相关论文: pyModRev: a Python Tool for Model Revision of Bool…
PhysiBoSS is an open-source platform that integrates agent-based modeling of cell populations with intracellular stochastic Boolean networks, enabling multiscale simulations of complex biological behaviors. To promote model sharing and…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Many business process models contain control flow errors, such as deadlocks or livelocks, which hinder proper execution. In this paper, we introduce a new tool that can instantaneously identify control flow errors in BPMN models, make them…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
Discrete modelling frameworks of Biological networks can be divided in two distinct categories: Boolean and Multi-valued. Although Multi-valued networks are more expressive for qualifying the regulatory behaviours modelled by more than two…
LLMs are increasingly deployed as agents, systems capable of planning, reasoning, and dynamically calling external tools. However, in visual reasoning, prior approaches largely remain limited by predefined workflows and static toolsets. In…
Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…
Model checking is a fundamental technique for verifying finite state concurrent systems. Traditionally, model designs were initially created to facilitate the application of model checking. This process, representative of Model Driven…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
Machine learning models are essential tools in various domains, but their performance can degrade over time due to changes in data distribution or other factors. On one hand, detecting and addressing such degradations is crucial for…
This document contains the mathematical introduction to RORPack - a Python software library for robust output tracking and disturbance rejection for linear PDE systems. The RORPack library is open-source and freely available at…
Most available tools propose simulation frameworks to study models of biological systems, but simulation only explores a few of the most probable behaviours of the system. On the contrary, techniques such as model checking, coming from…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Data generated in studies of cellular regulatory systems are often qualitative. For example, measurements of signaling readouts in the presence and absence of mutations may reveal a rank ordering of responses across conditions but not the…
Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of biological systems. Nonetheless, it might be difficult to gather enough data to precisely capture the behavior of a biological system into a set of…
Motivation: Laboratory gene regulatory data for a species are sporadic. Despite the abundance of gene regulatory network algorithms that employ single data sets, few algorithms can combine the vast but disperse sources of data and extract…
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…