
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, opensource, 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 opensource 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 firstprinciples electronicstructure 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 opensource program package ... treated, which allows to simulate molecular quantum dynamics beyond the BornOppenheimer 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 highperformance opensource Quantum Monte Carlo (QMC) simulation code ... electronic structure calculations of molecular, quasi2D and solidstate systems. Variational Monte Carlo...

turboTDDFT
 Referenced in 2 articles
[sw06833]
 molecular systems made of up to several hundred atoms. turboTDDFT is an opensource software...

CUIK
 Referenced in 3 articles
[sw21885]
 opensource toolbox for motion analysis of closedchain 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 opensource 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 openaccess 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 opensource spinadapted 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 opensource spinadapted 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 opensource program for linearscaling electronic structure calculations. Ergo ... which the computational cost increases linearly with system size for all parts of the calculation ... supports linearscaling computation of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital...

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