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Convex polyhedral abstractions of logic programs have been found very useful in deriving numeric relationships between program arguments in order to prove program properties and in other areas such as termination and complexity analysis. We…
Protein Contact Network (PCN) is a powerful tool for analysing the structure and function of proteins. In particular, PCN has been used for disclosing the molecular features of allosteric regulation through PCN clustering. Such analysis is…
We present the \texttt{NeuMC} software package, based on \pytorch, aimed at facilitating the research on neural samplers in lattice field theories. Neural samplers based on normalizing flows are becoming increasingly popular in the context…
Scikit-network is a Python package inspired by scikit-learn for the analysis of large graphs. Graphs are represented by their adjacency matrix in the sparse CSR format of SciPy. The package provides state-of-the-art algorithms for ranking,…
PySINDy is a Python package for the discovery of governing dynamical systems models from data. In particular, PySINDy provides tools for applying the sparse identification of nonlinear dynamics (SINDy) (Brunton et al. 2016) approach to…
The Controlled Molecule Imaging group (CMI) at the Center for Free Electron Laser Science (CFEL) has developed the CMIstark software to calculate, view, and analyze the energy levels of adiabatic Stark energy curves of linear, symmetric top…
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…
A common technique in the study of complex quantum-mechanical systems is to reduce the number of degrees of freedom in the Hamiltonian by using quasi-degenerate perturbation theory. While the Schrieffer--Wolff transformation achieves this…
Over the last few years, with the growth of time-series collecting and storing, there has been a great demand for tools and software for temporal data engineering and modeling. This paper presents a generic workflow for time series data…
Discrete mesoscale network models, in which explicitly modeled polymer chains are replaced by implicit pairwise potentials, are capable of predicting the macroscale mechanical response of polymeric materials such as elastomers and gels,…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
In this paper, we introduce Pysimfrac, a open-source python library for generating 3-D synthetic fracture realizations, integrating with fluid simulators, and performing analysis. Pysimfrac allows the user to specify one of three fracture…
Imbalanced-learn is an open-source python toolbox aiming at providing a wide range of methods to cope with the problem of imbalanced dataset frequently encountered in machine learning and pattern recognition. The implemented…
Python for Power System Analysis (PyPSA) is a free software toolbox for simulating and optimising modern electrical power systems over multiple periods. PyPSA includes models for conventional generators with unit commitment, variable…
Process mining extends far beyond process discovery and conformance checking, and also provides techniques for bottleneck analysis and organizational mining. However, these techniques are mostly backward-looking. PMSD is a web application…
PyOD is an open-source Python toolbox for performing scalable outlier detection on multivariate data. Uniquely, it provides access to a wide range of outlier detection algorithms, including established outlier ensembles and more recent…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
Polymerization and formation of crosslinked polymer networks are important processes in manufacturing, materials fabrication, and in the case of hydrated polymer networks, synthesis of biomedical materials, drug delivery, and tissue…