota! Subscription / Unsubscription 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. Dr. h.c. Dirk Heinz - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

3 years, 2 months

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NFDI4Microbiota - Happy new year + training and event announcements

by Goetz, Barbara

Dear NFDI4Microbiota community, Happy new year to all of you! We are looking ahead to the year 2023 under the motto "Community Engagement". Today we would like to point out some event and training highlights : · Love Data Week 2023<https://forschungsdaten.info/fdm-im-deutschsprachigen-raum/love-data-week/> 2023-02-16, 15:00-17:00, in person (University of Bremen) with zoom option During this international action week, we participate in the panel discussion 'Wind of change - sharing is caring! How to improve research data and its benefits in the Life Sciences'<https://nfdi4microbiota.de/news/2023-01-13-lovedataweek2023> with NFDI4Biodiversity, NFDI4Health and DataPlant at University of Bremen. · NFDI4Microbiota world café on Electronic Lab Notebooks (ELNs) 2023-02-24, 10:00 - 12:00, online To identify the needs of the German microbiology research community on Electronic Lab Notebooks (ELNs), we are organizing a world café on 2023-02-24 10:00 - 12:00. After an introduction, we will discuss topics such as General Needs, Interoperability, Ergonomics and Processes & Workflows. Ultimately, we would like to help the microbiology sub-communities to select and implement an ELN in their research group. To participate, please register here<https://us02web.zoom.us/meeting/register/tZAqceyppjwpHdRHg7uF7AqPb6Yxq4Phq3…>. · Workshop: Mapping the crosstalk of heterologous ECF sigma factors to the host genome 2023-02-20 - 24 08:00 - 16:00, in person and online 2023-03-06 - 10 08:00 - 16:00, in person and online Five places available for attendance + online participation, more details<https://nfdi4microbiota.de/training/training>. Our third newsletter will be shared with you in the end of January with news from our consortium. Kind regards Barbara Götz --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 3 months

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NFDI4Microbiota - Merry Christmas + Outlook 2023

by Goetz, Barbara

Dear NFDI4Microbiota community, We thank you for your helpful contributions in 2022! We are looking back on a very successful year and are pleased to announce that there will be a special focus on 'community engagement' in 2023. In the beginning of 2023 we will announce a few events and planned activities for 2023, as well as our next newsletter. In addition, you will have plenty possibilities to meet us in person at conferences in 2023 and actively participate in events together with other NFDI consortia. We wish you and your families a Merry Christmas, happy holidays and a Happy New Year and look forward to work with you in 2023. [cid:image003.jpg@01D9160E.61469870] On behalf of the Board of Directors and Administration Unit Kind regards Barbara Götz --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 4 months

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NFDI4Microbiota Newsletter October

by Paulmann, Carmen

Welcome Dear Reader, With our second NFDI4Microbiota newsletter, we would like to share news about our community activities such as the ambassador program or conferences we have participated in. In this issue, you can also read about Use Cases which will be implemented this year and about our recently published articles. Moreover, we continue presenting upcoming training courses, report on the release of our new web portal and much more. Let us know if you are interested in additional topics that we should cover. We are happy to hear from you<https://nfdi4microbiota.de/contact-form/>! Enjoy reading the newsletter! [cid:f9c998d6-06f8-4b0f-a5d8-168571dbe4bb] —————————————————————————————————————————— Community and Training Ambassador program: Monthly Coffee Talks series has started! Our mission is to be the central hub in Germany for supporting the microbiology community with access to data, analysis services, data/meta data standards and training. Therefore, the connection and interaction with the German microbiology community is key for our success and the goal of the NFDI4Microbiota ambassador program. The ambassadors will help to efficiently assess and communicate the needs of their community and provide them with suitable solutions generated by the consortium. A bilateral exchange with the ambassadors as well as presentations on different topics take place during the monthly Coffee Talk series. More information and the registration link for the ambassador program can be found here<https://nfdi4microbiota.de/ambassador/>. [cid:a4f0adb6-a9df-4862-8ecd-0a06eb519ce5] [cid:8ad45b62-6fd6-4273-9257-380fce5f27e9] Conferences NFDI4Microbiota has presented our activities at various conferences, including ISMB<https://www.iscb.org/ismb2022>, ISME<https://isme18.isme-microbes.org/>, GCB<https://gcb2022.de/>, ECCB<https://eccb2022.org/>, Targeting Microbiota<https://www.microbiota-site.com/> and DGHM<https://www.dghm-kongress.de/>. Moreover, together with representatives of other NFDI consortia, namely NFDI4Health, NFDI4Biodiversity, and KonsortSWD, we participated in the panel discussion ‘Everything FAIR and Open? Restrictions on data publications’ at JCDL 2022<https://2022.jcdl.org/nfdi-satellite-event/>. [cid:0fa23154-ecf4-4dde-8854-76eab66f3742] [cid:0c9091c0-01a6-42ff-8245-ff21cc6b585c] [cid:edc9b149-561e-4244-a57e-c2c41a91983a] [cid:da257049-02f6-40fd-9acb-3c750663b544] Upcoming training and events Within NFDI4Microbiota the support of the community by education and training is an important goal. Therefore, the consortium offers training<https://nfdi4microbiota.de/training/training> on several topics and for different disciplines. Moreover, we are regularly organizing or attending events<https://nfdi4microbiota.de/latest/events.html> such as the first BioHackathon Germany<https://www.denbi.de/de-nbi-events/1454-biohackathon-germany>. The workshop ‘Extending the NFDI4Microbiota Knowledge Base<https://www.denbi.de/de-nbi-events/2-uncategorised/1480-extending-the-nfdi4…>’ will be held during that event from 12th to 16th December 2022 in Wittenberg. NFDI4Microbiota has initiated a dedicated Knowledge Base that will contain information on Research Data Management and Reproducible Data Analysis in the broad field of microbiology. The Knowledge Base is developed in an open, collaborative process on GitHub<https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/RDM/introd…> and offered under a permissive license (CC-BY 4.0). Several NFDI4Microbiota members will participate in the BioHackathon and use that time as a content spring. The BioHackathon will offer a great opportunity to engage in discussions with other participants on various topics such as best practices, bioinformatical tools, Electronic Lab Notebooks and privacy issues. [cid:28221e70-0133-4062-8af4-7c841d8355dc] Registration is open for the following workshops and courses: Title Location Date Link Lecture on Research Data Management Online 2022-11-03, 9.00 to 11.00 a.m. Information and registration<https://www.zbmed.de/en/about/press/latest-news/article/einfuehrung-fdm0/> Single Cell Workshop Online 2022-11-21 to 2022-11-22 Information and registration<https://docs.google.com/forms/d/e/1FAIpQLSeLZjdsoEGEXycWZbsKNRR92lGcpFGcBV-…> Training Course on Metagenome Analysis Bielefeld University 2022-11-23 to 2022-11-25 Information and registration<https://www.denbi.de/training/1494-joint-de-nbi-nfdi4microbiota-training-co…> 1st BioHackathon Germany - Extending the NFDI4Microbiota Knowledge Base Lutherstadt Wittenberg - Leucorea 2022-12-12 to 2022-12-16 Information and registration<https://www.denbi.de/de-nbi-events/1454-biohackathon-germany> ____________________________________________________________________________ Networking and Collaborations Use Cases We are pleased to announce that NFDI4Microbiota currently has six active Use Cases: MULTI: Integration of multi-omics data of microbial species AmpliBench: Replacement or Extension: Systematic Assessment of Differences in Taxonomic Profiling Between Amplicon Sequencing Variants and Operational Taxonomic Units MetaProt: Functional profiling and routine diagnosis of humane microbiomes by metaproteomics Strain-ID: Collecting and matching microbial strain identifiers GUT: Crowd-sourcing high-quality descriptions of novel taxa MetaENVO (preliminary name): Metagenomic databases Learn more about the individual Use Cases and how you can contribute on our web portal<https://nfdi4microbiota.de/latest/usecase> or look forward to the Use Case showcase<https://www.eventbrite.co.uk/e/nfdi4microbiota-use-case-showcase-online-att…> during the NFDI4Microbiota Conference on 9th of November. Here, the project background and core aims of each Use Case will be shortly presented thereby providing the opportunity to give feedback, brainstorm further cooperation and discuss integration possibilities within NFDI4Microbiota. ____________________________________________________________________________ Publications Next steps after 15 stimulating years of human gut microbiome research – Published in microbial biotechnology Gut microbiome research has bloomed over the past 15 years. We have learned a lot about the complex microbial communities that colonize our intestine. Promising avenues of research and microbiome-based applications are being implemented, with the goal of sustaining host health and applying personalized disease management strategies. Despite this exciting outlook, many fundamental questions about enteric microbial ecosystems remain to be answered. Organizational measures will also need to be taken to optimize the outcome of discoveries happening at an extremely rapid pace. This article highlights our own view of the field and perspectives for the next 15 years. READ MORE<https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.13970> <https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.13970> Publication of the feedback from NFDI4Health, GHGA and NFDI4Microbiota on the positions and recommendations of the German Council of Science and Humanities NFDI4Health, GHGA and NFDI4Microbiota particularly welcome the positions and recommendations of the German Council of Science and Humanities on digitization and data use for health research and care and have formulated a joint response to this. Here, the consortia appreciate the strategic goal of establishing a decentralized, research-compatible, networked and interoperable health data infrastructure with a central health research data portal. The plea of the German Council of Science and Humanities for a data protection compliant facilitation of data access with the possibilities of the opt-out procedure is explicitly supported by the participating NFDI consortia. Additionally, improved possibilities for the linkage of different data sources (record linkage) on a national level are pleaded for. READ MORE<https://repository.publisso.de/resource/frl:6434341> (German) [Inline image OWAPstImg645685] NFDI4Microbiota - Enabling data-heavy research on microorganisms and their communities – Published in de.NBI brochure (pages 38-41) Our consortium is engaged in the support of microbiome research and for this builds on the high-performance cloud infrastructure provided by de.NBI. The de.NBI computational infrastructure supplies the network with computational resources on the one hand and massive storage capacities on the other. Furthermore, de.NBI and other partners work together to develop best practices and standards for metadata, training programs and community building. In conclusion, the de.NBI network represents a key component in the provision of NFDI4Microbiota’s solution. READ MORE<https://www.denbi.de/images/Downloads/deNBI_Cloud_Brochure_web.pdf> ______________________________________________________________________ Services and Infrastructure New Release of the NFDI4Microbiota web portal A new version of the NFDI4Microbiota portal<https://nfdi4microbiota.de/> has been released in August 2022. The NFDI4Microbiota services and useful information about the consortium appear in a new design and with an improved structure. New exiting features are an overview of the current Use Cases<https://nfdi4microbiota.de/latest/usecase> and our help desk<https://nfdi4microbiota.de/contact-form/>. Currently, our developer team works on a Content Hub that will function as a Knowledge Base in the future. Here, important resources on research data management and for reproducible data analysis will be available. [cid:43bd7426-43ce-4500-9324-ac6d22c69f8c] Survey on the use of Electronic Lab Notebooks Electronic Lab Notebooks (ELNs) play an important role in documenting research data: they provide clear documentation of experiment planning and implementation and of data generation and processing. One of our aims is is to ensure research data are captured as early in the process as possible in order to feed them directly into the analysis pipeline. In order to understand why or why not researchers use an ELN, and what are/were their hurdles in implementing or using an ELN, we conducted a survey on the use of ELNs which was intended for NFDI4Microbiota partners and participants. Only around 26% of respondents are currently using a ELN indicating a clear need to build awareness. Moreover, the ELNs being used varies greatly and are in need of improvements. To further support the use of ELNs and identify the needs of our community, we will soon organise a workshop. Ultimately, we would like to recommend a single ELN and guide researchers in the selection and implementation of the appropriate ELN for their research. The FAIR annotation of bacterial genomes The annotation of microbial genomes is a key task in bioinformatics and a requirement for many genome-based downstream analyses. Available contemporary command line annotation software tools, however, only provide mere functional descriptions for coding genes instead of linking known sequences to their related public database records. In particular, for proteins of unknown functions, i.e. hypothetical proteins, public databases can provide useful additional information. To address these challenges and to foster FAIR principles in general, the new software tool Bakta systematically assigns database accession numbers from e.g. UniRef and RefSeq to known protein sequences and related UniRef protein clusters as well as functional categories like COG, KEGG Orthology and GO. Recently, even Torsten Seemann, the developer of the famous Prokka tool, endorsed Bakta. It has been published in Microbial Genomics and is available via Docker and Conda as well as online here<https://bakta.computational.bio>. ____________________________________________________________________________________________________________________________________________ Social links and Contact Follow us on Twitter<https://twitter.com/nfdi4microbiota?lang=en> and GitHub<https://github.com/NFDI4Microbiota>! Questions or suggestions<https://nfdi4microbiota.de/contact-form/>? Learn more<https://nfdi4microbiota.de/> about NFDI4Microbiota! Subscription / Unsubscription<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…> 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. Dirk Heinz - komm. Administrative Geschäftsführerin: Elisabeth Gerndt Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

3 years, 5 months

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NFDI4Microbiota - Showcase of active Use Cases

by Magel, Maja

Dear all, this year, 6 Use Cases<https://nfdi4microbiota.de/latest/usecase> have been selected by NFDI4Microbiota. During the Use Case showcase on the 9th of November 08:30-10:00 AM, you will be able to learn what each Use Case entails. To attend, please use the following link to register for the online part of this hybrid event: https://www.eventbrite.co.uk/e/nfdi4microbiota-use-case-showcase-online-att…<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.event…> The showcase will include pitches on the topics * "Integration of multi-omics data of microbial species" (MULTI) * "Crowd-sourcing high-quality descriptions of novel taxa" (GUT) * "Replacement or Extension: Systematic Assessment of Differences in Taxonomic Profiling Between Amplicon Sequencing Variants and Operational Taxonomic Units" (AmpliBench) * "Functional profiling and routine diagnosis of humane microbiomes by metaproteomics" (MetaProt) * "Collecting and matching microbial strain identifiers" (Strain-ID) * "Provenance and usage of metagenome data" (MetaProv) As well as a general introduction to Use Cases in NFDI4Microbiota. Use Cases are generally real scientific projects in the broad field of microbiome research that were selected to aid NFDI4Microbiota facilitate and stimulate data sharing according to FAIR principles concerning microbial data and their associated metadata. The focus of the event is to give you a short overview and to enable future community engagement. NFDI4Microbiota is looking forward to seeing you online. Kind regards, Maja Magel Projektkoordination NFDI4Microbiota Institut für Medizinische Mikrobiologie Research Group Functional Microbiome [cid:image001.png@01D8E93B.E6CA27A0] ________________________________________ 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 Maja Magel Projektkoordination NFDI4Microbiota Institut für Medizinische Mikrobiologie Research Group Functional Microbiome [cid:image001.png@01D8E93B.E6CA27A0] ________________________________________ 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

3 years, 6 months

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TODAY: BacDive & MediaDive Workshop

by Isabel Schober

Hello everyone, this is a reminder that this year's *Bac/Dive/ <https://bacdive.dsmz.de/> Workshop and Q&A* will take place *today, * *6th October 2022*, *2 - 4 PM CEST online*! Topics: * *Introduction to **Bac**/Dive/**Advanced Search* <https://bacdive.dsmz.de/advsearch> Learn how to build complex queries using the Bac/Dive/ advanced search options and retrieve a custom data set for your research. * *Introduction to the**Bac <https://api.bacdive.dsmz.de/>**/Dive/**API* <https://api.bacdive.dsmz.de/> Learn how to programmatically access Bac/Dive/ data for large scale analysis. * *Introduction to**Media <https://mediadive.dsmz.de/>**/Dive/* <https://mediadive.dsmz.de/> Learn how to find new media recipes for your cultivation in Bac/Dive/'s new sister database and how to use its API to programmatically access media data for large scale analysis. * *Q&A with the developers* Any questions left? You can ask the Bac/Dive/ and Media/Dive/ developers directly! *No registration is needed! *Just join us on Zoom.* * Login details: https://dsmz-de.zoom.us/j/3818375651?pwd=OUVMMEtSZnh3SGxmcEJRUS9oTkcrdz09 /Meeting ID: 381 837 5651// //Passcode: m8j819/ We are looking forward to seeing you there! The Bac/Dive/ Team -- Dr. Isabel Schober Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstr. 7 B 38124 Braunschweig Germany Tel. +49531-2616-423 Fax +49531-2616-418 www.dsmz.de Directors: Prof. Dr. Joerg Overmann; Bettina Fischer Local court: Braunschweig HRB 2570 Chairman of the management board: MR Dr. David Schnieders DSMZ - A member of the Leibniz Association www.leibniz-gemeinschaft.de

3 years, 6 months

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Invitation to BacDive & MediaDive Workshop | 6th Oct 2022

by Isabel Schober

Dear NFDI4Microbiota community, we are happy to announce that this year's *Bac/Dive/ <https://bacdive.dsmz.de/> Workshop and Q&A* will take place on* * *6th October 2022*, *2 - 4 PM CEST online*! Topics: * *Introduction to **Bac**/Dive/**Advanced Search* <https://bacdive.dsmz.de/advsearch> Learn how to build complex queries using the Bac/Dive/ advanced search options and retrieve a custom data set for your research. * *Introduction to the**Bac <https://api.bacdive.dsmz.de/>**/Dive/**API* <https://api.bacdive.dsmz.de/> Learn how to programmatically access Bac/Dive/ data for large scale analysis. * *Introduction to**Media <https://mediadive.dsmz.de/>**/Dive/* <https://mediadive.dsmz.de/> Learn how to find new media recipes for your cultivation in Bac/Dive/'s new sister database and how to use its API to programmatically access media data for large scale analysis. * *Q&A with the developers* Any questions left? You can ask the Bac/Dive/ and Media/Dive/ developers directly! *No registration is needed! *Just join us on Zoom.* * Login details: https://dsmz-de.zoom.us/j/3818375651?pwd=OUVMMEtSZnh3SGxmcEJRUS9oTkcrdz09 /Meeting ID: 381 837 5651// //Passcode: m8j819/ We are looking forward to seeing you there! The Bac/Dive/ Team -- Dr. Isabel Schober Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstr. 7 B 38124 Braunschweig Germany Tel. +49531-2616-423 Fax +49531-2616-418 www.dsmz.de Directors: Prof. Dr. Joerg Overmann; Bettina Fischer Local court: Braunschweig HRB 2570 Chairman of the management board: MR Dr. David Schnieders DSMZ - A member of the Leibniz Association www.leibniz-gemeinschaft.de

3 years, 6 months

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NFDI4Microbiota - Training announcement

by Goetz, Barbara

Dear NFDI4Microbiota community, from now on, we will present to you upcoming courses and workshops for the NFDI4Microbiota community on a bimonthly base. Please feel free to (additionally) check out our training calendar on our web portal<https://nfdi4microbiota.de/training/training>. Today, we would like to draw your attention to our next Git workshop on the 26th of September: git/GitHub for Microbiologists Workshop @ NFDI4 Microbiota - ONLINE event Git is the most commonly used version control system. Git tracks the changes you make to files, so you have a record of what has been done, and you can revert to specific versions should you ever need to. Git also makes collaboration easier, allowing changes by multiple people to all be merged into one source. So regardless of whether you write code that only you will see, or work as part of a team, Git will be useful for you. For this workshop the following topics will be covered: · understanding of the possibilities of Reproducible Research and data processing · basic skills in the Unix-Shell, version control with git and using GitHub · will have found out about live-coding and compared notes with colleagues The workshop will include short tutorials alternating with practical exercises, so please bring your laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). This is an introductory course, so you don't need to have any previous knowledge of the tools that will be presented at the workshop. For example, do you know how to use the terminal? If you do not, come and join us! Registration is open<https://www.eventbrite.de/e/git-for-microbiologists-workshop-nfdi4-microbio…> until 21st of September. The class size for this workshop is limited. In order to reserve a seat, purchase a (free of charge) ticket from the workshop Eventbrite page. We will maintain a waiting list so, if you reserve a place and are unable to attend please let us know as soon as possible so someone else can take your place. Kind regards Your NFDI4Microbiota administration unit Barbara Götz and Carmen Paulmann --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 7 months

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NFDI4Microbiota Newsletter

by Sauerland, Kristin

Welcome to NFDI4Microbiota [cid:fc814ed6-36a5-47f8-9928-c17931aacf06] Here it is: the first NFDI4Microbiota Newsletter! Our consortium officially took up its work in October 2021 and a lot of exciting things have been happening since then. First of all: We are growing! In our ten partner institutions alone, we already have 65 people working enthusiastically on our mission to become the central hub in Germany for supporting the microbiology community with access to data, analytical services, data/metadata standards and training. Furthermore, there are more than 50 participants and 33 ambassadors actively supporting our work and providing the community with our solutions. We are currently working on a procedure to incorporate new participants. So if you are interested in becoming a part of NFDI4Microbiota, please contact us via email (contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de>). For general information about NFDI4Microbiota please have a look at our new web portal<https://nfdi4microbiota.de/>. There, we will continuously extend our services. We are also quite active on twitter<https://twitter.com/NFDI4Microbiota>, so if you have not by now, do take the chance to follow us for regular updates on our work, training etc. At our first general assembly in November 2021, Prof. Dr. Konrad Förstner<https://www.zbmed.de/kontakt/konrad-foerstner/> (ZB MED) and Prof. Dr. Alice McHardy<https://www.helmholtz-hzi.de/de/forschung/forschungsschwerpunkte/bakteriell…> (HZI) were elected to be the official consortial speaker and deputy of our consortium. In this function they will represent our consortium within the association National Research Data Infrastructure Germany (NFDI e.V.).If you want to learn more about the NFDI initiative driven by the Deutsche Forschungsgemeinschaft e.V. you can watch this short video<https://youtu.be/uJ01g9m8uE4>. [cid:6776db8d-e35d-4b74-ad84-7869dfcb9553] [cid:9f042b1c-2df8-49f1-b6b4-1b105248dcb3] Prof. Dr. Konrad Förstner Prof. Dr. Alice McHardy ——————————————————————————————————————————————————— How to get in touch with NFDI4Microbiota You can contact us via the contact form<https://nfdi4microbiota.de/contact-form/> on our web portal. Please choose the most fitting issue type and your request or question is automatically directed to the right contact person within our consortium. —————————————————————————————————————————— Community, Networking and Training Training Announcement Calendar One of the first services we established at the beginning of the year is our training announcement calendar<https://nfdi4microbiota.de/trainings/all-trainings> that we launched on our NFDI4Microbiota web portal. The calendar gives an overview of past and future training events within the consortium and will be updated regularly. Within the first quarter of 2022 we already carried out nine trainings/workshops successfully. If you want to offer training related to NFDI4Microbiota topics or if you miss a certain training offer, please get in touch via our contact form<https://nfdi4microbiota.de/contact-form/>, choosing the issue type “Training”. Upcoming Training events Title Organizer Date Link Introduction to deep learning with R HZI 13 - 15/06/22 Registration link<https://docs.google.com/forms/d/e/1FAIpQLSfdI1FG1jgOob_nqSJhNU53TPs0-bzop1Z…> Workshop on RDM in (Bio-)Medicine ZB MED 20 & 22/06/22 forschungsdaten(a)zbmed.de<mailto:forschungsdaten@zbmed.de> Train the Trainers (Carpentry or ELIXIR) EMBL Bio-IT 18-22.07.2022 to be announced Metagenomics JLU Giessen 06 - 07/09/22 tbc Community Workshop and Ambassador program The NFDI4Microbiota community is growing! Our 5th Community Workshop took place virtually, launching the NFDI4Microbiota Ambassador program. Our ambassadors are a direct and bilateral connection between NFDI4Microbiota and the community by helping to identify and communicate the needs of their local community and, in return, provide the community with suitable solutions generated by the NFDI4Microbiota consortium. More information and the registration link for the ambassador program can be found here<https://dc.2ask.com/preview/c/TGFB8CX1ZPCFR/?_init=true#>. Further requests and questions can be sent to ambassador(a)nfdi4microbiota.de<mailto:ambassador@nfdi4microbiota.de>. [cid:53d153b0-dd63-42a3-b01c-17278bce7742] Screenshot of the 5th Community Workshop Conferences NFDI4Microbiota has been present at various conferences, including VAAM<https://vaam.de/> and ViBioM (EVBC<https://evbc.uni-jena.de/>), and we are looking forward to many more possibilities to promote our activities and get in touch with the community. Next, we will be present at the JCDL – NFDI Satellite event<https://2022.jcdl.org/nfdi-satellite-event/> (June 23rd) and discuss the topics FAIR and open data and the restrictions of data publications together with NFDI4Health, NFDI4Biodiversity and KonsortSW. In September we will join the DGHM conference<https://programm.conventus.de/index.php?id=dghm2022&tx_coprogramm_programm%…> in Berlin and hold a workshop on NFDI4Microbiota on the 7th of September. [cid:c8cdcd14-e3e9-4aad-9ba8-31310e697c4d] NFDI4Microbiota is official partner of the DGHM conference 2022 Further conferences that we will attend: Intelligent Systems for Molecular Biology (ISMB<https://www.iscb.org/ismb2022>), Poster Sessions, July 10 - 14 German Conference on Bioinformatics (GCB<https://gcb2022.de/>), Talk, September 06 - 08 European Conference on Computational Biology (ECCB<https://eccb2022.org/>), Poster Session, September 19 - 20 ProkaGENOMICS<https://www.prokagenomics.org/general-information/welcome-note>, Poster Session, September 25 - 28 ____________________________________________________________________________ Networking and collaborations Base4NFDI We participated in the joint DFG application Base4NFDI for NFDI-wide basic services. Base4NFDI is a unique joint effort supported by all NFDI consortia to develop and deploy such services in order to increase efficiency and seamless user experience in research data management within and beyond the NFDI. Base4NFDI involves institutions from all relevant infrastructure domains and from all major research organizations in Germany. The proposal has been submitted and we expect the final decision by the DFG in November 2022. NFDI InfraTalk Together with NFDI4Biodiversity, DataPLANT and FAIRagro we gave an NFDI InfraTalk on the "Current developments in the global Genome Commons and challenges for service provision in NFDI". Thereby, we expressed the importance of digital sequence information (DSI) for researchers in the microbiological field. We do support the DSI Scientific Network, organized by Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH. You are wondering why this might be important to you? „DSI is used by researchers in a wide of contexts including for studying and monitoring biodiversity, understanding ecosystem impacts from climate change, improving crops, developing new medicines, and tracking the spread and evolution of new infectious diseases. Access to DSI is therefore crucial to research supporting many of the UN Sustainable Development Goals. A wide range of organizations and experts have called for DSI policy solutions that provide equitable benefit-sharing through multilateral mechanisms that protect open access DSI.” We invite all scientists to sign this open letter initiated by the DSI Scientific Network to protect open access of DSI. Source, possibility to sign the letter, and more information<https://www.dsiscientificnetwork.org/open-letter/>. If you missed the InfraTalk, you can watch it here<https://www.youtube.com/watch?v=odNBeqav2eQ>. [cid:295cfbfa-3bdc-4e9a-a022-70dedf60d76b] NFDI4Microbiota at the NFDI InfraTalk on restrictions of digital sequence information Use Cases We launched our first two Use Cases<https://nfdi4microbiota.de/index.php/use-cases/> („MULTI“ and „GUT“) during the 1st NFDI4Microbiota Use Case Workshop. Further information on current and planned Use Cases will be made available on our web portal. Are you interested in submitting a new Use Case? New Use Cases by partners and participants can be submitted until 20th of June. Please get in touch through our contact form<https://nfdi4microbiota.de/contact-form/>, choosing the issue type “Use Cases”. Publication Congratulations to Dr. Lorenz Reimer, Dr. Konrad Förstner and Dr. Jörg Overmann, who just published the first paper for and about NFDI4Microbiota in Biospektrum. The paper is dealing with the advantages of open and FAIR data for the microbial community. The German paper can be found here<https://link.springer.com/article/10.1007/s12268-022-1725-6>. ______________________________________________________________________ Policies & Standards Microbiome Working Group An important point within the scope of NFDI4Microbiota is the establishment of working groups for leading national and international scientists. They will be invited to engage with the NFDI4Microbiota network to discuss emerging topics, foster creativity, and identify cutting-edge trends in microbiota research. On the 17th of May, we kicked-off our Microbiome Working Group, taking a look at different workflow management systems and discussing their usage within our consortium and by international partners. Do you have questions or want to get involved? Please get in touch with us via contact(a)nfdi4microbiota.de.<mailto:contact@nfdi4microbiota.de.> ______________________________________________________________________ Services Data Quality & Provenance Services Data quality is a major prerequisite for qualified, interpretable, and valid research results. Another often underrated aspect is data provenance, which allows the tracing of data sources and processing steps. Well-documented provenance helps to confirm the authenticity of data and allows researchers to assess the comparability of studies. Therefore, we developed a first concept for provenance tracking & data quality checks and are now working on its implementation. Long-term preservation As long-term preservation of data is crucial for future research, we started to create and collect training material on long-term preservation. The intended audience is researchers who would like to learn about digital preservation and data storage in trusted repositories. In the future, all training materials will be made accessible on the NFDI4Microbiota web portal. For questions regarding our services, please get in touch through our contact form<https://nfdi4microbiota.de/contact-form/>, choosing the issue type “Services”. ____________________________________________________________________________ Technical Infrastructure Data Storage Platform We are also working on a scalable and easily accessible domain-agnostic data storage platform. As the requirements and technologies used for this measure are highly similar to the infrastructure which is being developed within the NFDI4Biodiversity consortium, we collaborate very closely with NFDI4Biodiversity. The first conceptual design of the storage platform will serve as a prototype, which is currently being extended to include the needs of NFDI4Microbiota. An alpha version of the platform has been deployed on the de.NBI Cloud infrastructure. Infrastructure Software Components This measure will provide ready-to-use computational frameworks for data analysis and computing services to the NFDI4Microbiota community. Initial deployment and the start of beta testing of core infrastructure components have been established. This includes a? platform as a service (PaaS) solution, providing easy access to an HPC cluster in cloud computing environments. Bottlenecks and limitations identified during this first testing phase have led to feature requests which are currently being integrated. For questions around our technical infrastructure, please get in touch through our contact form<https://nfdi4microbiota.de/contact-form/>, choosing the issue type “Software” or “Others”. ________________________________ 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. Dirk Heinz - komm. Administrative Geschäftsführerin: Elisabeth Gerndt Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

3 years, 10 months

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2026

2025

2024

2023

2022

Nfdi4microbiota-announce