Dear readers,

In this newsletter, we would like to give you an overview of our current course and consulting offers and inform you about the latest developments in the field of research data and research software management.

As usual, we briefly introduce ourselves in the first article “What is zedif” and would like to draw your attention to our practical courses in the winter semester 2024/25. By participating in certain courses, you will again have the opportunity to obtain a Carpentries certificate. We would also like to invite you to visit our booth at the Long Night of Science in November and talk to us!

We also present the zedif transcription service, the Repository for Research Data in Thuringia (REFODAT) and the current status in providing eLabFTW as a Thuringia-wide electronic laboratory notebook.

As digitisation and access to scientific results play an increasingly important role in research, we would like to inform you in this newsletter about the strategy paper on “Digitality in Science” of the Alliance of Science Organisations in Germany, the new “Open Code Policy” of Springer Nature and the Coffee Lectures of the Thuringian Competence Network for Research Data Management with a focus on the European Commission’s digital strategy. We also recommend that you familiarise yourself with the basic legal aspects of research data management.

In our series ‘News from the National Research Data Infrastructure (NFDI)’, we report on the emerging basic services of the Base4NFDI consortium.

We also look back on the Thuringian RDM Days 2024 and would like to draw your attention to the Data Fellowship Meeting in Jena next spring.

Last but not least, we ask you to take part in our mini-questionnaire on the possible use of a local ShareLaTeX/Overleaf instance at the university.

Enjoy reading, educating and networking!

Your zedif team

zedif is short for “Competence Center Digital Research“. We provide open doors and helping hands for all digital concerns of researchers.

We are the main point of contact for researchers and scientists from the University of Jena and other members of the Michael Stifel Center Jena, who are looking for help with any digital issues they may face during their research.

We provide assistants on the topics of teaching and training, funding requests, as well as with information on how to implement or develop digital tools. We are looking forward to every request, be it small, quickly answerable phone calls or year-long cooperations. If you are unsure on who to contact with your issues, we will help you find the correct contact person and provide additional consultations where needed.

Get in contact:

• Servicedesk: https://serviceportal.uni-jena.de/zedif
• Matrix Chat: https://matrix.uni-jena.de/#/room/#zedif-consultation:uni-jena.de
• E-Mail: zedif@uni-jena.de or researchdata@uni-jena.de
• Telephone: +49 3641 9-46435 or 9-46340

You can find us at the 21st floor of the JenTower. Please make an appointment beforehand so the best suited consultant will be available for you.

In the winter semester 2024/2025, zedif once again offers numerous courses that teach basic knowledge and skills in digital tools, research data management, and programming. There are also courses on containerisation with Docker, using an HPC cluster, and tools to help scientific writing. A special offer is the Carpentries’ certificate workshop. A new offer is a multi-day workshop on all aspects of software development.

Would you like a course on a topic that we do not offer yet? Feel free to send us a short (or long) email to zedif@uni-jena.de with the subject: course wish: topic.

This semester we are offering the following courses:

Research Data Management

• Research Data Management – Make your data count! (as part of the qualification programme of the graduate academy)
• Research data management in the humanities and social sciences (as part of the qualification programme of the graduate academy)

Data processing and analysis

• Spreadsheet Workshop
• Data cleansing and quality improvement with OpenRefine
• Introduction to the Database Query Language SQL
• A brief Introduction to R
• Introduction to the Command Line
• Basic Version Control with Git: A Beginner’s Workshop
• First Hands-on Experience with an HPC Clusters
• Introduction to Containerisation with Docker
• Working with Tabular Data in Python and Pandas
• Software Development: Beyond Programming
• Spring School: Introduction to Programming for the Humanities and Social Sciences

Publication and Presentation

• Scientific Writing with LaTeX

Carpentries Certificate Courses

The Carpentries are an internationally active, non-profit organisation. Their aim is to to make basic data and software skills accessible to increase efficiency, openness and reproducibility in science, and research. The Carpentries offers three programmes with different focuses: Data Carpentry, Library Carpentry and Software Carpentry. We offer the following course in the summer semester:

• Data Carpentry Workshop (Spreadsheets, OpenRefine, SQL, R)

By participating, you can acquire a Carpentries certificate.

All details about the courses and registration can be found in our catalogue within the Qualification Portal. The courses are open for all members and students of scientific institutes in Jena. The course language is generally English.

If you have any ideas or wishes for further courses, feel free to contact us.

On November 22, 2024, the Long Night of Science will take place in Jena, starting at 6 PM. In the foyer of the campus at Carl-Zeiß-Straße 3, zedif and its partners will present interactive offerings on the topics of research data and software, artificial intelligence and scientific computing. The zedif is joined by the Thuringian Competence Network Research Data Management (TKFDM), the Data Literacy Project Jena (DaLiJe), and the Thuringian Centre for Learning Systems and Robotics (TZLR).

Zedif and the TKFDM will show you in a playful way what (research) data management is all about: Try the prize wheel, build with Lego bricks, and read terrifying horror stories. We also present some of our consulting cases, illustrating how zedif collaborates with researchers at the university. With TinyDraco, we have a supercomputer in miniature format with us. It runs an interactive fluid simulation, which demonstrates how such high-performance computers work.

At the Data Literacy Project booth, you can sharpen your data skills with the help of sweets and test your knowledge in a data quiz.

The TZLR booth will explore what is behind the much discussed topics of machine learning and artificial intelligence. You can take a look inside an artificial neural network while teaching the machine to read and distinguish handwritten numbers.

Panel (f.l.t.r): simulation software „TinySPH“ (SPH = smoothed-particle hydrodynamics), © Uni Jena, E. Kadasch; sorted chocolate beans, © Nik on Unsplash.com; analysis software and source code, © Uni Jena, S. Hell and P. Schäfer; Lego minifigure with tools, © CCO.

In many scientific disciplines, the analysis of conversations, speeches, or interviews is central for gathering qualitative data and insights. Transcribing such recordings is a crucial step in this process. The zedif now provides an IT service that lets researchers automatically transcribe audio recordings quickly, ensuring privacy protection and delivering high-quality results, free of charge.

The service was successfully trialled during a pilot phase, so we now want to make it available to a wider audience and adapt it further to your needs. If you need audio transcription for your research or want to explore the service’s quality, feel free to register. More information can be found in our user documentation.

Why Use This Service?

We use open-source software for transcription that processes your recordings exclusively within the university’s secure network. This ensures that your sensitive data remains private, is only processed on university-owned computers, and is deleted immediately afterwards. The service can distinguish between multiple speakers and supports various languages — including Spanish, Italian, English, Portuguese, and German — which enables its use in a wide range of research contexts.

How It Works

You can access the service through your computer’s file manager by placing the files to be transcribed in a pre-configured location in the central storage system (German only) of the university. The media files are automatically picked up and transferred to the university’s high-performance computing cluster Draco for transcription. Once completed, you will receive the transcripts along with the associated media files in an output folder on the central storage system

How Was the Service Created?

The transcription service was born out of a collaboration between researchers from the Thuringian Water Innovation Cluster Jena and the zedif team. Peter Schulz, leading the QuaWaKon (German only) project, approached us with the desire to transcribe interviews for his sociological research quickly and automatically. He and his colleagues in five other research projects planned over 100 interviews with scientists, government representatives, and citizens of Jena.

After an initial meeting and subsequent analysis of available solutions, we determined that the open-source software noScribe, based on OpenAI’s speech recognition model Whisper, provided a solid foundation for the project. zedif then made the necessary modifications to run the software on the university cluster, developed automation scripts, and set up a server that connects the university’s central storage system with the job scheduling system of the university cluster.

What’s Next?

Looking ahead, we want to further enhance the service together with the University Computing Center. Therefor, the Computing Center and the zedif have initiated a project to make the service even more user-friendly and to reach additional user groups.

The prototype is currently subject to some limitations. For example, the transcript is currently created using one specific model and set of parameters and we provide one output format only. In the future we want to let users select models and customise transcription options to fine-tune transcript quality. We also plan to support multiple output formats, making it easier for researchers to integrate transcripts into their workflows. Additionally, we are working to simplify the registration process to make it easier for researchers to access the service.

Researchers at Thuringian universities will soon be able to use a new service to publish and preserve their research data. The Repository for Research Data Thuringia (REFODAT) offers a generic publication platform for data from all subject areas, especially for those for which no suitable subject-specific repository is available. Publication is free of charge for all researchers at Thuringian universities.

Datasets can be submitted at any time via the REFODAT website. An editorial team supports the submission process and ensures that the data comply with the FAIR principles. In addition, the repository provides interfaces that allow the transfer of collected and possibly curated collections from other systems (e.g. work platforms) that cannot guarantee permanent availability. DOI assignment, linking of authors and datasets with additional identifiers and resources (including ORCIDs, ROR, GND), and export and citation functions (such as JSON-LD or BibTeX) are supported. Datasets from researchers at Thuringian universities that have already been published in other subject-specific repositories can be registered in the repository, with the metadata transferred.

The service was developed by the Thuringian Competence Network for Research Data Management (TKFDM), the Library Service Centre (BSC) and the IT Centre of the Thuringian Universities (HS-ITZ). It is funded within the framework of the Strategy for Digitisation in Higher Education (2021-2025). The Thuringian University and State Library (ThULB) in Jena is responsible for the ongoing operation.

Further information can be found in the concept paper on the Repository for Research Data Thuringia(German only. For a first insight into the repository, we recommend you watch the following video(German only).

In experimental sciences, a transition from paper-based lab notebooks to digital documentation of experiments with so-called “Electronic Lab Notebooks” (ELNs) is currently taking place. With the Chemotion ELN, such an ELN is already offered at the University of Jena, which was developed especially for chemistry and related disciplines.

To satisfy the need for a generic ELN, zedif, the Thuringian Competence Network for Research Data Management (TKFDM), and the University Computer Center (URZ) have jointly evaluated various offers. The ELN eLabFTW emerged as a suitable candidate. The open-source software eLabFTW offers an appropriate range of functions, supports collaboration in teams, is intuitive to use and is being actively developed. In addition, there is a growing community of universities, particularly in Germany, which is driving development forward and facilitates a helpful exchange of experience.

Currently, we aim for the provision of eLabFTW as a service of the IT Centre of the Thuringian Universities (HS-ITZ) for all Thuringian universities. To this end, zedif is coordinating the creation of the technical, legal, and organisational requirements in consultation with the responsible bodies.

If you are interested in using eLabFTW, you are welcome to subscribe to the mailing list. There you will be kept up to date on the status of developments and will hopefully soon be informed about the launch of the service.

The Alliance of Science Organisations in Germany has published the Strategy paper on the focus area “Digitality in Science”: “Shaping Digitality - Advancing Openness and Sovereignty” (German only) (adopted 2023). The objectives are the timeliness in the coordination process of relevant topics, public access to scientific results and increasing sovereignty in the use of digital tools in science.

In February 2024, Springer Nature announced a new open code policy. It requires authors of journal article to include a “Code Availability” section for software that has been newly developed as part of the underlying research. The publisher claims to encourage and support article and book authors to make this software openly available.

The Thuringian Competence Network for Research Data Management (TKFDM) is continuing its popular Online Coffee Lecture series in the winter semester 2024.

These 30-minute events will take place once a month on Wednesdays from 14:00 to 14:30. This time, the laws of the EU Digital Strategy as well as their significance for science and specifically for the handling of research data, will be presented. Make yourself a cup of coffee or tea and drop by virtually! Participation is free of charge. Registration and further information can be found the website of the TKFDM. The TKFDM records all Coffee Lecture presentations and makes them permanently available on YouTube. It is also worth taking a look at the Coffee Lecture Playlist, where you will find all past series on topics such as RDM basics, tools in RDM and metadata. Have fun browsing!

Researchers are confronted with a variety of legal aspects in the course of their research activities. It is essential to be aware of the basic legal requirements, especially when it comes to the publication of research results or the subsequent use of data and results from other studies.

To provide researchers with an overview of the most important legal aspects in the different phases of the data life cycle, the FAIRmat consortium has published a practical guide on legal aspects of research data management (1). The guide is aimed at students, PhD candidates, postdocs and principal investigators. Topics such as copyright, licensing, international data transfer, contract law, data security and data protection, as well as research ethics and open access agreements are presented in an easy-to-understand manner.

1. “FAIRmat Guide to Legal Aspects in Research Data Management”, version 1.1, March 22, 2024. Zenodo: https://doi.org/10.5281/zenodo.11083303

In this series, we present the newest developments from the NFDI. This time we talk about the Base4NFDI consortium. Base4NFDI integrates and establishes basic services as interoperable solutions for the National Research Data Infrastructure (NFDI). Already existing services are adapted or extended to be usable for researchers from other disciplines.

The IAM4NFDI (Basic Service for Identity and Access Management) and TS4NFDI (Basic Service for Harmonisation and Mapping of Terminologies) projects were already approved in 2023 as part of Base4NFDI.

This year, four new basic services were accepted by Base4NFDI:

Jupyter4NFDI aims to provide a centralised JupyterHub service that provides access to various software stacks and computing resources across the NFDI consortia.

DMP4NFDI is the centralised base service for data management plans (DMP) and software management plans (SMP). It will host the open source DMP tool RDMO, coordinate the standardisation of templates and provide support and training to the NFDI consortia.

KGI4NFDI will be a service hub to help consortia, institutions and researchers create and link knowledge graphs to ensure interoperability within the NFDI and beyond.

nfdi.software aims to design, implement, and test a central marketplace for research software to improve the accessibility of NFDI research data via domain-specific software and enable more complex re-use of metadata and software.

There will be a Services Roadshow on December, 4th 2024 at 2 p.m., showcasing all currently funded services.

Please do not hesitate to reach out to Base4NFDI with any question via base4nfdi-office@lists.nfdi.de.

The Thuringian Competence Network for Research Data Management (TKFDM) organised the Thuringian Research Data Management Days (FDM Days) for the sixth time on June 18 and 19.

This year’s two-day online conference for researchers in Thuringia took place under the motto ‘Becoming literate in the Data Universe - From data literacy to the application of AI’. On the first day, participants were given an introduction to research data management and an overview of Thuringia’s activities in this area. Among other things, the work of the data stewards and the new Thuringian research data repository REFODAT were presented (see the separate article in this newsletter). A highlight of the event was the presentation of the Thuringian FAIRest Dataset Award. This year’s prize, endowed with 2,000 €, went to Georg Stolz and his team for their dataset published on zenodo. There will be another Fairest Dataset competition from the TKFDM in 2025; you will find more information on this in our next newsletter at the beginning of March.

The second day of the event started with a keynote by the German Research Foundation (DFG) on the influence of artificial intelligence (AI) on science and the DFG’s funding activities. Also included were interesting sessions on the topics of data literacy, effective research data management for AI applications and the ethical implications of using AI. All presentations and recorded lectures of the Thuringian RDM Days are permanently available online, you can find the corresponding materials via the event page of the TKFDM.

Would you like to be informed about future events of the Thuringian Competence Network for Research Data Management? Then subscribe to the TKFDM mailing list.

The Data Fellowship Meeting will take place in Jena from April 1 to 2, 2025. It is a face-to-face event with input workshops and networking opportunities for anyone who works as a data steward, feels like one or is interested in the topic!

The event is co-organised by zedif and TKFDM and aimed at all data stewards, trainers, data managers, curators and similar roles that promote research data management for scientists of all fields and disciplines.

The conference will have 3 main themes:

• Data Steward Beginners’ Jumpstart: overview of the landscape, stakeholders, support and networks.
• The life of a data steward: Tips & tricks, failures, variety of tasks
• Changing the culture of research data management: what, why, how?

On April 3, there will also be a satellite workshop on “Introduction to research data management”, which is aimed at researchers in the life sciences.

If you are interested in the event and would like to stay up-to-date, please subscribe to the newsletter mailing list.

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