Related papers: MOLS 2.0: Software Package for Peptide Modelling a…

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…

Designing compounds with desired properties is a key element of the drug discovery process. However, measuring progress in the field has been challenging due to the lack of realistic retrospective benchmarks, and the large cost of…

This paper describes the Parametrized Derivative-Free Model Predictive Control pdf-mpc package, a matlab coder-based set of subroutines that enables a model predictive control problem to be defined and solved. the pdf-mpc is made available…

To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…

We introduce MOS, a software application designed to facilitate the deployment, integration, management, and analysis of mathematical optimization models. MOS approaches mathematical optimization at a higher level of abstraction than…

This paper presents LIBTwinSVM, a free, efficient, and open source library for Twin Support Vector Machines (TSVMs). Our library provides a set of useful functionalities such as fast TSVMs estimators, model selection, visualization, a…

We have successfully ported under GNU Linux ATLAS 9, the widely used stellar atmosphere modeling code, as well as both the SYNTHE suite of programs, its ``companion'' for spectral synthesis, and WIDTH, used to derive chemical abundances…

Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpora of malicious binaries, obtaining high-quality corpora of…

Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding…

ROScopter is a lean multirotor autopilot built for researchers. ROScopter seeks to accelerate simulation and hardware testing of research code with an architecture that is both easy to understand and simple to modify. ROScopter is designed…

Automated documentation of programming source code is a challenging task with significant practical and scientific implications for the developer community. We present a large language model (LLM)-based application that developers can use…

A supplemental paper detailing the QuillenSuslin package for Macaulay2. The QuillenSuslin package for Macaulay2 provides the ability to compute a free basis for a projective module over a polynomial ring with coefficients in Q, Z or Z/p for…

Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to…

Generative models for molecules have shown considerable promise for use in computational chemistry, but remain difficult to use for non-experts. For this reason, we introduce open-source infrastructure for easily building generative…

This paper presents the philosophy, design and feature-set of Neural Network Distiller, an open-source Python package for DNN compression research. Distiller is a library of DNN compression algorithms implementations, with tools, tutorials…

OpenML is an online machine learning platform where researchers can easily share data, machine learning tasks and experiments as well as organize them online to work and collaborate more efficiently. In this paper, we present an R package…

Deriving LoD2 models from orthophoto and digital surface models (DSM) reconstructed from satellite images is a challenging task. Existing solutions are mostly system approaches that require complicated step-wise processes, including not…

Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…

One of the most widely used simulation environments for mobile wireless networks is the Network Simulator 2 (NS-2). However NS-2 stores its outcome in a text file, so there is a need for a visualization tool to animate the simulation of the…

Spectropolarimetry, the observation of polarization and intensity as a function of wavelength, is a powerful tool in stellar astrophysics. It is particularly useful for characterizing stars and circumstellar material, and for tracing the…