Showing 123 open source projects for "c-bus"

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  • 1
    The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!
    Downloads: 0 This Week
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  • 2
    FAUNUS is an object oriented class library for molecular simulation, written in C++. It contains routines and utility programs for, Metropolis Monte Carlo sampling (NVT, NPT, NmuT ensembles), Macromolecules, Proton Titration, Widom Analysis etc.
    Downloads: 0 This Week
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  • 3
    This tool is a free software tool for analyzing chemotactical or migration data.
    Downloads: 0 This Week
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  • 4
    Disco (DIStribution of COnformations) is a software package for the estimation of solution conformations of organic molecules. It is rewritten form of NAMFIS method and can be used with the input files generated by Janocchio.
    Downloads: 1 This Week
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  • 5
    CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.
    Downloads: 0 This Week
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  • 6
    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.
    Downloads: 3 This Week
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  • 7
    Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
    Downloads: 0 This Week
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  • 8
    SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.
    Downloads: 0 This Week
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  • 9
    Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.
    Downloads: 0 This Week
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  • 10

    Cell++

    A novel stochastic simulation environment for biochemical modeling

    UPDATE(2017-07-24) This repository has moved to BitBucket: https://bitbucket.org/parkinsonlab/cell-2017 Cell++ is a novel stochastic simulation environment which is capable of modeling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signaling.
    Downloads: 0 This Week
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  • 11
    sdf file viewer
    Downloads: 1 This Week
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  • 12
    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.
    Downloads: 0 This Week
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  • 13
    RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.
    Downloads: 0 This Week
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  • 14
    Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/
    Downloads: 1 This Week
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  • 15
    StochFit utilizes stochastic fitting methods to model specular x-ray reflectivity or neutron reflectivity data. It provides an easy to use graphical user interface for both model dependent and model independent methods.
    Downloads: 0 This Week
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  • 16
    GParticles is a tool to simulate the growth behaviour of two- and three-dimensional nano particles based on a simple grid model, with adjustable (time-dependent) concentrations of the particle's different components.
    Downloads: 0 This Week
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  • 17
    Contains various algorithms that maps short reads produced from Illumina (Solexa) Genome Analyzer, or Applied Biosystems' SOLiD System, to a reference sequence or a set of reference sequences.
    Downloads: 0 This Week
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  • 18
    DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
    Downloads: 1 This Week
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  • 19
    CDL provides a generic C++ framework to write algorithms for the calculation of molecular descriptors. CDL provides efficient substructure search, fingerprints and pharmacophore algorithms, and many more for the calculation molecular descriptors.
    Downloads: 0 This Week
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  • 20
    4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
    Downloads: 0 This Week
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  • 21
    QRasMol is a reimplementation of RasMol in C++ with updated CMake build systems.
    Downloads: 0 This Week
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  • 22
    TARIS (Tree Analysis and Representation of Isopotential Surfaces) is a software package designed for molecular similarity purposes in the field of Computational Chemistry. Users are allowed to compare molecules through their MEP loading .cube files.
    Downloads: 0 This Week
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  • 23
    A Folding@Home integrated monitoring environment, designed for Linux, *nix systems and Windows, which is intended to be easy-to-use and provide a flexible, customiseable and "user-friendly" environment for reviewing the status of active F@H clients.
    Downloads: 0 This Week
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  • 24
    This program simulates the performance of the supersonic continuous wave chemical laser by solving 2D-system of Navier-Stokes equations in slender-jet approximation that includes multi-component diffusion, non-equilibrium chemical reactions and radiation
    Downloads: 5 This Week
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  • 25
    Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.
    Downloads: 0 This Week
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