» Be FAIR – Open Your Data

The Open Science Platform of the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw (ICM UW), provides an informational website for users of the University of Warsaw Research Data Repository. The service was created with researchers in mind, offering practical information on using the University of Warsaw Research Data Repository, as well as guidelines for managing data at every stage of its life cycle.

The website is available at: info.danebadawcze.uw.edu.pl/en/

What kind of information can you find on the website?

The information website for the repository is a result of collaboration between the Open Science Platform team and the ICM UW communications team. We warmly encourage you to use the materials provided, share the website link on UW departments pages, and submit your suggestions for additional content that could support your work with research data.

The University of Warsaw Research Data Repository is a service enabling free, long-term storage and open access sharing of data from all fields of science. The resources collected there include data produced as part of research conducted at the University of Warsaw or in collaboration with the university. Depositing and sharing research results helps increase their visibility, enables reuse, and allows compliance with funder requirements.

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The 4EU+ Against Cancer Summer School returns for its 2025 edition, taking place from July 7 to 9 at Sorbonne University in Paris. This intensive three-day program offers 20 hours of instruction and awards 4 ECTS credits. It is designed for students from the 4EU+ Alliance universities who are eager to deepen their understanding of oncology through a multidisciplinary approach.

The 4EU+ Against Cancer Summer School is part of the 4EU+ Alliance’s Flagship 1: Urban Health and Demographic Change program. This flagship addresses major societal challenges related to health and well-being, demographic transitions, and the urban environment. The Summer School is supported by grants awarded to oncology educational projects, with beneficiaries including the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw, Assistance Publique-Hopitaux de Paris at Sorbonne University, and the Czech Academy of Sciences and Charles University in Prague.

This international programme offers students an overview of modern oncology research – from basic, translational, and clinical studies to bioinformatics, computational biology, drug development, and science funding opportunities.

Participants will explore key areas of cancer research, including:

Lectures and sessions will be led by experts from 4EU+ universities: Charles University, Sorbonne University, University of Warsaw, University of Milan, University of Copenhagen, Heidelberg University, and University of Geneva.

How to apply?

The summer school is open to students from the 4eu+ European University Alliance with a Bachelor or Master 1 degree or equivalent. Please send your motivation letter and your curriculum vitae to all 3 leading faculty by June 15, 2025.

Find more details here.

The Open Data Repository RepOD has been awarded the CoreTrustSeal certification. This certificate confirms the high quality of the service, which has been supporting Polish researchers for the past ten years. RepOD is one of the services offered by the Open Science Platform at the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw (ICM UW).

The status of a Trustworthy Digital Repository is granted to repositories that successfully pass an evaluation process coordinated by the CoreTrustSeal Standards and Certification Board. CoreTrustSeal is an international non-governmental organization promoting reliable research data infrastructures. As part of the certification, a repository is assessed for compliance with sixteen requirements, covering areas such as security standards and service interoperability.

The content of the application is available at: https://amt.coretrustseal.org/certificates.

Why is it worth using the RepOD repository?
→ Researchers choose to use the service to increase the visibility of their research and the chances of their datasets and related publications being cited.
→ Institutions are motivated by the opportunity to collect and share, in one place, data produced through the research of their employed scholars.
→ The repository allows for open and free sharing of all types of research data, in accordance with FAIR principles.
→ Depositors can meet the requirements of funding bodies, such as the National Science Centre or the European Commission, which recommend using trusted, certified repositories.
→ The service enables compliance with open access policies of academic institutions and scientific journals.

The RepOD research data repository is operated by the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw and is available at: https://repod.icm.edu.pl/. From the begining, RepOD has functioned as a free and openly accessible platform. It is available to both individual researchers and institutions interested in managing their own collections.

More about the Open Science Platform projects can be found at: https://pon.edu.pl/

The Open Science Platform at the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, cordially invites you to join in celebrating the 40th anniversary of the Free Software Foundation’s work in defending the freedom of computer program users.

The local celebration will take place on May 29th, from 6:00 PM to 9:00 PM at the University of Warsaw Library (BUW, room 256). The event doors open at 5:30 PM at the Library entrance. Admission is free.

During the event, you’ll learn what free software is and how the Free Software Foundation has been defending its users’ freedoms for the last forty years.

The gathering will open with an interactive quiz the audience, followed by a panel discussion on freedom in the realm of machine learning applications. Afterwards, there will be a short improvisational theatre performance by Spoko Moment, inspired by the evening’s theme.

The panel will be moderated by Krzysztof Siewicz (Licensing and Compliance Manager, FSF), and the discussion (held in English) will feature:

There will also be time for informal conversations and networking in a relaxed atmosphere.

We hope to see you there!

Learn more about FSF

Free Software Foundation

Free Software Foundation Europe

On May 7th, 2025, dramatic events took place on the Main Campus of the University of Warsaw, deeply affecting the entire academic community.

Our hearts go out to the Family and Loved Ones of the murdered Employee and the severely injured UW Security Guard. In these difficult moments, we wish to express our deepest sympathy and support to all those affected by this tragedy.

With heartfelt sorrow and solidarity,
The Management, Staff, and Students of the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw

See also

Commemoration of the Victim of the tragedy at the University of Warsaw

Support for the University of Warsaw academic community

A team led by the late Prof Piotr Bała, as part of the HEAP – Human Exposome Assessment Platform project funded by Horizon 2020, has developed a novel tool for rapid HPV viral sequence detection.

The paper entitled “HPV-KITE: sequence analysis software for rapid HPV genotype detection”, whose first author is Dr Marek Nowicki from ICM UW, has just been published in the prestigious journal Briefings in Bioinformatics.

Detecting HPV gene sequences is a major challenge due to the large number of closely related HPV genotypes, the presence of significant amounts of non-viral DNA in samples and the high variability and rapid mutation of viruses.

Dr Nowicki and co-authors have developed HPV-KITE, a tool that enables the detection of HPV genotypes from virtually any next-generation sequencing data. The method is based on k-mer analysis and uses the Tversky index, which allows for high scalability.

Publication link

HPV-KITE: sequence analysis software for rapid HPV genotype detection
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf155,

https://doi.org/10.1093/bib/bbaf155

The Human Exposome Assessment Platform project was co-financed by the European Union under the Horizon 2020 program (grant 874662) and by the Minister of Education and Science’s project called “Premia na Horyzoncie 2” (497700/PnH 2/2020).

Funding information: https://icm.edu.pl/heap-human-exposome-assessment-platform/

Project website: https://heap-exposome.eu/

The National Science Centre has awarded MAESTRO grants to experienced researchers. Seven applications received funding, including the research project of Prof. Dr. hab. Piotr Andrzej Gwiazda, which will be carried out at the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw.

The research project titled “Research Challenges of Partial Differential Equations Inspired by State-of-the-Art Statistical and Machine Learning Algorithms” has been granted NCN funding of 2,920,200 PLN, ranking third on the list in the group of exact and technical sciences.

A key advantage of the project is its innovative application and development of partial differential equation (PDE) techniques, well-integrated with statistical methods. This combination will enable significant advancements in optimization, sampling, inference, and machine learning. On one hand, statistical approaches such as Bayesian inference play a crucial role in identifying PDE parameters; on the other hand, emerging gradient flow methods show great potential in developing sampling algorithms. The research objectives of the project focus on four problems: parameter identification, sampling methods, parameter stability, and extended graphons.

MAESTRO is a competition organized by the National Science Centre for research projects led by experienced scientists, aiming to conduct pioneering scientific studies, including interdisciplinary research, that are significant for scientific progress, go beyond the current state of knowledge, and may result in scientific breakthroughs.

In the sixteenth edition of the MAESTRO competition, NCN received 69 applications. Seven projects received funding: one in the humanities, social sciences, and arts group, two in the life sciences group, and four in the exact and technical sciences group. The total value of the funded applications exceeds 29.7 million PLN.

NCN / ICM UW

We invite you to an open lecture by Dr. Jeffrey Burgdorf from Northwestern University, titled “New Horizons in the Analysis of Time Series: From Neurons to Behaviors”. The lecture is organized as part of a mentoring visit under the Excellence Initiative – Research University program (Action I.1.1/IV.1.1 “Mentor Program”).

Dr. Jeffrey Burgdorf is a world-class expert in the neurobiology of emotions, a co-author of groundbreaking research on the mechanisms of positive affect, and a pioneer in the study of ultrasonic vocalizations in rodents. He also works in the pharmaceutical industry, contributing to the development of rapastinel, a promising substance with antidepressant and neuroprotective properties.

His research focuses on the analysis of multi-scale oscillations that govern living organisms and their interconnections – from the pulsations of individual neurons to brain waves, physiological rhythms such as heart rate and respiration, vocalizations, behaviors, and even circadian cycles.

During the lecture, the emotional system and its fundamental role in the functioning of the entire brain will also be incorporated into this dynamic framework.

The lecture, open to the University of Warsaw community, will take place on Monday, March 3, 2025, from 2:00 PM to 3:30 PM at ICM UW, Pawińskiego 5A, in the seminar room on the 5th floor (ICM Library).

An article by Dr. Miron Kursa from ICM UW titled “Vistla: identifying influence paths with information theory” has been published in Bioinformatics. It describes the Vistla algorithm, which is used for analyzing data from observations of complex systems, particularly those found in living organisms, studied through high-throughput molecular methods.

A complex system consists of components that interact with each other in a multitude of intricate and non-trivial  ways. The network of these interactions, characterized by a high density of connections and, at first glance, a lack of clear structure, is commonly called a “haystack.” This complexity poses a significant challenge when attempting to decipher the specific mechanisms of the system’s behavior or when trying to steer its behavior toward a desired direction.

Vistla allows for the analysis of data from experiments in which the system was subjected to external intervention, such as the administration of a substance. The method tracks how the information about this event spreads through the system, passing between various components—resulting in a much easier-to-interpret graph with a tree-like topology.

The open-source implementation of the method for the R environment is available in the CRAN repository: https://doi.org/10.32614/CRAN.package.vistla

DOI: https://doi.org/10.1093/bioinformatics/btaf036

In mid-December, series of meetings for the MOSAIC project were held in Warsaw, bringing together three project partners: the African Conservation Centre (ACC), the Institut de Recherche pour le Développement (IRD), and the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw (ICM UW). The project, titled “Multi-site application of Open Science in the creAtion of healthy environments Involving local Communities (MOSAIC),” involves a total of 15 institutions from around the world and is funded by the Horizon Europe program: Environment and Health – Planetary Health.

The centerpiece of the meetings was a two-day workshop (December 16–17) dedicated to data repositories, prepared by a team of scientists and developers from ICM UW. The event, conducted by Łukasz Dumiszewski and his team under the title “MOSAIC-WP4 Repository Systems Workshop: Data Analysis, Functional Requirements, and Collaboration Principles,” was attended by:

“Our series of meeting in Warsaw follows two field visits: in Kenya, within the Amboseli Ecosystem—a cross-border region with Tanzania—and in Brazil, at two locations: (1) Tabatinga and Leticia, in the tri-border area of Brazil, Colombia, and Peru, and (2) Oiapoque, a region where Brazil borders French Guiana. In each of these locations, we were met with the warm openness of local communities. We personally witnessed the great hopes placed on the outcomes of our project. Now, in Warsaw, we gather at a moment when local, traditional, and scientific knowledge must be integrated into a formalized structure on a shared platform,” commented Dr. Aneta Afelt, Assistant Professor at ICM UW and leader of the Polish MOSAIC team.

On the days preceding the workshop (December 12–13), project consultations were also held between the ICM UW and African Conservation Centre teams. These meetings focused on the challenges faced by cross-border communities that can be addressed through dedicated IT tools. The team from Kenya also had the opportunity to explore the University of Warsaw’s HPC infrastructure and learn about ICM UW’s data science expertise.

MOSAIC (Multi-site application of Open Science in the creAtion of healthy environments Involving local Communities) – focuses on open, multimodal, and replicable information ecosystems supporting cross-border communities. MOSAIC secured funding from the European Union’s Horizon Europe framework program: Environment and health – Planetary health (HORIZON-HLTH-2023-ENVHLTH-02-01). The task is being carried out by an international consortium of 15 institutions led by the French institute IRD (Institut de Recherche pour le Développement). The role of ICM UW is to prepare data infrastructure and software for stakeholders. The leader of the Polish MOSAIC team is Dr. Aneta Afelt (assistant professor at ICM UW, member of Espace-DEV research group affiliated with IRD).

Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.

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