Showing 43 open source projects for "simulation biology"

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    Catalyst.jl

    Catalyst.jl

    Chemical reaction network and systems biology interface

    Catalyst.jl is a symbolic modeling package for analysis and high-performance simulation of chemical reaction networks. Catalyst defines symbolic ReactionSystems, which can be created programmatically or easily specified using Catalyst's domain-specific language (DSL). Leveraging ModelingToolkit and Symbolics.jl, Catalyst enables large-scale simulations through auto-vectorization and parallelism. Symbolic ReactionSystems can be used to generate ModelingToolkit-based models, allowing the easy...
    Downloads: 0 This Week
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  • 2
    DEVS-Suite Simulator

    DEVS-Suite Simulator

    Component, CA, and CCA models; superdense time, DB repo, testing, etc.

    Integrated component-based and cellular automata (CA) Parallel DEVS simulator: https://acims.asu.edu/devs-suite/ OFFERS: 1) synchronized execution & animation, 2) run-time linear/superdense I/O & state trajectories, 3) Action Level Real-Time modeling & simulation, 4) model checking, 5) ABM, 6) CA & composable CA playback, 7) KIB interaction modeling, 8) hierarchical model libraries, 9) Black-Box testing & debugging, 10) PostgreSQL repository, 11) FMU (OpenModelica), 12) OSATE (AADL...
    Downloads: 49 This Week
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  • 3
    SimThyr

    SimThyr

    A simulation program for thyroid homeostasis.

    SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.
    Downloads: 15 This Week
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  • 4
    The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters...
    Downloads: 1 This Week
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  • 5
    Tellurium

    Tellurium

    Model, simulate, and analyze biochemical systems using one tool.

    Tellurium (te.) is a Python environment supporting Spyder2 IDE and Jupyter Notebook aimed for large-scale systems and synthetic biology simulation. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via tePlugins. In addition other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support.
    Downloads: 2 This Week
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  • 6
    CyberUnits

    CyberUnits

    Class library for computational cybernetics

    CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal.
    Downloads: 2 This Week
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  • 7
    Pysces

    Pysces

    PySCeS is the Python Simulator of Cellular Systems

    PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis.
    Downloads: 1 This Week
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  • 8
    DBSolveOptimum

    DBSolveOptimum

    The software for systems biology/pharmacology modeling

    DBSolveOptimum is a stand-alone software tool for the construction and analysis of mathematical models of biological systems. It is a succession and extension of DBSolve 5 and DBSolve 7, which were popular tools for systems biology. In addition to the capabilities of these software packages, DBSolveOptimum is implemented with new tools for extended data analysis and multiple simulations, which are important for simulation of virtual clinical trials and application of modern modeling techniques...
    Downloads: 1 This Week
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  • 9
    This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
    Downloads: 3 This Week
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  • 10
    jlibsedml
    A Java library to facilitate SED-ML support for systems biology applications to read, validate, edit, and write SED-ML documents in compliance with MIASE guidelines. Also contains modules to execute simulation tasks and produce outputs. This project also contains the SED-ED editor application for SED-ML.
    Downloads: 0 This Week
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  • 11
    KMC-KaiC

    KMC-KaiC

    Kinetic Monte Carlo simulation of the in-vitro Kai Circadian clock

    ... clock", which is freely available at the open access journal PLOS Computational Biology: https://doi.org/10.1371/journal.pcbi.1005415 *UPDATE* We made a fully reversible version of our model, including the inverse reactions for ATP hydrolysis. This makes it possible to run the model at thermodynamic equilibrium. This version of the model can be downloaded under KMC_KaiC_Rev.zip. If you like to use our model for your own research, please cite our PLoS Computational Biology paper.
    Downloads: 0 This Week
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  • 12
    libRoadRunner

    libRoadRunner

    high performance SBML JIT compiler & simulation engine

    A high performance and portable simulation engine for systems and synthetic biology.
    Downloads: 12 This Week
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  • 13
    Systems Biology Simulation Core Library

    Systems Biology Simulation Core Library

    Accurate and efficient Java library that simulates biological models

    This project has been moved to https://github.com/draeger-lab/SBSCL.
    Downloads: 0 This Week
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  • 14

    MultiCellDS

    MultiCellular Data Standards Project

    MultiCellDS (Multicellular data specification), an outgrowth of the earlier MultiCellXML project, aims to create a data standard for sharing multicellular experimental, simulation, and clinical data. Our ultimate goal is to foster a community that develops user-friendly tools that can read, write, and recombine data into better simulations and analyses for multicellular biology and predictive medicine. As part of this effort, we are developing MultiCellDB: a repository for a curated libary...
    Downloads: 0 This Week
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  • 15
    TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
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    Downloads: 29 This Week
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  • 16

    Moose

    Multiscale Neuroscience and Systems Biology Simulator

    Moose is the core of a modern software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes. We have moved Github.com. This should be your source for the latest version of the code.
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    Downloads: 0 This Week
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  • 17
    SBSI
    SBSI (Systems Biology Software Infrastructure) is a suite of tools for systems biology, such as parallelized numerical algorithms, and a Java, Eclipse RCP based client for visualizing results, running simulations, and integrating SBML based plugins.
    Downloads: 0 This Week
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  • 18
    RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
    Downloads: 0 This Week
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  • 19

    LipidWrapper

    Create lipid-bilayer models of arbitrary geometry.

    ..., is capable of creating curved membrane models with geometries derived from various possible sources, both experimental and theoretical. We are hopeful that this utility will be a useful tool for the computational-biology community.
    Downloads: 0 This Week
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  • 20
    GenoCAD
    GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
    Downloads: 2 This Week
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  • 21

    ASEP

    Monte Carlo Simulations of Asymmetric Exclusion Processes

    Monte Carlo simulations of various classes of asymmetric exclusion processes (ASEP) with open and periodic boundaries. ASEP is a paradigmatic model of non equilibrium statistical mechanics. It can be utilized to model various non-equilibrium phenomena in Biology such as molecular motor transport and protein synthesis. The code's comments will be gradually expanded upon; if there are mistaken or unclear comments they will be corrected. We cannot give an estimation as to when because...
    Downloads: 0 This Week
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  • 22
    Terminology for Description of Dynamics
    The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
    Downloads: 0 This Week
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  • 23

    Top-down Modulated Pitch Model

    An implementation for the Top-Down pitch model by E.Balaguer et al.

    MATLAB implementation for the Top-Down Modulated Pitch model proposed by Balaguer-Ballester E., Clark, N., Coath, M., Krumholz, K. and Denham, S. L. in "Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation", published in "PLOS Computational Biology" in 2009
    Downloads: 0 This Week
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  • 24
    The Systems Biology Ontology project (SBO) goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. !!!! Important Announcement !!!! We have moved the curation and development of Systems Biology Ontology (SBO) to a git-hub repository https://github.com/EBI-BioModels/SBO. Hence, this SourceForge SBO project has also been retired. Please use the Git-Hub issue...
    Downloads: 0 This Week
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  • 25

    RaTrav

    mean first passage times and node occupancies calculations

    RaTrav tool was designed to support computational biology studies where mean first-passage times (MFPTs) between initial and single or multiple final states in network-like systems are used. The tool approves arbitrary networks (graphs) where a dynamics of the Markovian type takes place. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method. References: M...
    Downloads: 0 This Week
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