Open Source Simulation Software - Page 22
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FUMOLA - Functional Mock-up Laboratory
An FMI-based co-simulation framework.
FUMOLA is a co-simulation framework specifically designed to support the features offered by the FMI specification. It provides a flexible platform that allows to configure and execute co-simulation setups in an easy way. FUMOLA is developed on top of the Ptolemy II framework (https://ptolemy.eecs.berkeley.edu) and the FMI++ library (http://fmipp.sourceforge.net). The online documentation of FUMOLA is available here: https://sourceforge.net/p/fumola/wiki/Home/ -
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Famms is a Python module for applying the method of manufactured solutions (MMS) to PDE simulators written in C/C++, Fortran, and Python.
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FeMOS is a finite element method simulation of Double Gate MOSFET. The calculation uses Non-equilibrium Green's function method in fast uncoupled mode space approach.
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Note: New versions are not being posted to source forge. Please check the project homepage at: http://www.cove.org/flade A free library for simulating 2D physics in Flash using Verlet integration. It currently features particles, stick & angular constra
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Flint
A simulator for biological and physiological models
Flint is a simulator for biological and physiological models written in CellML, PHML and/or SBML. -
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A language and a compiler for the solution of differential equations (ODE). Both lumped and distributed variables (PDE) will be possible. The ability to solve DAEs is a long term goal. The compiler generates a Python program that does the computation.
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Frevo
Frevo is probably the simplest tool for evolutionary design
FREVO is an open-source framework developed in Java to help engineers and scientists in evolutionary design or optimization tasks. The major feature of FREVO is the componentwise decomposition and separation of the key building blocks for each optimization tasks. We identify these as the problem definition, solution representation and the optimization method. This structure enables the components to be designed separately allowing the user to easily swap and evaluate different configurations and methods or to connect an external simulation tool. The latest version in development is hosted at https://github.com/smartgrids-aau/Frevo -
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GPMfit
Gaussian Process Model Fitting
Gaussian Process model for fitting deterministic simulator output. Establish efficient and reliable likelihood optimization through hybridized DIRECT-BFGS and multi-start BFGS algorithms. Programming Language: Matlab. -
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GRAVITY ALPHA 1.05
Visualization of gravitational force effects between (two) objects
GRAVITY ALPHA is developed for visualization of gravitational force effects between (two) objects. In order to predict/calculate object properties in future time (of course, within the limits of calculation) one need initial position and speed at some initial moment of time . For calculating positions and velocities, numerical method for solving differential equations is used. There is no limitation in parameters - object will behave just like they behave in the real world. The only thing which is not ‘real’ is an option to increase the object sphere beyond physical meaning (unrealistic small density). So, be careful with initial data - you will see same behaviour as in real world with real objects - of course, within variables, calculation and display limitations. You can input the properties of object(s) via program interface or directly editing simple *.TXT file. -
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Gekko Timeseries Software
Timeseries handling, and solving of large-scale economic models
Gekko Timeseries Software is a free time-series oriented software package for timeseries handling, and solving and analyzing large-scale economic models. Since 2009, Gekko is being used by Danish ministeries, banks, interest groups and universities, for the simulation of economic and energy-related models. The software runs under Windows (.NET), and is open source (GNU GPL) -
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GenCodeGenerator
C++ class to generate biologically plausible genetic codes
The "GeneticCode" C++ class is designed to generate versions of the genetic code subject to the requirements of the three major models of the genetic code origin and evolution (about these models see, e.g., Koonin & Novozhilov, 2009, IUBMB Life). This class was written specifically to perform statistical test for the paper Makukov & shCherbak (2017), but it might be used for a wider class of studies related to the genetic code. By default, the class "GeneticCode" generates alternative genetic codes, with the reqirement of block structure, and, optionally, with the assumption of stereochemical or biosynthetic models (to impose the assumption of the adaptive model, simply filter the codes using the error_cost() function). See Appendix in Makukov & shCherbak (2017) for the description of the algorithm. The code requires Qt 5. To compile the provided example, run 'qmake' to produce the Makefile, and then run 'make' to compile the executable file. License: Public Domain. -
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Genetic Evolution Project
Evolution with Genetic algorithms
This project is meant to simulate Evolution using genetic algorithms and unity engine. -
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Genetic algorithm for EOM
A python GA code for EOM in SAXS/WAXS
Because GAjoe of ATSAS cannot deal with WAXS range, and no parameters can be modified. I made a code by myself to use GA for finding best EOM for SAXS/WAXS. The project need ATSAS crysol and a folder with multiple pdb files to use. -
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A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8
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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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Hyperfit
Software for calibration of hyperelastic constitutive models
This software allows to fit various hyperelastic constitutive models. Optimal set of parameters of a selected constitutive model can be identified. Many advanced setting, methods and corrections are available to get optimal results according to the user's preference. -
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IPSA - Inventor Physics Simulation API
Easy to use physics simulation combining ODE with OpenInventor.
Create phyiscal simulations easily through IPSA which combines the OpenInventor 3D API with the Open Dynamics Engine (ODE). Scenes are read from .iv files and simulated in the supplied viewer applications. Find it at: http://ipsa.sourceforge.net -
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Ideal Gas Simulator
An ideal gas simulator 2D developed in Java
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Insensitive
NMR spin dynamics simulation
Insensitive (Incredible Nuclear Spin EvolutioN SImulation Tool Intended for Visual Education) is an application to simulate the NMR experiment based on the quantum mechanical density matrix formalism. It is available for Mac OS X 10.6 and above and iOS 5.1.1 and above. Please refer to the paper published in Concepts In Magnetic Resonance, 2011, 38A (2), 17-24. -
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This project hosts the 'Simulation Tool', an extensible, interactive environment for carrying out simulation experiments of SBML models. This project can use RoadRunner or SBW enabled simulators to carry out simulations.
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Ising model
Ising model framework for Ms Windows
ising models are a statistical thermodynamics toy system that physicists love to play about with. I've done all the fiddly graphics work for an Ising model so you can see it on the screen. You want to play with the file ising.c to make the model do various things other than just respond to temperature. If you can see the results, it's much easier to spot problems with code / interesting phenomena. -
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JABM is a Java framework for building agent-based simulation models using a discrete-event simulation framework.
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please don't hesitate to review the software below or email Paul Craig [pac8612@rit.edu] with larger descriptions/bugs/feature ideas. Our next scheduled release will contain (in addition to 2DE and MassSpec) a 1D Electrophoresis simulation as well as a tab containing ChemAxon's MarvinSketch [http://www.chemaxon.com/products/marvin/] along with some improved functionality. It should be out shortly as we complete the creation and modification of a permanent domain for the project.
