• CGAL

  • Referenced in 360 articles [sw00118]
  • goal of the CGAL Open Source Project is to provide easy access to efficient ... aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning...
  • Cytoscape

  • Referenced in 73 articles [sw09080]
  • Biomolecular Interaction Networks. Cytoscape is an open source software project for integrating biomolecular interaction networks ... other molecular states into a unified conceptual framework. Although applicable to any system of molecular...
  • NFsim

  • Referenced in 11 articles [sw22256]
  • free, open-source, biochemical reaction simulator designed to handle systems that have a large ... even infinite number of possible molecular interactions or states. NFsim also has advanced and flexible...
  • ABNER

  • Referenced in 6 articles [sw30049]
  • Entity Recognizer) is an open source software tool for molecular biology text mining ... core is a machine learning system using conditional random fields with a variety of orthographic...
  • GOMC

  • Referenced in 2 articles [sw27534]
  • Monte Carlo (GOMC) is open-source software for simulating molecular systems using the Metropolis Monte...
  • BN2DMD

  • Referenced in 1 article [sw16950]
  • large (hydrodynamic scale) molecular systems. We provide the open source code written ... BN2D water model implementation using Molecular Dynamics...
  • SIESTA

  • Referenced in 22 articles [sw05949]
  • efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA ... algorithms which can be applied to suitable systems. A very important feature of the code ... treating large systems with some first-principles electronic-structure methods has opened up new opportunities...
  • GeneWays

  • Referenced in 4 articles [sw23128]
  • integrated system that combines several such subtasks. It analyzes interactions between molecular substances, drawing ... consensus view of molecular networks. GeneWays is designed as an open platform, allowing researchers...
  • WavePacket

  • Referenced in 8 articles [sw19829]
  • Closed quantum systems and discrete variable representations. WavePacket is an open-source program package ... treated, which allows to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting ... well as for research projects in atomic, molecular and optical physics or in physical ... deals with the description of closed quantum systems in terms of Schr”odinger equations...
  • QMCPACK

  • Referenced in 6 articles [sw12953]
  • QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code ... electronic structure calculations of molecular, quasi-2D and solid-state systems. Variational Monte Carlo...
  • turboTDDFT

  • Referenced in 2 articles [sw06833]
  • molecular systems made of up to several hundred atoms. turboTDDFT is an open-source software...
  • CUIK

  • Referenced in 3 articles [sw21885]
  • open-source toolbox for motion analysis of closed-chain mechanisms. Many situations in Robotics require ... parallel manipulators, reconfigurable robots, or molecular compounds), there is a lack of general tools ... spaces of such systems. This paper describes the CUIK suite, an open-source toolbox...
  • SMEAGOL

  • Referenced in 6 articles [sw33755]
  • Spin and molecular electronics in atomically generated orbital landscapes. Ab initio computational methods for electronic ... transport in nanoscaled systems are an invaluable tool for the design of quantum devices ... direct sum- mation of both open and closed scattering channels together with a regularization procedure ... particular it allows us to tackle material systems with complicated electronic structures, such as magnetic...
  • MetaboLights

  • Referenced in 1 article [sw16939]
  • major open-access data providers in molecular biology. Metabolomic profiling is an important tool ... research into biological functioning and into the systemic perturbations caused by diseases, diet ... methods depends on the availability of public open data across a broad range of experimental...
  • Kwant

  • Referenced in 6 articles [sw19547]
  • quantum transport. Kwant is a free (open source) Python package for numerical calculations on tight ... models can describe a vast variety of systems and phenomena in quantum physics. Therefore, Kwant ... topological insulators, quantum Hall effect, superconductivity, spintronics, molecular electronics, any combination of the above...
  • CheMPS2

  • Referenced in 4 articles [sw17633]
  • CheMPS2: a free open-source spin-adapted implementation of the density matrix renormalization group ... nuclear structure and molecular electronic structure, it has significantly extended the system sizes that ... this work we present CheMPS2, our free open-source spin-adapted implementation of DMRG...
  • PSI3

  • Referenced in 1 article [sw36173]
  • open‐source Ab Initio electronic structure package. PSI3 is a program system and development platform ... initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input ... data such as basis‐set information or molecular orbital coefficients, and retrieving and storing binary ... software limitations on file sizes or file‐system‐sizes), especially multi‐index quantities such...
  • Simbody

  • Referenced in 3 articles [sw12963]
  • systems share many properties with mechanically engineered systems, and researchers have successfully employed mechanical engineering ... molecular dynamics are given. All methods and examples were implemented in Simbody TM , an open...
  • Ergo

  • Referenced in 2 articles [sw37384]
  • Ergo: An open-source program for linear-scaling electronic structure calculations. Ergo ... which the computational cost increases linearly with system size for all parts of the calculation ... supports linear-scaling computation of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital...
  • DP-GEN

  • Referenced in 2 articles [sw36442]
  • allow us to perform molecular dynamics simulations for large scale systems with quantum accuracy. However ... Deep Potential GENerator (DP-GEN), an open-source software platform that implements the recently proposed...