相关论文: MOLS 2.0: Software Package for Peptide Modelling a…

PyMilo is an open-source Python package that addresses the limitations of existing Machine Learning (ML) model storage formats by providing a transparent, reliable, and safe method for exporting and deploying trained models. Current…

The open source ALPS (Algorithms and Libraries for Physics Simulations) project provides a collection of physics libraries and applications, with a focus on simulations of lattice models and strongly correlated electron systems. The…

We present POMDPPlanners, an open-source Python package for empirical evaluation of Partially Observable Markov Decision Process (POMDP) planning algorithms. The package integrates state-of-the-art planning algorithms, a suite of benchmark…

The largenet2 C++ library provides an infrastructure for the simulation of large dynamic and adaptive networks with discrete node and link states. The library is released as free software. It is available at…

Docking is a crucial component in drug discovery aimed at predicting the binding conformation and affinity between small molecules and target proteins. ML-based docking has recently emerged as a prominent approach, outpacing traditional…

Network data mining has become an important area of study due to the large number of problems it can be applied to. This paper presents NOESIS, an open source framework for network data mining that provides a large collection of network…

Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results:…

In recent IoT (Internet of Things) and Web 2.0 technologies, a critical problem arises with respect to storing and processing the large amount of collected data. In this paper we develop and evaluate distributed infrastructures for storing…

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates…

This work introduces a new software package `Sesame' for the numerical computation of classical semiconductor equations. It supports 1 and 2-dimensional systems and provides tools to easily implement extended defects such as grain…

A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community,…

Machine learning interatomic potentials (MLIPs) enable atomistic simulations with near ab initio accuracy at significantly reduced computational cost, but their broader adoption is often limited by fragmented tooling, limited scalability,…

The purpose of this paper is the modeling of a repository for modules and interfaces that must include all integrated information system management of a port terminal.Modules will provide a basic framework necessary for automatic management…

PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…

We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…

PLOS and Mozilla conducted a month-long pilot study in which professional developers performed code reviews on software associated with papers published in PLOS Computational Biology. While the developers felt the reviews were limited by…

Motivation: Estimating model parameters from experimental observations is one of the key challenges in systems biology and can be computationally very expensive. While the Julia programming language was recently developed as a high-level…

Bodge is a free and open-source Python package for constructing large-scale real-space tight-binding models for calculations in condensed matter physics. "Large-scale" means that it should remain performant even for lattices with millions…

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…

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…