Search Results for "java open source" - Page 6
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Showing 530 open source projects for "java open source"
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!!! PTEROS DEVELOPMENT MOVED TO GITHUB !!! New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
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nmr-nessy
NMR relaxation dispersion spectroscopy analysis software
NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models. -
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Maui
Maui is the Maltcms User Interface
Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas. -
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In silico fragmentation evaluation
Comparative analysis of open source in silico fragmentation tools
We compared the performance of four publicly available in silico fragmentation tools that help in structure elucidation of metabolites (MetFrag, CFM-ID, MAGMa+ and MS-FINDER). Using the output of these tools we developed a voting/consensus model which is combining, re-ordering and re-ranking the candidates file and increases the correct hit percentage. We used 520 compounds from the 2016 CASMI challenge with 312 compounds for training and 208 compounds for validation purposes. -
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J-ICE stands for Jmol interface for crystallographic and electronic properties. Is an extension of the powerful, platform independent molecular visualizer Jmol, towards crystallographic and electronic properties. More info will be given soon.
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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
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Solution Percenter
Calculator for making solutions
Soluton Percenter is a program for making solutions percent. Maked by python and PyQt4 module. For chemists, mathematicians and barmans. Program can create advanced recipes and print them. -
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Grid-based Coupled Electron and Electromagnetic field Dynamics (GCEED) is an open-source software package for massively parallel first-principles calculations of electron dynamics in real time and real space. The program codes are written in the Fortran 90/95 language with MPI and OpenMP. Time dependent density functional theory (TD-DFT) calculations can be performed on 100,000 CPU cores of K Computer with high parallel efficiency.
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Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
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Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, biochemistry, or related areas
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XDrawChem
XDrawChem is an application for chemistry drawing and analysis.
XDrawChem is an application for drawing and analyzing chemical structures and reactions. Please visit the website for full details. Download source and binary releases here, and clone the source from GitHub at the external link above. -
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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Molecular Simulation Grid
Provides high performance computing power and state of the art tools
MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE. -
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The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
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An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
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BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.
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Spglib is a C-library written for finding crystal symmetry. Symmetry operation, space group, etc, can be obtained using this symmetry finder. It is easy to include this library to your code. For more information, See, http://spglib.sourceforge.net/
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orthos
Simulation of EPR spectra of nitroxide biradicals
The program Orthos is developed to performed simulation (including nonlinear least-squares fitting) of EPR spectra of nitroxide biradicals. The program capabilities include simulation of rigid-limit and slow-motional spectra, of both isotropic and aligned samples. The spectra of multiple paramagnetic species, both bi- and monoradicals can be modeled. NB: Please note that now (as of Nov 2016) the distribution is being updated so that to improve reliability, OS-universality, and the quality... -
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PyVib2 is a program for analyzing vibrational motion and vibrational spectra. It is an open source "all-in-one" solution for scientists working in the field of vibrational spectroscopy (Raman and IR) and vibrational optical activity (ROA and VCD).
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DISCUS is a set of programs to simulate the atomic structure of disordered materials and calculate experimental properties such as diffuse scattering or the atomic pair distribution function.
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pyxaid
PYthon eXtension for Ab Initio Dynamics
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WavePacket
Dynamics of quantum systems, controlled by external fields
WavePacket is a program package for numerical quantum-mechanics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations, as well as classical or quantum-classical Liouville equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate modern experiments involving ultrashort light... -
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LOOS
Analyze molecular simulation data
LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods. THIS PAGE IS NO LONGER UPDATED. Please see https://github.com/GrossfieldLab/loos for all recent developments -
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qcinteg
Integrals for Quantum Chemistry
This C library provides functions for evaluating basic integrals needed in quantum chemistry. It supports primitive cartesian Gaussian basis functions (GTO) of arbitrary angular momentum and is based on the Hermite Gaussian Expansion. The purpose of this library is to have a handy useful implementation.
