Search Results for "parallel" - Page 21
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Showing 924 open source projects for "parallel"
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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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Schnek
A C++ library for developing parallel simulations on Cartesian grids
NOTICE: The current version of Schnek is hosted on GitHub https://github.com/holgerschmitz/Schnek This repository on Sourceforge is no longer maintained! Schnek is a library for the fast development of parallel simulation codes using multidimensional arrays. It is designed to work both on single processor and massively parallel architectures. The library is intended mainly for use in physics simulations on regular grids but some of its features might be useful for other types of simulation codes. Features include - setup file reader with C style syntax - extendable for formulas in setup files - hierarchical structure of simulation components - mutli-dimensional grids - initialisation of grid from formulas in setup file - boundary cells and ghost cells - MPI support for parallelisation - MPI update of ghost cells to neighbouring processes - easy to use parallel and serial HDF5 output of grids -
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PhyloPart
automated partition of phylogenetic trees
Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. -
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P3BSseq
Parallel processing pipeline for analysis of bisulfite sequencing data
...Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding. We have developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards. P3BSseq outperforms the known BSseq mappers regarding running time, computer hardware requirements. ... -
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Pop Framework
Use Java bean as model of web page, reference beans in hyperlinks
...Views and Models are therefore loosely coupled in Pop. A model can have multiple views for different devices and different locales. Each view and each model can be maintained and optimized independently and in parallel. -
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ThéMA libs
Commons and utils Java classes used in ThéMA projects
This project contains 7 Java libraries developped in ThéMA laboratory : - common - data - parallel - drawshape - graph - network - msca -
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The English-Vietnamese Bilingual Corpus (EVBCorpus) is a collection of English and Vietnamese parallel translations and bitexts.
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AutoGen is designed to generate text files containing repetitive text with varied substitutions. Its goal is to simplify the maintenance of programs that contain large amounts of repetitious text, especially when needed in parallel tables.
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5.Kernelized qtl-haplotype mapping (HPC)
Fortran/R program for kernelized qtl-haplotype mapping by mixed model
Kernelized qtl-haplotype mapping (named KHAMMIX) is a Fortran/R program which performs parallel haplotype based scans of chromosomes, by mixed model analyses, for diploid organisms. Two kernels; the Gaussian and Van Raden kernels, are allowed for the mixed model analyses. The haplotypes are defined by a sliding window of L SNP markers (L is an integer greater or equal to 1). Hence, 2^L haplotypes can be (not necessarily) observed for a sliding window (e.g. 2^6=64 for L=6). -
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GMaVis: A DSL for Geo-Visualization
It is a domain-specific language for large data geo-visualizations
...GMaVis' compiler. It is used to recognize GMaVis' code and transform it in a geospatial data visualizations. Usage: bin/gmavis [-i/--input] <arg> [-o/--output] <arg> [-p/--parallel] <arg> Example: bin/gmavis -i my_gmavis_code.vis -o out.html -
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Hound
Elixir library for writing integration tests and browser automation
...It wraps the WebDriver protocol, allowing developers to write ExUnit tests that control browsers like Firefox, Chrome, or PhantomJS via Selenium or ChromeDriver. Hound supports parallel sessions, asynchronous test execution, JavaScript-heavy interactions, screenshots, and more—all directly in Elixir test suites. -
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VITAMINS
Visual and Insitu Analytics for Molecular Interactive Simulation
A framework to support the high performance analysis and visualisation of molecular dynamics trajectories directly acquired in-situ while the simulation is running, or read from files. Vitamins relies on the FlowVR software and comes with binding with Gromacs. Vitamins (Visual and In Situ Analytics for Molecular Interactive Simulation) is an open source framework for the analysis and visualisation of large molecular dynamics trajectories directly acquired in-situ while the simulation... -
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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. ... -
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SPRITE
Parallel SNP detection pipeline
SPRITE is an open-source software package providing a parallel implementation of the Single Nucleotide Polymorphisms (SNP) detection genomic data analysis workflow. It consists of three tools: PRUNE for read alignment, SAMPA for intermediate file processing, and PARSNIP for parallel SNP calling. -
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MSRE-HTPrimer
A high-throughput primer design tool for MSRE-assay in epigenetics
...MSRE-HTPrimer provides significant improvements over existing solutions with following unique features: 1) visualization of primer pairs in UCSC genome browser, 2) search each resulting primer pair in UCSC In-Silico PCR database, 3) flexible primer selection and filtering based on custom quality matrix and 4) parallel primer design for several target sequences. The pipeline is equipped with multiprocessing capability and uses custom inputs and parameters to design specific primers. -
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4. Bagging Nadaraya Watson Estim. (HPC)
Shell/R program to perform Bagging of the Nadaraya Watson Estimator
Shell/R program which performs bagging of the Nadaraya Watson Kernel estimator by parallel computing -
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...We employed an existing algorithm to analyze the modularity of directed graphs and a Boolean network model for robustness calculation. In particular, to ensure the robustness algorithm’s applicability to large-scale networks, we implemented it as a parallel algorithm by using the OpenCL library. A batch-mode simulation function was also developed to verify whether an observed relationship between modularity and robustness is conserved in a large set of randomly structured networks. The app provides various visualization modes to better elucidate topological relations between modules, and tabular results of centrality and gene ontology enrichment analyses of modules.
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Icarus Scene Engine
3D .NET engine for Windows, Linux, Mac
Icarus Scene Engine is a cross-platform, CLS-compliant 3D framework, integrating open source APIs into a cohesive all-open-source, all .NET solution. For Windows, MacOSX & Linux. Uses OpenTK, OpenGL, OpenAL APIs for graphics and audio. Runs on Mono/.NET. Links to FFMpeg for streaming video, and FreeType as a temporary conversion mod to bring fonts into a native XML format. Binary builds of Icarus will be infrequent, roughly every 18 months or so, the GIT code updates regularly on a... -
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Parallel Quicksort with MPI
Parallel Quicksort with MPI
...It was invented by C.A.R Hoare in 1961and is using the divide-and-conquer strategy for solving problems [3]. Its partitioning aspects make QuickSort amenable to parallelization using task parallelism. MPI is a message passing interface library allowing parallel computing by sending codes to multiple processors, and can therefore be easily used on most multi-core computers available today. The main aim of this study is to implement the QuickSort algorithm using the Open MPI library and therefore compare the sequential with the parallel execution. -
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2. Tune kernel Ridge MM (HPC parallel)
Shell/R program which tunes kernel Ridge by parallel computing
A shell/R program for HPC Linux clusters which allows users to estimate the optimal rate of decay parameter for kernel Ridge regression, within the mixed model framework, for prediction. The optimal rate of decay is estimated using K-folds cross validation parallelized using cluster nodes. -
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orbkit (Moved to Github)
A Modular Python Toolbox for Cross-Platform Post-Processing of Quantum
PLEASE NOTE ORBKIT HAS BEEN MOVED TO https://github.com/orbkit/orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (Output File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided. -
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baramonweb
OpenFOAM UI based on web
baramonweb은 php로 구현된 웹어플리케이션으로 웹 기반의 OpenFOAM 사용자환경입니다. OpenFOAM 입력 파일 생성, 솔버 및 유틸리티 구동을 지원합니다. -
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memP is a parallel heap profiling library based on the mpiP MPI profiling tool. The intent of memP is to identify the heap allocation that causes a task to reach its memory in use high water mark for each task in a parallel job.
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PanCGP
PanCGP: Pangenome and Comparative Genome Analysis Pipeline tool
Pan-genome and Comparative Genome analysis Pipeline tool is a high performance parallel computing analysis tool. The aim of developing this high performance and scalable pipeline is to reduce the time cost of calculating the pan-genomes from the given dataset of protein sequences of bacterial strains. The pipeline is able to compute pan-genome analysis from unpublished data-sets as well. Those results are interpreted in the form of pan-genome, core genome/proteins, dispensable genes/proteins, unique/strain-specific genes/proteins, new gene/protein families and total number of genes per strain of the specie. ... -
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ppienergy
Compute Protein Protein Interaction Energy Profile
...The distance energy plots of contact residues in the interacting regions of several experimentally validated protein-protein complexes were computed to generate energy landscapes. Cumulative energy profiles of protein-protein complexes were generated for observing trends in the context of geometry (parallel, terminal), surface areas (large, medium, small) and interacting partners (homomer, heteromer).
