Search Results for "parallel genetic algorithm"
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Showing 34 open source projects for "parallel genetic algorithm"
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Geophysical Library is a C++-library to handle geophysical data. At the moment the focus is on magnetotelluric and seismic data. It also includes a genetic algorithm for data inversion, signal processing and statistics routines.
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PPface
PPface is vector processor emulator / simulator
PPface is vector processor emulator / simulator (SIMD array processor with 1-bit processing elements). VEPRAN language used to design parallel algorithms and operate data slices. The system allows to visualize algorithm work by viewing vector memory and registers, it supports debugging and animated program execution. To run this app on 64-bit system please install Windows Virtual PC and Windows XP Mode. -
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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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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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This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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SWAPHI: Smith-Waterman on Intel Xeon Phi
The first protein sequence database search on shared-host Xeon Phis
The first parallel algorithm to accelerate the Smith-Waterman protein database search on shared-host multiple Intel Xeon Phi coprocessors. By searching against the UniProtKB/TrEMBL database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on a single Xeon Phi and up to 228.4 GCUPS on four Xeon Phis. -
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
...IEEE Transactions on Parallel and Distributed Systems, vol. 99, PrePrints, 2012 [2] Edans Sandes, Alba Melo. Smith-Waterman Alignment of Huge Sequences with GPU in Linear Space. IPDPS 2011: 1199-1211 [3] Edans Sandes, Alba Melo. CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences. PPOPP 2010: 137-146 The latest source code can be found in Github. -
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Glycosylation Microviewer
An application create, simulate and adjust N-linked glycosylation.
...The model used in the application is based on two significant papers: 1.1997 Pablo Umana, James E.Bailey A Mathematical Model of N-linked Glycoform Biosynthesis. 2.2005 Frederick J.Krambeck, Michael J.Betenbaugh A Mathematical Model of N-linked Glycosylation. The application allow to simulate the network in dynamic form with various ODE solvers(Euler, Runge-Kutta etc). Genetic Algorithm is used to adjust the kinetic parameters of Michaelis-Menten equations in glycosylation reaction network. A dynamic plot is supplied to show the value of mole amout and mole fraction of various glycoform. Thanks to Alexey Balakin and Alessandro Presta. Alexey Balakin supply mathgl(https://sourceforge.net/projects/mathgl) that make the implementation of dynamic plot in this application easily. ... -
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EurekaOptima is a framework for optimization containing the implementation of several algorithms like Genetic Algorithm (GA), Clonal Selection Algorithm (CLONALG), Grammatical Evolution (GE), Differential Evolution (DE), and Evolution Strategy (ES).
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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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FamSeq
Variant calling on the basis of pedigree information
...FamSeq accommodates de novo mutations and can perform variant calling at chromosome X. To accommodate variations in data complexity, FamSeq consists of three distinct implementations of the Mendelian genetic model: the Bayesian network algorithm, Elston-Stewart algorithm and Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA® graphics processing unit. -
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Ezys
Ezys 3D medical image registration program
Ezys is a non-linear 3D medical image registration program. Ezys fully exploits the parallel computing power of inexpensive commercial graphics processing units (GPU), resulting in a very fast and accurate program capable of running on desktop PCs and even some laptops. On these systems, non-linear image registrations take less than a minute to complete. Ezys implements a diffeomorphic inverse consistent image registration algorithm with a demons-style regularization based on a non-parametric free form deformation model. ... -
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PPSeq: Parallel NGS Analysis
Parallel Processing for Next-Generation Sequencing (NGS) Analysis
High-throughput next generation sequencing (NGS) technology has quickly emerged as a powerful tool in many aspects of biomedical research. However, along with its rapid development, the data magnitude and analysis complexity for NGS far exceed the capacity and capability of traditional small-scale computing facilities, such as multithreading algorithms on standalone workstations. To address this issue, here we present a solution using the ever-increasing supply of processing power by massive... -
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The parallelized FDTD Schrodinger Solver implements a parallel algorithm for solving the time-independent 3d Schrodinger equation using the finite difference time domain (FDTD) method. See the Hosted Apps > MediaWiki menu item for more information.
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Molecular Measurer
Parallel, Stochastic Measurement of Molecular Surface Area
A program to measure molecular surface area. The algorithm is GPU-accelerated using CUDA and is described in the research paper linked from the project home page. The input to the program is xyzr files, which can be generated from pdb files. -
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libfgen
Library for optimization using a genetic algorithm or particle swarms
libfgen is a library that implements an efficient and customizable genetic algorithm (GA). It also provides particle swarm optimization (PSO) functionality and an interface for real-valued function minimization or model fitting. It is written in C, but can also be compiled with a C++ compiler. Both Linux and Windows are supported. -
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Clusterfit
Show stellar evolution and open clusters in a color-magnitude diagram
...In addition, it can show the CMD of a large number of existing open clusters, based on scientific survey data, and overlay isochrones (the curve in a CMD from stars born at the same time) to determine the age, distance and interstellar reddening of the cluster. Determining these parameters can be done automatically with a global search algorithm (more specifically a genetic algorithm). This program requires the installation of the libfgen package, also available on SourceForge. -
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DecGPU: CUDA-based Error Correction
The first distributed and parallel short-read error corrector on GPUs
DecGPU (Distributed Error correction on GPUs) is a parallel and distributed error correction algorithm for large-scale short read assembly. It is implemented using CUDA C++ and MPI, running on a GPU cluster. -
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BIL++ is a set of standalone C++ packages for data processing in Bioinformatics (Graph mining, Bayesian networks, Genetic algorithm, Discretization, Gene expression data analysis, Hypothesis testing).
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Parallel Reinforcement Evolutionary Artificial Neural Networks (PREANN) is a framework of flexible multi-layer ANN's with reinforcement learning based on genetic algorithms and a parallel implementation (using XMM registers and NVIDIA's CUDA).
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Evolutionary Structural Optimization Package (ESOP) consists of software for viewing, analyzing, and optimizing structures containing beam, truss, and membrane plate elements utilizing OpenGL and the Genetic Algorithm (GA). Created for use in M.S. theses
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