Search Results for "ghost 4 linux"
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Showing 35 open source projects for "ghost 4 linux"
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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luscus
molecular editor and viewer
Luscus is the program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus can also visualize dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to point out a geometrical feature or a physical quantity. The program is developed as a graphical... -
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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RMGDFT
Real Space Multigrid based electronic structure code.
News: active RMG development has moved to github https://github.com/RMGDFT News: V4.1.0 released on 09/29/2020 News: V4.0.0 released on 09/01/2020 with major updates. News: V3.0.0 released on 06/09/2018 with major updates. News: V2.2.2 released on 10/14/2017 with minor bug fixes. News: V2.2 with performance enhancements, bug fixes and new features released on 06/26/2017. Sources are available with binaries to follow soon. News: V2.1 with many improvements released on... -
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ParamIT
a Toolset for Molecular Mechanical Force Field Parameterization
ParamIT is a toolkit aiding the development of molecular mechanical force field parameterization of small, drag like, molecules within CHARMM general force field (CGenFF) protocol. The developed toolkit helps the researchers in following ways: 1) automating the creation of multiple input files for quantum and molecular mechanics programs, 2) automating the output analysis and 3) substitute the use of full MM programs with a faster specialized one. The developed tools include: 1) generator of... -
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FullFun
A software package for fullerenes and their functionalized derivatives
FullFun (stand for Fullerene Functionalization) is an open source software package, licensed under the GNU General Public License (GPL). It provides an efficient and easy way to generate, analyze and predict fullerene-related structures. The package consists of four programs: CSIOpt, XSI, XSIOpt and bkcage. They are implemented using the C and C++ languages and distributed under an open source licence. The code can be compiled and executed on Linux, Mac OS X and Windows (via DOS) operating systems. The bkcage program for general purposes of generation, identification and nomenclature of fullerene structures. ... -
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Iphigenie
A fast and versatile molecular dynamics program
The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations. -
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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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Gecko Hamaker
Calculates Hamaker coefficient,interaction free energy,force,torque.
The Gecko Hamaker open-source software project is a full implementation of the fully retarded Lifshitz formulations for isotropic and anisotropic plane-plane and cylinder-cylinder interactions with intervening interlayer materials, planar systems of up to 99 layers, and graded interfaces for the modeling of grain boundaries or other continuously changing systems, accompanied by a database of material optical properties spectra. The machine-readable optical property database is available... -
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MDcore is an Open-Source library implementing the core functionality of a Molecular Dynamics engine. The engine is inherently multi-threaded and runs efficiently on multi-processor/multi-core shared-memory architectures.
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Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.
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ParaSim
Parallelized calculation of molecular similarities
Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently... -
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ASCEND is a modelling environment and solver for large or small systems of non-linear equations, for use in engineering, thermodynamics, chemistry, physics, mathematics and biology. Solvers for both steady and dynamic (NLA & DAE) problems, are provid
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islec
ISL Solid-Liquid Equilibrium Calculator
ISL Equilibrium Calculator,which process solid-liquid equilibrium calculation by using Harvie extended Pitzer's ion interaction electrolyte solution model and particle swarm optimization Gibbs free energy minimization (GEM). ISLEC is an efficient tool for solid-liquid equilibrium calculation, and can simulate the crystallization path of seawater and salt lake brines. ISLEC is suitable for related researches and process design. -
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Burrow-owl is a software package for visualizing multidimensional nuclear magnetic resonance (NMR) spectra, with an emphasis on spectra used in macromolecular structure determination.
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This project contains a custom version of the GROMACS molecular dynamics software package that helps users to choose parameters for the PME electrostatics model which produce a known error in the PME approximation for minimal computational cost.
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Ion Chromatography Data Analyzer for analyzing wasted oil. Can parse data file from HW2000 workstation.
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A system for symbolic chemical database for analysis and generation. The main use is to generation the information necessary for a oxidative combustion mechanism to be used in programs for combustion mechanisms.
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An editor for small organic molecules, written in C using gtk+. It can read and write SMILES and cml and can save to dia's file format. It is suitable for creating chemical molecule diagrams for lower level chemistry/ochem lab reports.
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QMGA is a Qt-based molecular graphics application for visualizing large ensembles of ellipsoids, spherocylinders or spheres. It is conceived for coarse-grained mesoscopic molecular simulation, but can be used for any kind of convex body systems.
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Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.
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A family of programs for building coarse-grained models (eg. of macromolecules), manipulating them (geometrical transformations and more) and calculating their X-ray scattering patterns (1D and 2D too). Uses PVM for parallelization.
