Dear readers,

in this newsletter, we would like to bring you up to date with the latest news from the Competence Center Digital Research (zedif). In addition to presenting our current course programme for the winter semester, we also congratulate the winner of the zedif Fellowship.

We look back on the Thuringian RDM Days — including the presentation of the winner of the ’FAIRest Dataset’ competition. In addition, we present new TKFDM materials such as the RDM checklists and a FAIR assessment tool, as well as the dates for the TKFDM Coffee Lecture Series ‘Research Tools 4 All: Smart Solutions for Thuringian Scientists’.

We also announce the next version of our transcription service and inform you about the possible uses of the ORCID at the University of Jena.

Exciting developments are also taking place at the European level, and we would like to introduce you to several European Commission initiatives in the field of research data. We are also pleased to announce that the second funding period for nine consortia of the NFDI, including contributions of the University of Jena, began in October 2025.

Have you ever considered publishing your research data in a data journal or wondered how to write a software management plan? Then our information articles on these topics are just what you need!

Finally, we invite you to take part in our mini-survey. Let us know: Are you using an electronic laboratory notebook (ELN) for documenting your research?

We hope you enjoy reading, and we wish you a great start to the winter semester!

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 central point of contact for researchers from the University of Jena, who are looking for help with digital issues they may face during their research.

We provide assistance on a wide variety of topics like teaching and training, grant applications, or selection or development of digital research tools and workflows. We are looking forward to every request, be it small and quickly answerable on the phone, or year-long cooperations. If you are unsure on who to contact, 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
• Telephone: +49 3641 9-46435 or 9-46340

You are also welcome to visit us at our Campus Inselplatz offices (Inselplatz 5, rooms 2027–2030). Due to changing home office arrangements, please contact us in advance to ensure that those who can best assist you are available.

This winter semester, we once again offer a range of courses that teach basic knowledge and skills in digital tools, research data management, and programming. Further courses focus on machine learning, the use of HPC clusters, and the electronic lab notebook eLabFTW.

All courses can be be credited towards our new certificate “Digital Research”. You can find more details on our website. You can also earn an internationally recognized Carpentries certificate by completing our Software Carpentry workshop series.

This semester we are offering the following courses:

Research Data Management

• Research Data Management – Make your data count!
• Research data management in the humanities and social sciences
• Introduction to Experiment Documentation with eLabFTW

Data processing and analysis

• Introduction to the Command Line
• Basic Version Control with Git: A Beginner’s Workshop
• Introduction to Programming with Python
• Scientifc Writing with LaTeX
• First Hands-on Experience with an HPC Cluster
• Basics of Machine Learning for Non-Computer Scientitst

Carpentries Certificate Courses

The Carpentries are an internationally active non-profit organisation. Their aim is to make basic data and software skills accessible to increase efficiency, openness and reproducibility in science and research. The Carpentries consist of three flavours with different focuses: Data Carpentry, Library Carpentry and Software Carpentry.

This semester, we offer a Software Carpentry Workshop, consisting of the three workshops marked above. By participating, you can acquire an internationally recognised 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.

In May, we introduced the zedif fellowship programm, which offered the opportunity to apply for a year of individual mentoring. Now, we are happy to announce our first fellow: Inmaculata Pérez Pérez from the Abbe Center of Photonics at Friedrich Schiller University.

Inmaculada Pérez Perz (used with permission, all rights reserved.)

Pérez Pérez previously earned her Master’s degree in photonics from Friedrich Schiller University. She currenlty pursues her doctorate continuing her research in quantum optics where she focuses (pun intended) on methods for quantum spectroscopy.

As part of her Master’s thesis, Pérez Pérez worked on photonics methods to detect single molecules, such as individual proteins or pollutants, without altering the respective samples, using their unique “light fingerprint”, their electromagnetic signature. The major challenge is that most of the molecules of interest have their electromagnetic signature in light wavelengths that are hard to detect by sensors.

To get around this, she used pairs of entangled photons, produced together with a fixed wavelength each. The presence of a probing molecule would affect the generation of photons with wavelengths similar to its own. Thanks to the fact that these entangled photons are produced together in pair, a production increase at this wavelength would be accompanied by an increase of the other photon in the entangled pairs, at a different wavelength. Designing the full detection system correctly, the partner photon can lay in a frequency range that is easy to detect.

Quantum imaging with undetected photons. (a) Illustration of the study system: A nanoparticle with a probing molecule is sensed through the detector. (b) Amount of detected photons with probing molecule absent. (c) Amount of detected photons with probing molecule present. Licensed under CC BY-SA 4.0.

This sensing scheme, known as “quantum imaging with undetected photons”, is not new. As part of her thesis, Pérez Pérez developed a Matlab code that enabled her to simulate that interaction.

During her fellowship, we will work on improving the code to both increase usability and accessibility for other researchers and students, as well as raise computational efficiency to accelerate the scientific feedback loop.

The Thuringian Competence Network for Research Data Management (TKFDM) hosted the Thuringian Research Data Management Days (RDM Days) for the seventh time on June 18 and 19. Under the motto “Empowering Research – Tools and Thuringian Case Studies”, this year’s two-day online conference on research data management was held entirely in English for the first time.

The first day began, as usual, with an introduction to research data management and concluded with an overview of current Thuringian activities in this field. A highlight of the day was the presentation of the Thuringian FAIRest Dataset Award. This year, the €2,000 prize was awarded to Tobias Gäbler (University of Jena/Fraunhofer IOF Jena) and his team for their dataset published on Zenodo. The next FAIRest Dataset Award will be organized by TKFDM in 2026. Further information will be available in our upcoming newsletter in early March.

On the second day, the focus was on software solutions for collaborative research data management. Among others, LaTeX and Overleaf were introduced, as well as the practical use of the electronic lab notebook elabFTW at the University of Jena. All presentations and recorded talks from the Thuringian RDM Days are available online for permanent access. You can find the corresponding materials on the TKFDM event page.

Would you like to stay informed about future events organized by the Thuringian Competence Network for Research Data Management? Subscribe to the TKFDM mailing list.

The Thuringian Competence Network for Research Data Management (TKFDM) has published checklists for successful research data management as well as a tool for evaluating datasets according to the FAIR principles.

The TKFDM has adapted materials originally developed by TU Berlin – including the overview “10 Steps to Successful Research Data Management (RDM)” and six additional checklists on specific aspects of RDM – and adapted them for the Thuringian context. These resources can be found on the TKFDM website, where the checklists are available to download as PDFs by clicking on the preview images. If you have any questions about the practical implementation mentioned in the checklists, please email zedif@uni-jena.de. The Research Data Management team at Friedrich Schiller University Jena will be happy to support you. In addition, zedif also plans to adapt the TKFDM checklists for use specifically at the University of Jena.

In July, the TKFDM also released a FAIR Evaluation Tool, based on the open-source survey tool developed by the Australian Research Data Commons (ARDC). The tool helps to assess the extent to which a published dataset complies with the FAIR principles. Introduced in 2016, these principles aim to improve the findability and reusability of research data. The acronym FAIR stands for findable, accessible, interoperable, and reusable. This video provides a brief introduction to the FAIR Assessment Tool.

In October, the new coffee lecture series of the TKFDM will start under the motto “Research Tools 4 All: Smart Solutions for Thuringian Scientists”. The series opens with a session by the Thuringian University IT Center, introducing AI applications available to Thuringian universities. Among others, the AI chatbot HAWKI, the translation service DeepL, and Ollama will be presented. The following coffee lectures will focus on further practical tools: the open-source platform Galaxy for data analysis, JupyterHub, and elabFTW, an electronic lab notebook that has been available at the University of Jena since this year.

The coffee lectures take place at 2 pm online via Zoom on the last Wednesday of every month (except December!). Participation is free of charge. Make yourself a cup of coffee or tea and join the event! Further information about the coffee lecture series, including details of how to register, is available on the event website.

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

A year ago, we introduced our transcription service, which allows researchers to transcribe audio recordings quickly, in a privacy-friendly manner, and free of charge in high quality. Since then, almost 30 researchers have registered for the service and and nearly 600 recordings have been transcribed. We are happy to announce that we now launched the next version as an official service of the University Computing Centre (URZ), offering faster transcription and much simplified access.

The new version

Together with colleagues from the University’s Multimedia Centre at the URZ, we have been working on a new version of the service over the past few months. It offers two major advantages over the previous one:

1. Registration and use have become much easier, as the service is integrated into the university cloud as a menu item. This eliminates the need for manual setup on the university’s central storage system.
2. Transcription is now significantly faster (5 h of audio in approx. 10 min), as we are using a much faster implementation of the Whisper model (WhisperX, https://arxiv.org/abs/2303.00747) in the new service.

As with the previous version of the service, your data remains within the university network and is processed on our computing cluster Draco. We continue to provide the transcript as a Word document.

Usage

To use the service, log in to the university cloud at cloud.uni-jena.de with your URZ account. You can transcribe audio recordings that you upload there with a click in the context menu of each audio file. After a short time, the corresponding transcript will appear next to the recording as a Word document.

You can find detailed instructions (German) on the Wiki of the University Computing Centre. If you have any questions regarding the transcription of your files, please use the ticket system and select the “Uni-Cloud” service.

Since July 2025, you have the opportunity to connect your contact details at the University Jena with your ORCID to increase the visibility of your research outputs. You can link your ORCID to your contact details at portal.uni-jena.de → Bibliographic IDs. Additionally, you can add your ORCID in the university’s bibliography, and link your publications to your personal university site. Find more information on the Wiki page of the URZ (German only) or directly in the ThULB’s handout.

Persistent identifiers (PIDs), such as ORCID, help researchers to link their work directly to their name, ensuring that research articles and data publications are correctly assigned and made more visible within the research community. Any publications you tag with your ORCID will be updated automatically on your profile. You can choose how publicly visible your data is on your profile settings. The ORCID or ORCID iD is a globally recognised standard for the identification and conncection of researcher and their research activities. It is also increasingly being used for verification purposes when registering for certain research-related tools and services.

Don’t have an ORCID, yet? Follow this link to register and create your own unique and free identification in just a few clicks.

1. Horizon Europe: New framework programme with four pillars

The European Commission is planning the next phase of the research framework programme Horizon Europe, which will run from 2028 to 2034 with a total budget of around €175 billion — the highest ever. For the first time, the programme will be structured around four instead of just three pillars: Alongside the familiar areas of Excellent Science, Competitiveness and Society, and Innovation, a new pillar focusing on the European Research Area will be created. This pillar will focus particularly on research and technology infrastructures. Furthermore, ambitious ‘moonshot’ projects are planned to secure Europe’s international leadership in strategic future fields such as data sovereignty.

2. Uniform rules for researchers: DSA data access

Another step involves granting researchers access to research data on large online platforms. As part of the Digital Services Act (DSA), the European Commission has adopted a delegated act that clearly regulates this process for the first time. This defines technical conditions and establishes harmonised procedures, obliging digital service coordinators (DSCs), very large online platforms (VLOPs) and very large online search engines (VLOSEs) to disclose key information. Of particular importance is the newly created DSA data access portal, which provides a central point of contact. There, researchers can view their data access requests, track their status, and exchange information with colleagues. This makes the previously fragmented process much easier and more transparent.

We also recommend the TKFDM’s Coffee Lecture ‘Data Access for Researchers under the Digital Services Act’ to anyone interested in this topic. It is available both as a video (German) and as a set of slides.

3. AI on Demand: A central platform for data, tools and networking

The EU is expanding its activities in artificial intelligence. As part of the AI Continent initiative, the AI on Demand (AIoD) platform provides new services for research and industry. Researchers can access specially curated data sets, AI tools, and powerful computing resources. The offering is intended not only as a technical tool, but also as a networking platform. Its purpose is to promote the use of artificial intelligence and networking across Europe, supporting both research and industry equally.

On 4 July, the Joint Science Conference (Gemeinsame Wissenschaftskonferenz, GWK) decided to continue funding all nine consortia from the first selection round of the National Research Data Infrastructure (NFDI), see the DFG press release. The consortia are developing discipline-specific solutions to make data findable, accessible, interoperable, and reusable in accordance with the FAIR principles. The federal and state governments are providing around 92 million euros to fund the consortia until the end of 2028.

The second funding period will begin in October 2025 for DataPLANT, GHGA, KonsortSWD, NFDI4Biodiversity, NFDI4Cat, NFDI4Chem, NFDI4Culture, NFDI4Health, and NFDI4ING.

You can find an overview of all NFDI consortia and their local contact persons here.

Research software is becoming an increasingly integral part of the research process, and we are placing greater emphasis on its overall quality, reproducibility and sustainability (see Guiding principles of the DFG in the development of research software, FAIR4RS principles). Software Management Plans (SMPs) are one tool that can help address this technical and cultural challenge.

SMPs describe a software project, covering aspects such as development, documentation, testing, release, and licensing. As such, they are “living” documents that can evolve to meet the needs of the project. They formalise internal processes, support the onboarding of new contributors, and ensure the sustainability of the software.

As with data management plans, funding organisations may require SMPs as part of funding applications or after approval in the future. While not yet mandating SMPs, the DFG emphasises their usefulness in the information for applicants (see also DFG’s Guidelines for Safeguarding Good Research Practice, guideline 13 on providing public access to research results).

You do not need to start from scratch when writing an SMP for your project. A number of resources are available to help you create an SMP. These resources are usually presented as questionnaires or templates. For example, the UK Software Sustainability Institute provides guidance with questions and a checklist for writing SMPs. Grossmann et al. (2024) provide an extensive list of supporting materials in their review Software Management Plans – Current Concepts, Tools, and Application.

It is also worth noting that not every script or piece of software requires an SMP, and the scope and level of detail should be proportionate to the scale and complexity of the software project. The German Aerospace Center (Deutsches Zentrum für Luft- und Raumfahrt, DLR), for example, categorizes software into four application classes: from class 0 (personal scripts or similar, with no planned publication) to class 3 (mission-critical software where errors must be avoided to reduce risks) in their Software Engineering Guidelines. The DLR then assignes a minimum application class to each of their recommendation, resulting in guidelines the extent of which grows with the class of application.

Finally, even if creating a software management plan for your research software project is not a formal requirement, working through one of the templates may still be worthwhile. This will give you an overview of current best practices, it can highlight areas of your development processes that have been overlooked, and may reveal opportunities for quick but meaningful improvements.

Data journals offer an innovative platform for publishing research data. Unlike traditional publications, which focus on results and their interpretation, data journals focus exclusively on providing a detailed description of datasets. Articles in these journals describe the scope, complexity, and data collection methods of the data, but do not interpret them.

This publication method is particularly well-suited to important datasets, as it facilitates their subsequent utilisation and raises the profile of scientific work. A major advantage is the peer review process, which ensures a high-quality standard. The data are usually accessible via a persistent identifier (e.g. a DOI), which is linked to the articles, and are published separately in data repositories.

In addition to data journals, there are also journals that publish descriptions of research software.

Data and software journals thus offer an excellent opportunity to increase the value of a dataset within the scientific community and to raise the profile of one's research through academic publications. We invite all researchers to explore this innovative form of publication and share their datasets with a broader audience.

The zedif information page data publication provides a list of data journals organised by discipline.

Do you use an electronic laboratory notebook (ELN) to document your research?

➡️ Answer