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>.
[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
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
---
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
---
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.
