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!
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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/>.
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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/>.
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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.
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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>
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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.
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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)
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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>
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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.
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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>.
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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
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
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________________________________________
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
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________________________________________
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
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
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
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.
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>.
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Prof. Dr. Konrad Förstner Prof. Dr. Alice McHardy
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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.
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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>.
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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.
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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
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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>.
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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>.
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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.>
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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”.
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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”.
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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
Dear NFDI4Microbiota community,
After we launched the NFDI4Microbiota project last October, we are happy to invite you warmly to our 5th NFDI4Microbiota community workshop.
It will take place on Friday, the 18th of March 2022 from 10:00 AM to 12:00 AM CEST and will be held online. During this workshop, we will also kick off our ambassador program (for more information, click on the registration link).
Here are the links to register until the 13th of March:
· 5th NFDI4Microbiota Community WS: https://t1p.de/hobfs
· NFDI4Microbiota Ambassador program: https://t1p.de/0602x
Shortly after the registration deadline, we will provide you with the Login details and the agenda.
Please feel free to invite your colleagues who might be interested in the NFDI4Microbiota consortium to the Community WS. If you have further questions, please do not hesitate to contact us.
We are looking forward to meet you soon!
Konrad Förstner and Alice McHardy, on behalf of the NFDI4Microbiota consortium.
Kind regards
Barbara Götz
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Barbara Götz, M.Sc. Microbiology
Project manager NFDI4Microbiota
www.nfdi4microbiota.de<http://www.zbmed.de/>
Reachable: Mon.-Thu. 7:30 AM - 4 PM
ZB MED - Informationszentrum Lebenswissenschaften
Gleueler Straße 60
50931 Köln
www.zbmed.de<http://www.zbmed.de/>
INFORMATION. WISSEN. LEBEN.
Mit freundlichen Grüßen
Barbara Götz
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Barbara Götz, M.Sc. Mikrobiologie
Projektmanagerin NFDI4Microbiota
www.nfdi4microbiota.de<http://www.zbmed.de/>
Erreichbarkeit: Mon.-Don. 7:30-16:00 Uhr
ZB MED - Informationszentrum Lebenswissenschaften
Gleueler Straße 60
50931 Köln
www.zbmed.de<http://www.zbmed.de/>
INFORMATION. WISSEN. LEBEN.
