Related papers: MPAT: Modular Petri Net Assembly Toolkit
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…
The emergence of data-driven computational materials science offers unprecedented opportunities to explore complex material landscapes, complementing experimental research with the discovery of novel compounds. To enable these developments,…
This paper describes a stand-alone, no-frills tool supporting the analysis of (labelled) place/transition Petri nets and the synthesis of labelled transition systems into Petri nets. It is implemented as a collection of independent,…
We introduce NetworKit, an open-source software package for analyzing the structure of large complex networks. Appropriate algorithmic solutions are required to handle increasingly common large graph data sets containing up to billions of…
This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. It builds on the…
AMDAT (Amorphous Molecular Dynamics Analysis Toolkit) is an open-source C++ toolkit for post-processing molecular dynamics trajectories, focused on high-performance static and dynamic analyses of amorphous, glassy, and polymer materials,…
Advances in high-throughput simulation (HTS) software enabled computational databases and big data to become common resources in materials science. However, while computational power is increasingly larger, software packages orchestrating…
We describe the open-source global fitting package GAMBIT: the Global And Modular Beyond-the-Standard-Model Inference Tool. GAMBIT combines extensive calculations of observables and likelihoods in particle and astroparticle physics with a…
This paper presents ADAMANT, a set of software modules that provides grasp planning capabilities to an existing robot planning and control software framework. Our presented work allows a user to adapt a manipulation task to be used under…
In response to a concerning trend of selectively emphasizing metrics in medical image segmentation (MIS) studies, we introduce \texttt{seg-metrics}, an open-source Python package for standardized MIS model evaluation. Unlike existing…
It is well known that the complex system operation requires the use of new scientific tools and computer simulation. This paper presents a modular approach for modeling and analysis of the complex systems (in communication or transport…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
In this paper, we present nmtpy, a flexible Python toolkit based on Theano for training Neural Machine Translation and other neural sequence-to-sequence architectures. nmtpy decouples the specification of a network from the training and…
We present theoretical rudiments of Petri nets over ontological graphs as well as the designed and implemented Python toolkit for dealing with such nets. In Petri nets over ontological graphs, the domain knowledge is enclosed in a form of…
It is known for decades that computer-based systems cannot be understood without a concept of modularization and decomposition. We suggest a universal, expressive, intuitively attractive composition operator for Petri nets, combined with a…
Recent advances in computing hardware and modeling software have given rise to new applications for numerical optimization. These new applications occasionally uncover bottlenecks in existing optimization algorithms and necessitate further…
The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…
The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…
Petri Nets (PN) are extensively used as a robust formalism to model concurrent and distributed systems; however, they encounter difficulties in accurately modeling adaptive systems. To address this issue, we defined rewritable PT nets…
As the field of data science continues to grow, there will be an ever-increasing demand for tools that make machine learning accessible to non-experts. In this paper, we introduce the concept of tree-based pipeline optimization for…