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

We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…

Liquid Chromatography Mass Spectrometry (LC-MS) is an indispensable analytical technique in proteomics, metabolomics, and other life sciences. While OpenMS provides advanced open-source software for MS data analysis, its complexity can be…

The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…

Developing reusable software for mobile robots is still challenging. Even more so for swarm robots, despite the desired simplicity of the robot controllers. Prototyping and experimenting are difficult due to the multi-robot setting and…

Selecting an effective docking algorithm is highly context-dependent, and no single method performs reliably across structural, chemical, or protocol regimes. We introduce MolAS, a lightweight algorithm selection system that predicts…

Wearable biosensors can enable continuous human data capture, facilitating development of real-world Human-Robot Interaction (HRI) systems. However, a lack of standardized libraries and implementations adds extraneous complexity to HRI…

SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…

In order to facilitate the production of codes using WiSARD-based models, LabZero developed an ML library C++/Python called wisardpkg. This library is an MIT-licensed open-source package hosted on GitHub under the license.

RevelsMD is a new open source Python library, which uses reduced variance force sampling based estimators to calculate 3D particle densities and radial distribution functions from molecular dynamics simulations. This short note describes…

SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…

There has always been much motivation for sharing code and solutions among teams in the RoboCup community. Yet the transfer of code between teams was usually complicated due to a huge variety of used frameworks and their differences in…

semanticSBML 2.0 is an online collection of services for the work with biochemical network models in SBML format.

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources…

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely…

In this work, we present MOLPIPx, a versatile library designed to seamlessly integrate Permutationally Invariant Polynomials (PIPs) with modern machine learning frameworks, enabling the efficient development of linear models, neural…

PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…

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…

In this technical report, we describe a new version of SimpleSBML which provides an easier to use interface to python-libSBML allowing users of Python to more easily construct, edit, and inspect SBML based models. The most commonly used…

We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…