5th International Workshop on Reaction Systems

Important dates

• Abstract submission: June 15, 2025

• Brainstorming topic: August 15, 2025

• Workshop: September 2, 2025

• Main conference UCNC 2025: September 1-5, 2025

About the workshop

The 5th edition of the Reaction Systems Workshop takes place at the Université Côte d'Azur, Valrose Campus, Nice, France on September 2, 2025. The workshop is planned as an on-site/in-person full day event. It is co-located with the 22nd International Conference on Unconventional Computing and Natural Computing UCNC 2025, which features a broad and stimulating scientific program, including topics such as self-organizing robot swarms, molecular self-assembly, and cellular automata.  

Since their introduction nearly 20 years ago, reaction systems have evolved into a broad inter-disciplinary research area, driven by both biological motivations as well as the need to understand interactive computation. Research in this field is extensive and diverse, spanning theoretical foundations, applications and software tools. It encompasses various types of reaction systems, their mathematical properties, and their connections to other fields.  In response to the growing interest, a series of workshops and schools on reaction systems has been established to present state-of-the-art developments, exchanging research ideas, foster new collaborations, and strengthen existing ones.

Previous editions of the workshop: 

• Fourth edition: Pisa, Italy, September 2024.

• Third edition: Jacksonville, Florida, USA, March 2023. 

• Second edition: Torun, Poland, June 2019. 

• First edition: Milano, Italy, June 2018. 

Invited speakers

Roberto Bruni, University of Pisa, Italy.

Title of the talk: Reaction Systems analysis with BioReSolve.

Abstract. BioResolve (http://www.di.unipi.it/~bruni/LTSRS/) is a Prolog interpreter for Reaction Systems that offers a flexible playground for their analysis. BioReSolve has been designed by exploiting a process algebraic version of Reaction Systems, which allowed to seamlessly enhance basic Reaction Systems with additional features, like delays, duration, monitoring, dynamic slicing and various kinds of contexts (guarded, nondeterministic and recursive). The talk will provide an overview of the many facets of BioReSolve related to the simulation, analysis and verification of Reaction Systems. 

Short bio. Roberto Bruni is Full Professor at the Computer Science Department of the University of Pisa. His research ranges from the modeling and verification of concurrent, distributed, adaptive, and open systems, to natural computing and bio-inspired models of computation. He has contributed to several areas including Petri nets, rewriting logic, process calculi, Reaction Systems, service-oriented computing, multiparty interactions, abstract interpretation and program logics. He has co-authored over 150 publications, including textbooks and research monographs, and has been actively involved in numerous international research projects and program committees.

Wojciech Penczek, Institute of Computer Science, Polish Academy of Sciences, Poland.

Title of the talk: Model checking for temporal and epistemic properties of Reaction Systems.

Abstract. In this talk, we address the problem of model checking temporal and epistemic properties in reaction systems — a computational model inspired by the biochemistry of living cells. We introduce two dedicated temporal logics: rsCTL and rsLTL, counterparts of Computation Tree Logic (CTL) and Linear Temporal Logic (LTL), and discuss the complexity of their model checking procedures. We also present a synthesis method for rsLTL applied to partially defined reaction systems. To incorporate reasoning about knowledge and interaction, we extend the formalism toward distributed reaction systems with agency. This leads to the development of rsCTLK, an epistemic extension of rsCTL, and its corresponding model checking algorithm. We report on experimental results using a biological benchmark and demonstrate the effectiveness of our ReactICS toolkit, comparing it with the MCMAS model checker for multi-agent systems. 

Short bio. Wojciech Penczek is the Director of the Institute of Computer Science at the Polish Academy of Sciences (PAS), a corresponding member of PAS, and the Chair of the PAS Committee on Informatics. He served as General Chair of the conferences ICATPN 2010, TIME 2018, and ACSD 2019, and has recently been a Program Committee member for over 110 international conferences in computer science. He has co-authored more than 250 peer-reviewed publications on topics including Petri nets, distributed and timed systems, reaction systems, model checking, temporal, epistemic and strategic logics, security verification, and web services. According to Google Scholar, his work has been cited over 4050 times, and his H-index is 35. He received Best Paper Awards at AAMAS 2004 and SEFM 2015, as well as a Best Paper Nomination at AAMAS 2018. His teaching experience includes invited lectures at the Advanced Course on Petri Nets (2010), ESSLLI (2010), and EASSS (2006, 2007, 2017), as well as tutorials at PRIMA 2022 and ECAI 2024.

Program (tentative)

8.00 - 8.50 Registration (Amphitheater JAD, Department of Mathematics)

8.50 - 9.00 Opening

Session 1 9.00 - 12.50 (Amphitheater JAD, Department of Mathematics)

• 9.00 - 9.50 Invited talk. Roberto Bruni, Reaction Systems analysis with BioReSolve

• 9.50 - 10.15 Juliana Bowles, Linda Brodo, Roberto Bruni, Moreno Falaschi, Roberta Gori, Paolo Milazzo, Arend Rensink. Refinement of clinical guidelines for patients with multimorbidities

• 10.15 - 10.40 Linda Brodo, Roberto Bruni, Moreno Falaschi, Ion Petre. Simulation and Analysis of Distributed Reaction Systems

• 10.40 - 11.10 Coffee break

• 11.10 - 11.35 Paolo Bottoni, Anna Labella, Victor Mitrana, Ion Petre. Quantitative reaction systems

• 11.35 - 12.00 Paolo Bottoni, Anna Labella, Victor Mitrana, Ion Petre. Reaction systems with valences and polarities

• 12.00 - 12.25 Luca Manzoni. TBA

• 12.25 - 12.50 Daniela Genova. TBA

Lunch break and steering committee meeting 12.50 - 14.20

Session 2 14.20 - 16.50 (Amphitheater JAD, Department of Mathematics)

• 14.20 - 15.10 Invited talk. Wojciech Penczek, Model checking for temporal and epistemic properties of Reaction Systems.

• 15.10 - 15.35 Lukasz Mikulski and Maciej Koutny. Encoding reaction systems in Petri nets

• 15.35 - 16.00 Coffee break

• 16.00 - 16.25 Marcin Piatkowski. ReactICS: a model checking tool for distributed reaction systems

• 16.25 - 16.50 Anna Kuczik, Gyuri Vaszil. Chemical Reaction Automata and the Theory of Bayesian Rough Sets

Session 3 16.50 - 18.00 (Amphitheater JAD, Department of Mathematics)

• 16.50 - 17.20 Brainstorming & demos 

  • Linda Brodo, Roberto Bruni, Moreno Falaschi. Bioresolve: simulation and analysis of RS models.

  • Marcin Piatkowski. ReactICS: a model checker environment for reaction systems. 

  • Paolo Milazzo. The Zotero bibliography on reaction systems: how to search it, how to use it for your own articles, integration with Latex, Word, Google Docs.

  • Ion Petre. Brainstorming on the functioning of the reaction systems community: website, bibliography and events.

• 17.20 - 18.00 General assembly meeting

Call for contributed talks

We welcome talks on all aspects of reaction systems, including, but not limited to: 

• new variants of reaction systems; 

• mathematical and computational properties of reaction systems; 

• biologicla aspects of reaction systems;

• relationships to other areas;

• software tools;

• applications and case-studies. 

Talks may present novel, unpublished research results as well as research published in peer-reviewed journals and conferences since 2023. To propose a talk, send an email to ion.petre@utu.fi with an extended abstract (up to 2 pages). If the proposal is based on an already published article, include the bibliographical reference in the proposal. 

 The workshop will not publish a proceedings volume. A special issue based on the workshop is planned to be organized in Natural Computing. A separate call for novel, unpublished research will be issued, and submissions will undergo a separate peer-review process.

Submission deadline: June 15, 2025.

Call for discussion topics for the brainstorming & demo session

We invite contributions to the brainstorming session, where participants can propose and explore topics of mutual interest. This session aims to foster discussions, spark new research directions, and encourage collaborations. Discussions will take place in parallel in small groups, and all workshop participants are encouraged to join. We welcome suggestions on a broad range of topics, including but not limited to:

• theoretical developments;

• applications;

• novel connections to other areas;

• software tools;

• open challenges and future directions. 

 Submit your proposal by email to ion.petre@utu.fi as a 1-page description including the title of the topic and a brief description of its background and significance. 

Submission deadline: August 15, 2025. 

Organizers

• Paolo Bottoni, Sapienza University of Rome, Italy

• Moreno Falaschi, University of Siena, Italy

• Enrico Formentti, University of Nice, France

• Daniela Genova, University of North Florida, USA

• Roberta Gori, University of Pisa, Italy

• Jetty Kleijn, University of Leiden, the Netherlands

• Maciej Koutny, Newcastle University, UK

• Wojtek Penczek, Polish Academy of Sciences, Poland

• Ion Petre, University of Turku, Finland and National Institute of R&D for Biological Sciences, Romania (chair) 

• Grzegorz Rozenberg, University of Leiden, the Netherlands