Search Results for "parallel" - Page 31
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Showing 1671 open source projects for "parallel"
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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CUDA-Quicksort
CUDA-Quicksort: A GPU-based implementation of the quicksort algorithm
..."Two GPU-based implementations of the quicksort were presented in literature: the GPU-quicksort, a compute-unified device architecture (CUDA) iterative implementation, and the CUDA dynamic parallel (CDP) quicksort, a recursive implementation provided by NVIDIA Corporation."[*]. CUDA-quicksort is an iterative GPU-based implementation of the quicksort algorithm. "Experiments performed on six sorting benchmark distributions show that CUDA-quicksort is up to four times faster than GPU-quicksort and up to three times faster than CDP-quicksort."[*]. ... -
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jAgg
jAgg - Java Aggregation Operations
jAgg is a Java 5.0 API that supports “group by” operations on Lists of Java objects: aggregate operations such as count, sum, max, min, avg, and many more. It supports Super Aggregation: Rollups, Cube, and Grouping Sets. It supports analytic operations such as lag/lead and row number and more. It also allows custom aggregate and analytic operations. -
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Shawn's AutoCAD Scripter
AutoCAD batch scripting
...-The window can be resized so full paths can be read (EZscript doesn't do this) -A radio button can switch between using full blown AutoCAD to run scripts and using the console to run scripts. The console is much faster, and it works for most scripts. -Batch scripting with the console can be done in parallel, so multiple drawings are being scripted at the same time. This feature is limited to splitting jobs based on directory, so scripting drawings in 5 directories would run 5 console instances. -
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aCompute
Aims to enable researcher to tap in to mobile computing capability
This is a software agent based computing program that will enable researchers and other users to tap in computing power of machine available by sharing work load on the fly with zero configuration on network & resources A self organizing agent program that will understand network and its resource. where as the only job left to researcher is to split up jobs in several chunks of programs either parallel or sequential jobs and go issue the job (A visual Modeler or Scripting support need to be yet designed) Software agents will automatically manage the rest or resource management, sharing , cloning of tasks etc. new resources can be added and removed from the system on fly; in layman terms the project will create an agent program that enable sharing & execution of program among all the available resources whether it be desktop, laptop, pda . thereby one can accelerate research to the very extent of resource availability with out bothering about anything... ... -
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PANET, a Cytoscape plugin is developed to efficiently analyze the robustness-related dynamics and feed-forward/feedback loop structures of biological networks. This is an advanced plugin of NetDS (http://netds.sourceforge.net/). We employed OpenCL library to make the time-consuming parts of NetDS are processed in parallel. Finally, in comparison to the original NetDS, PANET performed large-scale robustness calculation and feed-forward/feedback loop examination faster by several hundred times for a human signaling network with 1609 nodes and 5063 links.
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EPparallel
Tool for EnergyPlus parallelization
...EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model energy and water use in buildings: http://apps1.eere.energy.gov/buildings/energyplus/. EPparallel splits a single annual EnergyPlus simulation into 12 simulations, runs them in parallel over a cluster of 12 nodes, and collates the results once the simulations are finished. It uses Message Passing Interface API and runs on Linux. It is based on the earlier studies done on the methodology for speeding EnergyPlus simulation by splitting an annual EnergyPlus simulation into multiple smaller simulations: http://www.tandfonline.com/doi/abs/10.1080/19401493.2010.531142 -
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parSRA
Portable Framework for the Parallel Execution of Short Read Aligners
...It uses the following techniques in order to improve scalability: 1) a fast splitting of the input reads using the FUSE kernel module available in most of current Linux distributions; 2) a balanced on-demand distribution of the reads based on the shared locks of UPC++, an extension of C++ for parallel computing that follows the Partitioned Global Address Space (PGAS) paradigm. parSRA is portable as its configuration file allows the users to parallelize the execution of existing SRA tools without the need to modify the source code of parSRA or the aligner. -
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GTkNN
GPU-based Textual kNN (GT-kNN)
The following code is a parallel kNN implementation that uses GPUs for the high dimensional data in text classification. You can use it to classify documents using kNN or to generate meta-features based on the distances between a query document and its k nearest neigbors -
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Ichnaea
Performance Timing Tools
Ichnaea is a set of tools that aid in collecting and tracking parameters and timings for parallel applications. The Performance Modelling Timing Module, PMTM, is a library that wraps system timing calls to abstract these from code developers and aid portability. It also has functionality to store parameters and print those, along with the timing information to a comma separated variable file. The Performance Modelling Analysis Tool, PMAT, is coming soon. -
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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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MPJ Express is an implementation of an MPI-like API—standardized by the Java Grande forum—used to write parallel Java applications, which can execute on a variety of parallel platforms ranging from multicore processors to compute clusters/clouds.
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JPOP is a pure java parallel optimization package based on the Optimization Java Package. It supports analytical gradients and Hessians for non-linear optimization. JPOP is based on uncmin in Fortran but employs java arrays and object oriented code.
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Distributed Video Transcoding
Distributed Video Transcoding
...Also we want to build this solution on top of CentOS and ffmpeg. So I decided to design and develop "Simple Scalable, Parallel, Multi-bitrate Video Transcoding System" by myself. -
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Agilefant
The scalable open source tool for lean and agile project management
Agilefant is a simple but powerful web based tool for lean and agile project management. It is the most versatile open source solution of its kind today, with a rapidly growing user base of more than 10k users around the world in thousands of organizations. Based on more than ten years of solid scientific research within real world organizations, Agilefant's unique model scales from personal todo-lists to large-scale multi-team development and long-term product and portfolio... -
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COMRAD-MPI
Compression of Large Genomic Datasets using Parallel Computing
COMRAD-MPI is a parallel computing algorithm for reducing the computational time for compressing the large genomic data sets based on COMRAD algorithm. It captures the long range repeat redundancies in large genomes there by providing a way to compress the large DNA data set. Three stages- Substitution, Clean up and Huffman encoding have been parallelized using message passing library. -
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Fast Sweeping GPU
Fast Sweeping Method on GPU using Cuda
This is a simple demo of a parallel implementation of the fast sweeping method using Cuda. -
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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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RPlite
RankProduct implementation for differential expression analysis
...It allows the user to perform meta-analysis of different transcriptomic datasets (with different protocols, platforms, technologies, batch, etc.). This implementation computes both up and down regulations in one pass. It is parallelized (dependency: parallel) and memory-optimized: the user can specify the maximum size of the matrices in memory (parameter size) for the unpaired test. -
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
...Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. 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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AVR HV Programmer
High voltage parallel programmer for AVR microcontrollers.
AVR-HV is high voltage parallel programmer for Atmel AVR series microcontrollers. AVR-HV allows programming, reading, verifying and configuring AVR microcontrollers with its high voltage programming interface and it connected with PC using USB interface. -
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BOM Management Software
Manage your Excel Bill of Materials (BOM) in one centralized database
The Bill of Materials Management System (BMMS) is a real time collaborative software application designed specifically for organizing and managing electronic component and bill of materials data. It enables multiple users to work in parallel and supports advanced features including version control. It is fully integrated with the Ciiva Electronic Component Search API, seamlessly bringing together the component library and bill of materials with all other related information sources in one centralized database. -
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Postgres-XC is a write-scalable synchronous multi-master PostgreSQL cluster with the following features. 1) Both read and write scalability. 2) Configured with more than one server. 3) Complete global transaction and visibility management.
