Related papers: JAK/STAT signalling - an executable model assemble…
Petri nets are a mathematical language for modeling and reasoning about distributed systems. In this paper we propose an approach to Petri nets for embedding reversibility, i.e., the ability of reversing an executed sequence of operations…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…
Synthesis automatically generates a process model from a behavioural specification. When the target model is a Petri net, we address synthesis through region theory. Researchers have studied region-based synthesis extensively for…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
SMPT (for Satisfiability Modulo Petri Net) is a model checker for reachability problems in Petri nets. It started as a portfolio of methods to experiment with symbolic model checking, and was designed to be easily extended. Some distinctive…
Interacting systems are increasingly common. Many examples pervade our everyday lives: automobiles, aircraft, defense systems, telephone switching systems, financial systems, national governments, and so on. Closer to computer science,…
Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require…
Sensing and reciprocating cellular systems (SARs) are important for the operation of many biological systems. Production in interferon (IFN) SARs is achieved through activation of the Jak-Stat pathway, and downstream upregulation of IFN…
State-of-the-art models represent proteins and molecules in separate embedding manifolds, limiting the modeling of systemic biological processes. We introduce ReactEmbed, a lightweight, plug-and-play module that bridges this gap. ReactEmbed…
We present a Python package called Modular Petri Net Assembly Toolkit (MPAT) that empowers users to easily create large-scale, modular Petri Nets for various spatial configurations, including extensive spatial grids or those derived from…
During the last decade, various approaches have been put forward to integrate business processes with different types of data. Each of such approaches reflects specific demands in the whole process-data integration spectrum. One particular…
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…
Supply chains involve geographically distributed manufacturing and assembly sites that must be coordinated under strict timing and resource constraints. While many existing approaches rely on Colored Petri Nets to model material flows, this…
Real-world processes operate on objects that are inter-dependent. To accurately reflect the nature of such processes, object-centric process mining techniques are needed, notably conformance checking. However, while the object-centric…
We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the…
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law…
Petri Nets are an increasingly used modeling framework for the spread of disease across populations or within an individual. For example, the Susceptible-Infectious-Recovered (SIR) compartment model is foundational for population…
Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…