相关论文: Python Unleashed on Systems Biology

Over the past decade, the Python-based Simulations of Chemistry Framework (PySCF) has developed into a widely used open-source platform for electronic structure theory and quantum chemical method development. This article reviews the major…

Python is a particularly appealing language to carry out data analysis, owing in part to its user-friendly character as well as its access to well maintained and powerful libraries like NumPy and SciPy. Still, for the purpose of analyzing…

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…

This paper introduces the practicalities and benefits of using SimPy, a discrete event simulation (DES) module written in Python, for modeling and simulating complex systems. Through a step-by-step exploration of the classical Dining…

PySPH is an open-source, Python-based, framework for particle methods in general and Smoothed Particle Hydrodynamics (SPH) in particular. PySPH allows a user to define a complete SPH simulation using pure Python. High-performance code is…

In this paper we present an open source framework developed in Python and consisting of three distinct classes designed to manipulate in a simple and intuitive way both symbolic representations of neutrosophic sets over universes of various…

An open source software package for performing dynamic RMS simulation of small to medium-sized power systems is presented, written entirely in the Python programming language. The main objective is to facilitate fast prototyping of new wide…

High-level programming languages such as Python are increasingly used to provide intuitive interfaces to libraries written in lower-level languages and for assembling applications from various components. This migration towards…

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…

The usage of the high-level scripting language Python has enabled new mechanisms for data interrogation, discovery and visualization of scientific data. We present yt, an open source, community-developed astrophysical analysis and…

This article describes lcpy, an open-source python package that allows for advanced parametric Life Cycle Assessment (LCA) and Life Cycle Costing (LCC) analysis. The package is designed to allow the user to model a process with a flexible,…

Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…

We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…

The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…

We present PyThaiNLP, a free and open-source natural language processing (NLP) library for Thai language implemented in Python. It provides a wide range of software, models, and datasets for Thai language. We first provide a brief…

Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…

As camera pixel arrays have grown larger and faster, and optical microscopy techniques ever more refined, there has been an explosion in the quantity of data acquired during routine light microcopy. At the single-molecule level, analysis…

Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for…

We present PyOECP, a Python-based flexible open-source software for estimating and modeling the complex permittivity obtained from the open-ended coaxial probe (OECP) technique. The transformation of the measured reflection coefficient to…

We introduce SLIRP, a module generator for the S-Lang numerical scripting language, with a focus on its vectorization capabilities. We demonstrate how both SLIRP and S-Lang were easily adapted to exploit the inherent parallelism of…