Search Results for "parallel genetic algorithm"
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Showing 23 open source projects for "parallel genetic algorithm"
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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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Mendel’s Accountant is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection.
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PF_HP
Prediction of proteinfolding in 2D HP model
Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings). Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. Hier implementieren wir einen brute-force Algorithmus zur Lösung kurzer Eingabesequenzen (0-1-Bitstrings) für die Proteinfaltung. ... -
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As of August 2018 Spheral++ has moved to Github -- please see the current repository at https://github.com/jmikeowen/spheral We are leaving a frozen version here on SourceForge for historical reasons. Spheral++ provides a steerable parallel environment for performing coupled hydrodynamical & gravitational numerical simulations. Hydrodynamics and gravity are modelled using particle based methods (SPH and N-Body).
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GenCodeGenerator
C++ class to generate biologically plausible genetic codes
...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. -
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diauxic growth model ensemble
An ensemble of models showing diauxic growth behavior
...Carbon catabolite repression (CCR) is the main mechanism controlling carbohydrate uptake in bacteria, and therefore also controlling whether or not different carbon sources are metabolized in parallel or sequentially. Although described as a paradigm of the regulation of bacterial metabolism, the underlying mechanisms remain controversial. The models in the ensemble can be categorized according to regulatory, stoichiometric, and physiological constraints and differ from each other on only a single aspect. We distinguish four groups of models: (1) flux balance models that only define reaction kinetics for substrate uptake and by-product excretion, (2) kinetic models without and (3) kinetic models with regulation on the metabolic and/or genetic level, and (4) resource allocation models. -
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cupSODA
Deterministic simulator of mass-action based models
cupSODA is a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm, LSODA -
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gametes
Generate complex SNP models and heterogeneous datasets
Genetic Architecture Model Emulator for Testing and Evaluating Software (GAMETES) is an algorithm for the generation of complex single nucleotide polymorphism (SNP) models for simulated association studies. GAMETES is designed to generate epistatic models which we refer to as pure and strict, that constitute the worst-case in terms of detecting disease associations, since such associations may only be observed if all n-loci are included in the disease model. -
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ESTReMo
An evolutionary simulator of transcription regulatory networks
ESTReMo is a genetic algorithm-based simulator to explore the evolution of transcription factors and their binding motifs on realistic genomic backgrounds. -
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fPotencia
Power flow library in C++
fPotencia is the fruit of free time and passion for power systems simulation. After observing the lack of ready-to-implement libraries for power system analisys, and that the existing ones focus on command line workflow, I decided myself to start a project to fill the gap. Since Power system simulations have started needing to be executed in parallel, the old C-like designs are outdated; modular design is now needed to launch many simulations at the same time based on a base... -
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Java Evolutionary Computation Library
As of 2012-12-18, this project may now be found at Google Code.
As of 2012-12-18, this project may now be found at http://http://code.google.com/p/paba JECO is a Evolutionary Computation Library deveoloped in Java. It includes a variety of evolutionary optimization techniques such as genetic algorithm, genetic programming, evolutionary mapping methods, particle swarm optimization, ant colonies, etc. -
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A genetic algorithm in Python for evolving programs that write a given string to an allocated dataspace, using a made-up machine language with only 7 instructions and flow reversal.
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This project is a complete cross-platform (Windows, Linux) framework for Evolutionary Computation in pure python. See the project site at http://pyevolve.sourceforge.net or the blog at http://pyevolve.sourceforge.net/wordpress
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This easy to run and change program for developers, it contains several evolutionary based strategies allowing you try among some function samples
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PGAF provides a framework tuned, user-specific genetic algorithms by handling I/O, UI, and parallelism. It is designed for optimizing functions that take a "very long time" to evaluate.
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A 2D rigid physics simulator and set of genetic algorithm tools. Evolve cute little walking creatures.
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The Automatic Model Optimization Reference Implementation, AMORI, is a framework that integrates the modelling and the optimization processes by providing a plug-in interface for both. A genetic algorithm and Markov simulations are currently implemented.
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The Distributed Genetic Programming Framework is a scalable Java genetic programming environment. It comes with an optional specialization for evolving assembler-syntax algorithms. The evolution can be performed in parallel in any computer network.
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Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.
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aVolve is an evolutionary/genetic algorithm designed to evolve single-cell organisms in a micro ecosystem. It currently uses the JGAP Genetic algorithm, but does include a primitive genetic algorithm written in Python.
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GAZES - Genetic Algorithm Zombie Eradication Simulation Grid-based simulator for zombie scenario. The units will use genetic algorithm to determine their actions on a cycle by cycle basis. This is a school project, so is likely on hiatus for summer.
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Profiled Endwall Design
A genetic algoritm based system for generating profiled endwalls.
This code is based on the Durham Endwall Design System used to produce endwall designs for low speed linear cascades. It consists of a number of Octave scripts which run mesh generators and flow solvers and uses a genetic algorithm to find the optimal solution.
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