- Nfdi4microbiota-announce

[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, 3 months

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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, 4 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, 5 months

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NFDI4Microbiota seasonal greetings

by Goetz, Barbara

Dear NFDI4Microbiota Community members, on behalf of the Board of Directors and the whole NFDI4Microbiota consortium I sent you seasonal greetings! In 2023, we could meet, interact, and connect with many of you on the different conferences we attended (i.e. VAAM, DGHM, etc.). In addition, you helped us by giving feedback on your needs and wishes, which was rewarded for some of the participants with a giant microbe and some merchandise. Some of you even applied for the NFDI4Microbiota 2024 Flex Funds call. We appreciate the effort and interest in our work by all of you! For 2024, we wish and hope for an even closer interaction and would like to draw your attention to a few interesting events in 2024: 1. Our 6th NFDI4Microbiota Community Workshop online on the 5th of February 2024 from 10:00 to 12:00 CEST. 2. This community workshop will be followed by a Knowledge Base Content/Coding Sprint on the 15th of February (10:00 - 17:00 CEST) and 16 February (09:00 - 16:00 CEST) both online and in Cologne. Details will be shared in the beginning of 2024. 3. The 3rd NFDI4Microbiota conference will take place in Leipzig from the 4th to the 6th of December 2024. Details will follow ASAP. We wish you lovely holidays, Merry Christmas and a Happy New Year! [cid:image001.jpg@01DA3415.4B54B0D0] 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/> Mastodon: nfdi.social/@NFDI4Microbiota<https://nfdi.social/@NFDI4Microbiota> LinkedIn: linkedin.com/company/nfdi4microbiota/<https://www.linkedin.com/company/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.

2 years, 5 months

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Open Call for new NFDI4Microbiota Use Cases - until January 31st 2024

by Magel, Maja

Dear Partners, Participants, Ambassadors, and interested microbiology researchers, NFDI4Microbiota looks forward to receiving your Use Case submissions for the 2024 call! Submissions are open until January 31st, 2024. You can find the document links and more information about the submission procedure here<https://nfdi4microbiota.de/latest/ucsubmissioncall>. [cid:image002.png@01DA328C.9A4E1670]<https://nfdi4microbiota.de/latest/ucsubmissioncall> Wondering what Use Cases are? In a nutshell, Use Cases will help NFDI4Microbiota to * test and fine-tune solutions developed within NFDI4Microbiota based on ongoing scientific projects and generate scientific results or reusable tools. * bring the expertise of several stakeholders involved in the Use Cases together to create elaborate solutions that can be easily adapted by other research projects to make their work more efficient. * nurture ideas for the consortium to implement additional measures to address newly detected needs. At the end, the Use Case outcomes will benefit the broad microbiology research community. We look forward to your Use Case. On behalf of the NFDI4Microbiota Use Case measure team, I wish you all the best and a relaxing start to the New Year! Kind regards, Maja Magel PS: Feel welcome to forward this mail to your collaborators. Please excuse double postings to your mail. Projektkoordination NFDI4Microbiota Institut für Medizinische Mikrobiologie Research Group Functional Microbiome [cid:image001.png@01DA328A.E429A0E0] ________________________________________ E-Mail: mmagel(a)ukaachen.de<mailto:mmagel@ukaachen.de> (I'll be back on January 2nd to answer your questions) Aufzug D4, Etage 5, Raum 34 Universitätsklinikum Aachen Pauwelsstraße 30 52074 Aachen

2 years, 5 months

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NFDI4Microbiota - Community survey deadline extended until October 14th

by Goetz, Barbara

Dear NFDI4Microbiota community, You haven't had a chance to fill out the survey yet? No problem! We have extended the deadline until October 14th! We need your help to get better! Therefore, we have designed a 15-minute survey to gain a better understanding of the knowledge and needs of our community. As an incentive and compensation for your time, NFDI4Microbiota merchandise packages and some microbiology-related items will be raffled among all participants. Please do not hesitate to forward the link to other microbiologists! The survey is open and accessible via this link: https://www.2ask-survey.com/c/6238RCG6EJY12/ We count on you! 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> Mastodon: nfdi.social/@NFDI4Microbiota<https://nfdi.social/@NFDI4Microbiota> LinkedIn: linkedin.com/company/nfdi4microbiota/<https://www.linkedin.com/company/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.

2 years, 8 months

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Invitation to BacDive, MediaDive and StrainInfo Workshop | 11th Oct 2023

by Isabel Schober

Hello everyone, we are happy to announce that this year's *Bac/Dive/ <https://bacdive.dsmz.de/>, Media/Dive/ <https://mediadive.dsmz.de/> and StrainInfo <https://straininfo.dsmz.de/> Workshop* will take place on* * * * *11th October 2023*, *2 - 4 PM CEST online!* *2 PM - Websites* Introductions to BacDive, MediaDive and StrainInfo websites. Learn how to use the search functions and read and retrieve data. *3 PM - APIs* Introductions to the BacDive, MediaDive and StrainInfo webservices. Learn how to programmatically access data for large scale analysis. Any questions left? You can ask the developers directly! *No registration is needed! *Just join us on Zoom.* * *https://dsmz-de.zoom-x.de/j/3818375651?pwd=OUVMMEtSZnh3SGxmcEJRUS9oTkcrdz09 Meeting-ID: 381 837 5651 Kenncode: 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 Phone +49531-2616-423 isabel.schober(a)dsmz.de 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

2 years, 8 months

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DataXplorar - cross-consortia hackathon

by Hege, Cordula Almut Selma

(English version below) Liebe NFDI4Microbiota-Interessierte, wir möchten Euch herzlich zu unserem spannenden Mitmach-Event der NFDI-Konsortien NFDI4Biodiversity<https://www.nfdi4biodiversity.org/en/>, NFDI4Earth<https://www.nfdi4earth.de/> und NFDI4Microbiota<https://nfdi4microbiota.de/> einladen, bei dem sich – natürlich – alles um die Arbeit an und mit Daten dreht. Unsere DataXplorers-Webseite<https://www.nfdi.de/dataxplorers-hackathon/> ist nun online und Registrierungen darüber bis zum 01. Oktober möglich. Mit einem online Kick-Off-Event am 23. Oktober 2023 startet der Hackathon für Nachwuchs- und erfahrende Wissenschaftler:innen aus den Feldern Erdsystem-, Biodiversitäts- und Mikrobiologieforschung sowie Interessierte aus anderen Feldern, etwa Informatik oder Design. Chat-Bots programmieren, die Fragen zu Forschungsdatenmanagementthemen beantworten, Data Cubes erstellen, die Klima – mit Biodiversitätsdaten verbinden – was kann entstehen, wenn neugierige Köpfe verschiedener Disziplinen zusammenkommen und gemeinsam Neues kreieren? Wir wollen es gemeinsam mit Euch herausfinden! Der Hackathon ermöglicht es den Teilnehmenden, sich in Gruppen (von max. 5 Personen) zusammenzutun und (begleitet von Profis) ihrer Kreativität freien Lauf zu lassen. Ihr könnt euch entweder als Team oder auch alleine anmelden. Das Organisationsteam hat dafür sechs verschiedene Challenges zu unterschiedlichen Themen vorbereitet, denen Teilnehmende sich je nach Interesse zuordnen können. Für die remote Bearbeitung der Aufgaben ist mehrere Wochen Zeit, bis am 5. und 6. Dezember 2023 in Frankfurt am Main die Ergebnisse präsentiert werden. Es ist möglich an der Abschlussveranstaltung sowohl in Person, als auch online teilzunehmen. Alle weiteren Informationen zum Ablauf des Hackathons, die detaillierten Challenge-Beschreibungen finden sich auf unserer DataXplorers Homepage: https://www.nfdi.de/dataxplorers-hackathon/. Für die Teilnahme an einer Challenge und an der Veranstaltung in Frankfurt ist eine Registrierung erforderlich. Die Formulare finden sich unter dem entsprechenden Link auf unserer Webseite und hier<https://events.gfbio.org/event/38/>. Wir freuen uns, Ihr selbst dabei seid und möchten Euch auch dringend bitten, die Veranstaltung an geeignete Empfänger:innen weiterzuleiten. Auch Interessierte, die selber keine Challenge bearbeiten, sind herzlich eingeladen am Kick-Off Event und der Abschlussveranstaltung teilzunehmen. Bei Fragen könnt Ihr Euch direkt an mich und das Organisationsteam wenden: nfdi4earth-academy(a)groups.tu-dresden.de<mailto:nfdi4earth-academy@groups.tu-dresden.de> Viele Grüße, Kristin Sauerland und Cordula Hege ----- Dear NFDI4Microbiota-enthusiasts, We would like to invite you to our exciting hands-on event of the NFDI consortia NFDI4Biodiversity<https://www.nfdi4biodiversity.org/en/>, NFDI4Earth<https://www.nfdi4earth.de/> and NFDI4Microbiota<https://nfdi4microbiota.de/>, which - of course - is all about working on and with data. Registrations via our DataXplorers website<https://www.nfdi.de/dataxplorers-hackathon/> can be made until October 01st. The hackathon starts with an online kick-off event on October 23, 2023 and adresses young and experienced scientists from the fields of Earth system, biodiversity and microbiology research as well as interested people from other fields, such as computer science or design. Programming chat bots that answer questions on research data management topics, creating data cubes that connect climate and biodiversity data - what can happen when curious minds from different disciplines come together and create something new? Together with you, we are going to find this out! The Hackathon allows participants to get together in groups (of max. 5 people) and (accompanied by professionals) give free rein to their creativity. You can register either as a team or alone and get to know new people. The organizing team has prepared six different challenges on various topics, to which participants can assign themselves according to their interests. There will be several weeks to work on the tasks remotely until the results are presented in Frankfurt am Main on December 5 and 6, 2023. It is possible to participate in the final event both in-person and online. All further information about the hackathon and the detailed challenge descriptions can be found on our DataXplorers homepage: https://www.nfdi.de/dataxplorers-hackathon/. Registration is required to participate in a challenge and in-person in the event in Frankfurt. The forms can be found under the corresponding link on our website and here<https://events.gfbio.org/event/38/>. We hope that many of you participate and would like to ask you to forward the event to suitable recipients. Interested people that do not wish to participate in a challenge, are also welcome to participate in the kick-off event and in the closing event. If you have any questions, please contact me and the organising team directly: nfdi4earth-academy(a)groups.tu-dresden.de<mailto:nfdi4earth-academy@groups.tu-dresden.de> Kind regards, Kristin Sauerland und Cordula Hege [cid:1937d5ea-b3e5-4ed6-bcd1-de12c902d198] 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, 8 months

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NFDI4Microbiota - Community survey open until 30th of September

by Goetz, Barbara

Dear NFDI4Microbiota community, We need your help to get better! Therefore, we have designed a 15-minute survey to gain a better understanding of the knowledge and needs of our community. As an incentive and compensation for your time, NFDI4Microbiota merchandise packages and some microbiology-related items will be raffled among all participants. Please do not hesitate to forward the link to other microbiologists! The survey is open until the 30th of September and accessible via this link: https://www.2ask-survey.com/c/6238RCG6EJY12/ We count on you! 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> Mastodon: nfdi.social/@NFDI4Microbiota<https://nfdi.social/@NFDI4Microbiota> LinkedIn: linkedin.com/company/nfdi4microbiota/<https://www.linkedin.com/company/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.

2 years, 8 months

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NFDI4Microbiota Newsletter #5

by NFDI4Microbiota

[Im Browser öffnen](https://b18ad.r.a.d.sendibm1.com/mk/mr/sh/OycXxko2a8zXPIR5m9M7ojCw/… NEWSLETTER ---------- Dear Reader, With our fifth NFDI4Microbiota newsletter, we would like to share news about conferences, Use Cases, training and available online videos. If you are interested in other topics we should cover, please let us know.[We are happy to hear from you!](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo1eQuZUu03s625SA/… And now: Enjoy reading the newsletter! ###Community engagement – events and conferences ###Upcoming conferences In September 2023, we will be attending many conferences in order to present our work and to meet our various target communities. Please come by to meet us if you are attending – we look forward to meeting you in person! You can find our contributions to all events below and [on our web portal](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo1kTcoJzby1bbhK… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGarTU3MznueikKVCI/7NYh…"). - [VAAM Annual conference 2023](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo1qWL395DsB7BJDC/… "https://vaam-kongress.de/programme-abstracts/scientific-programme#c6756") – oral presentation, poster and booth - [36th Workshop of the European Helicobacter and Microbiota Study Group](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo1wZ3HyApmKckv5i… "https://www.workshop.ehmsg.org/") (EHMSG) – poster - [1st Conference on Research Data Infrastructure](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo22blWn… "https://www.nfdi.de/cordi-2023/") (CoRDI 2023) – oral presentation, poster and booth - [German Conference on Bioinformatics](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo28eTlc… "https://gcb2023.de/") (GCB) 2023 – poster - [75th Annual Conference of the DGHM 2023](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo2EhC0RRfUn9TkjG/… "https://dghm-kongress.de/en/") – poster - [Jahrestagung der Deutschen Gesellschaft für Epidemiologie](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo2KjuFGX… "https://2023.dgepi.de/") (DGEpi) – poster ###NFDI4Microbiota will attend the 2023 Digital-Gipfel (Digital Summit) The 2023 Digital-Gipfel (Digital Summit) will take place in Jena from November 19th-21st. Various NFDI consortia including the NFDI4Microbiota will come together on the themes of the summit. [See more here.](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo2QmcU5ctJ6AcyUI… "https://initiatived21.de/veranstaltungen/digital-gipfel-2023") ###Upcoming hackathon: DataXplorers – Cross-community hackathon Together with NFDI4Biodiversity and NFDI4Earth, NFDI4Microbiota is organizing a hackathon. **The hackathon will start with an online kick-off event on October 23rd and will end with a hybrid final event on December 5th-6th in Frankfurt.** The main target group are early career researchers (PhD students and postdocs) from the fields of earth system sciences, biodiversity and microbiology – but we also strongly encourage participation from other fields, such as informatics, bio-/media-informatics, and design. More experienced individuals are also welcome to participate. Challenges will be provided and mentored by partners from the consortia of NFDI4Earth, NFDI4Biodiversity and NFDI4Microbiota. Topics include developing an annotation tool for metaproteomics experiments, building of data cubes and developing machine learning methods for image annotation. You can register on our[ hackathon website](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo2WpKiuiVDFgCa… "https://www.nfdi.de/dataxplorers-hackathon/"), where we will also publish the challenge descriptions. ###Successful Workshop on "Automating Virus Taxonomy" was held in Jena The [Workshop "Automating Virus Taxonomy"](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqJHsMvatjmqq2Ba/UIlgxIX3UGmF "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZeDhCmpvvSJauqNq/Alhq…"), which took place from July 31st to Aug 2nd in Jena, Germany, was a great success. The hybrid event was co-organized by members of the International Committee for the Taxonomy of Viruses [(ICTV)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZFGUXZslPb3DsR… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGa3Atrzn6RJZxxFTy/2DdB…"), European Virus Bioinformatics Center [(EVBC)](https://evbc.uni-jena.de/ "https://evbc.uni-jena.de/"), and the NFDI4Microbiota. About 400 people from 46 countries registered, highlighting the global interest in this important topic. After the workshop the ICTV Executive Committee discussed this year’s taxonomic proposals and approved most of the additions to the virus taxonomy. For those interested, one can find these under “Taxonomy > Proposals” on the[ ICTV website](https://ictv.global/ "https://ictv.global/"). On the third day of the workshop, a pop-up hackathon and Hands-On Workshop co-organized by Dr. Noriko Cassman (NFDI4Microbiota, FSU Jena) and David Lähnemann (DKFZ Heidelberg/DKTK site Essen-Düsseldorf) took place. About 100 online and 20 onsite participants learned how to write Snakemake workflows and/or created pipelines to automate virus classification. We are pleased to share the results of the hackathon: two Snakemake workflows for Caudoviricetes classification that follow best coding practices! Take a peek at the [mashup-phage](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGaS86XCk… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbG2VrcebytN54SmM/zUFe…") and [download-and-reannotation-of-phage-genomes](https://b18ad.r.a.d.sendibm1.co… "https://github.com/ICTV-VBEG/download-and-reannotation-of-phage-genomes") workflows on the [GitHub repository of the ICTV Virus Bioinformatics Enthusiasts Group](https://github.com/ICTV-VBEG "https://github.com/ICTV-VBEG"). Also available are the Snakemake [material](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbeziWpbmUkd… "https://snakemake.readthedocs.io/en/latest/tutorial/tutorial.html") and [slides](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc3wvC2Yx0btp9… "https://slides.com/johanneskoester/snakemake-tutorial"). ###NFDI4Microbiota Use Cases ###NFDI4Microbiota is looking for your input on the Use Cases We are delighted to invite you to explore our active [Use Cases](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGcSu7rFW7WTACBg… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqPKabkgVdwMPe46/pi9R…"). Whether you are a microbiologist, bioinformatician, or computer scientist, your expertise can be a valuable addition to these projects. Engage with our Use Cases, explore innovative ideas, and contribute to solutions that drive innovation in the field of microbiome research. For each Use Case you will find graphical abstracts, project descriptions, contact details of the project leaders and how to get involved [on our web portal](https://nfdi4microbiota.de/latest/usecase "https://nfdi4microbiota.de/latest/usecase"). Discover the different topics our Use Cases cover, from metaproteomics and metagenomics to multi-omics data integration: - MetaProt: Functional profiling and routine diagnosis of human microbiomes by metaproteomics - MetaProv: Provenance and usage of metagenome data - MockBench: Systematic assessment in metagenomics using high diversity Mock samples - MULTI: Integration of multi-omics data of microbial species - Strain-ID: Collecting and matching microbial strain identifiers - TAXA: Descriptions of novel taxonomic lineages Ultimately, the outputs from these projects will help you to be more effective in your daily research. Here are some examples from across the Use Cases where your input is needed and/or how you can benefit from them: You are a … - **Microbiologist** trying to identify and match culture collection numbers to a given strain: Use the service [StrainInfo](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZFMXFohr1… "https://straininfo.dsmz.de/") and [provide feedback](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZeJjv1f1XMT… "https://nfdi4microbiota.de/usecases/strain-id"). - **Microbiologist** with experience in transcriptomics or proteomics analyses: Check out the [preliminary guidelines on data processing, analysis, and integration of genomics, transcriptomics, and proteomics data](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGa3GwaEcC3DjTWrM… "https://gitfront.io/r/user-6306825/uUtkLPVoZfbX/multi/") and [give feedback](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGaSE9FRZMZ4z… "https://nfdi4microbiota.de/usecases/multi"). - **Bioinformatician** curating metagenomes datasets: Provide curated data and metadata from human gut microbiome samples. [(Use Case “MetaProt”)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGarBLueWX4wGDbfYk/vRlpO11H_BGC "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGcT0AZULD8NJhlHxG/msmW…") - **Metagenome analyst** frustrated with numerical bacteria names lacking functional insights: [Use the tool](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbG8YZrThanWae4e… "https://nfdi4microbiota.de/usecases/taxa") to generate functional descriptions and curate information in a human-readable format. - **Metagenome researcher** looking for sequence data: Find a unified and standardized metadata database from SRA (sequence read archive) metagenomic sequences where you can easily select relevant samples according to your research question. [(Use Case “MetaProv”)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbf5lF4Qs6emxgTl0/33R3fNXxds4O "https://nfdi4microbiota.de/usecases/metaprov") - **Bioinformatic software developer** interested in evaluating your tools: Specify the application scenario for which your tool is most likely to be used and, consequently, indicate what challenges are to be expected from a typical target microbial community in terms of complexity and diversity. What key parameters should an appropriate evaluation dataset feature? [(Use Case “MockBench”)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc42xuHO2cW3Kisr8/pk2BTZQRiSj- "https://nfdi4microbiota.de/usecases/mockbench") ###Metaproteomics Workshop organized by the NFDI4Microbiota Use Case “MetaProt” Are you interested in metaproteomics and a hands-on training workshop and getting to know the faces behind the NFDI4Microbiota [Use Case “MetaProt”](https://nfdi4microbiota.de/usecases/metaprot "https://nfdi4microbiota.de/usecases/metaprot")? Join the**“Applied Metaproteomics Workshop Magdeburg 2023”** for training on experimental design, sample preparation, LC-MS measurements, data analysis and metadata suggestions based on standards developed by the MetaProteomics Initiative and NFDI4Microbiota. **Organizers:** Dirk Benndorf, Patrick Hellwig, Kay Schallert, Robert Heyer, Nico Jehmlich **Date:** September 18th-22nd, 2023 **Location:** Otto von Guericke University Magdeburg, Germany **Registration fee:** 100 € (including coffee and snacks) **More information:**The agenda and registration details are available at [mpa@ovgu.de](mailto:mpa@ovgu.de?subject=Applied%20Metaproteomics%20Workshop%20Magdeburg%202023 "mailto:mpa@ovgu.de") ###NFDI4Microbiota Services ###Upcoming training and workshops Supporting the community through education and training is an important goal of our work. Therefore, we provide a comprehensive training program to equip the community with the skills and literacy required for efficient and data-driven microbial research. Upcoming training courses can be found in [our training calendar](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqVNIqZm7Y5… "https://nfdi4microbiota.de/training/training") and below. - [Workshop on Computational Pangenomics](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZFSZy3Ww… "https://www.denbi.de/training/1588-workshop-on-computational-pangenomics") (online, Sep 20th-21st, 2023) - Workshop on BacDive, MediaDive and StrainInfo (Oct 11th, 2023, *more details coming soon*) - [Workshop on Deep Learning with R](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZePmdGU79Gcc448s/z… "https://www.dzif.de/en/event/introduction-deep-learning-r") (online, Oct 11th-13th, 2023) - [Workshop: How to describe biological data?](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGa3MzITRHf7sz6T… "https://biometadata-01.sciencesconf.org/") A primer to a FAIR approach for now and the future (RWTH Aachen, Oct 16th-17th, 2023, see the next article for more details) - [Workshop on Basic statistics with R](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGaSKBxgOSAz9M8sL8/d… "https://www.dzif.de/en/event/basic-statistics-r") (online, Oct 25th-27th, 2023) - Joint de.NBI & NFDI4Microbiota Training Course on Metagenome Analysis (online, Nov 7th-9th, 2023, *more details coming soon*) ###Workshop: How to describe biological data? A primer to a FAIR approach for now and the future Confused about FAIR, ontologies and metadata and how they can help you and your datasets? Begin with our hands-on workshop about description of biological data on October 16th-17th in Aachen and [register here by September 20th](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGarHOctLcgqPjBHR… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbGEbI6InChg6DgXO/PmaV…"). **The workshop is intended for:** - People with knowledge about microbiology - Late-stage (wet lab) researchers with datasets that are in preparation to be submitted to repositories - Early-stage researchers that will be generating large datasets - Researchers having difficulties to apply existing ontologies and metadata fields to their data set - Data stewards or broker responsible for submitting data You will learn how to use terms based on existing ontologies and controlled vocabulary. Your engagement and continuous use of these terms will help to increase future machine-actionable analyses. After the workshop, you will have successfully described your own datasets and prepared the necessary metadata for future deposition of your described datasets. **But beware during this workshop, we will not upload or publish your data, analyze/ re-analyze your data, develop an ontology or set-up an automatic transfer of your metadata to repositories.** ###Publications ###The NFDI4Microbiota Grant Proposal has been published We are pleased to announce that our DFG [grant proposal](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbfBnxJFxiYw… "https://riojournal.com/article/110501/") “NFDI4Microbiota – national research data infrastructure for microbiota research” has been published in the journal [Research Ideas and Outcomes (RIO)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc490cWD8EQCqIUj… "https://doi.org/10.3897/rio.9.e110501"). Here you can find all information about our structure, partners, objectives, work program and strategies. ###Reading recommendation: How to make your scientific data accessible, discoverable and useful - Nature In June 2023, Nature published a Technology Feature article entitled “How to make your scientific data accessible, discoverable and useful” asking data scientists about their best practices for publishing usable, high-quality data. Here, specialists offer seven tips for effectively sharing data. [Read the full article here.](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGcT6DHjAIkHTDKt… "https://www.nature.com/articles/d41586-023-01929-7") ###Media ###NFDI4Microbiota is now part of the LinkedIn network After having profiles on X (former Twitter) and Mastodon, [you can follow us now also on LinkedIn!](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqbQ15OrjS… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZFYcgIM2FJVkbGvG/s7Ez…") We are looking forward to get in touch with you there. ###Short introduction video of NFDI4Microbiota published A two-minute introduction video of NFDI4Microbiota is [now available online](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZeVpLVJClAm7d… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGa3T20iGNH22Ug57W/Z6M6…"), giving an insight into our vision and mission, and how we aim to democratize the access to microbiota data and high-end computational analyzes. ###Online video: NFDI4Microbiota lecture talk - Training and education One focus of our consortium is the democratization of access to data and workflows for the field of microbiology. Training and education, as well as building a knowledge base on topics related to this field, are some of the means to achieve these goals. [This presentation was originally given at the second NFDI4Microbiota annual conference (April 2023).](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGaSQEfvDXmtIri… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGarNRL8AiIkZEktJm/Guda…") It provides an overview of the overall goals for training and education within NFDI4Microbiota and details on the first steps we have taken to reach these goals. We also introduce the NFDI4Microbiota Knowledge Base as part of our educational efforts. ###Online presentation: NFDI4Microbiota - Services to make data FAIR and Open The presentation "NFDI4Microbiota - Services to make data FAIR and Open" held by Barbara Goetz, member of NFDI4Microbiota, at the fifth Thuringian RDM Days on 20-21 June 2023 [has been recorded and is available online](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbfHqfY53KT5yp… "https://www.youtube.com/watch?v=cvy5nhDBYbE"). The slides of the presentation [can be found here](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbGKe0L7sobpbnIP… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc4F3Kl2DqKMLs6cA/7VNS…"). ###Jobs The members of the NFDI4Microbiota consortium offer specialist positions throughout Germany. The content and funding of all positions are the responsibility of the individual members. **Our partner at the Friedrich Schiller University Jena is looking for a**[**“Postdoctoral researcher (m/f/d) or PhD Candidate (m/f/d) in Frontend development of virus database and community engagement”**](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGcTCFzx… "https://jobs.uni-jena.de/jobposting/d070b59d5f1c7eaa6e77f0e1eebbdb2238de461…")**.** The application deadline is November 1st, 2023. [All vacancies are posted on the NFDI4Microbiota website as they become available.](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqhSjKDxL… "https://nfdi4microbiota.de/latest/jobs") Learn More About Us: -------------------- **This newsletter is brought to you by NFDI4Microbiota** Mail: [contact@nfdi4microbiota.de](mailto:contact@nfdi4microbiota.de) If you no longer wish to receive this newsletter, [click here to unsubscribe.](mailto:contact@nfdi4microbiota.de?subject=Unsubscribe&body=Dear%20NFDI4Microbiota-Team%2C%0AI%20would%20like%20to%20unsubscribe%20from%20your%20newsletter.%0A%0AKind%20regards "click here to unsubscribe") [Privacy Policy](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbGQgiZwyQVz7M… • [Impressum](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbfNtNmu8wN… • [Disclaimer](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc4L62zrJS…

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