Search Results for "throughput" - Page 12
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Showing 350 open source projects for "throughput"
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TCP Segment Retransmission Viewer
View, graph, record TCP segment retransmission rates
View, graph, and record TCP segment retransmissions to quickly see network congestion / problems TCP segment retransmissions are a sign of network congestion and reduced throughput. A segment is retransmitted from a client if there is no corresponding acknowledgment from the receiving host. Further analysis can be done in Wireshark at the packet level if a problem is suspected. Trends can be seen over time graphically with the graph function, which allows panning, zooming, etc. If you find this tool useful please let me know! -
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We developed a novel mining pipeline, inGAP, which is guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms.
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VariantMaster
Extract causative variants for monogenic and sporadic genetic diseases
There is a fast growing interest in clinical genetics to the utilization of High Throughput Sequencing data for accurate diagnosis of monogenic diseases. To improve the identification of the variants from HTS, we developed VariantMaster, an original program that accurately and efficiently extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. ... -
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JPerf
Java Performance and Scalability Testing
JPerf is a simple framework for writing and running automated performance and scalability tests. It's like JUnit but for performance. Simple write a class that implements PerfTest then create a PerfTestRunner instance to run the test. *** JPerf has moved! Please go to https://github.com/andygrove/jperf for the current version *** -
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TriageTools
Tools for partitioning and prioritizing fastq data
TriageTools is a collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. The project wiki contains usage information. -
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This is a simple CPU burn program for the major UNIX systems: AIX, BSD, HP-UX, Linux, Solaris etc (full list in the source file #defines) and Windows. It will discover the number of available CPU cores and fork enough threads to create a load on all cores by default. The number of threads and memory block size can be changed from the command line.
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Parallel GENSENG is a parallel implementation of the GENSENG software for detecting copy number variations from high-throughput sequencing data. This software runs exactly as the original code does, except that it utilizes multiple threads where possible. OpenMP was used for multi-threading so changes to the original code were minimal. For a demo, please download the sample data linked to below and follow the README from the tarball. Example read count data: http://www.cs.unc.edu/~wangwb09/GENSENG/reviseddata4hmm_300bpSlides_chr1.txt Suggested transition matrix file http://www.cs.unc.edu/~wangwb09/GENSENG/transition_init.dat The original code can be found at these locations: v0.1: http://www.cs.unc.edu/~wangwb09/GENSENG/GENSENG_download_page.html v0.3: https://sourceforge.net/projects/genseng/
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Arron-IMSA
Integrated Metagenomic Sequence Analysis for Next Gen Datasets
We present Integrated Metagenomic Sequence Analysis (IMSA), a flexible, fast, and robust computational analysis pipeline that is available for public use. IMSA takes input sequence from high throughput datasets and uses a user-defined host database to filter out host sequence. IMSA then aligns the filtered reads to a user-defined universal database to characterize exogenous reads within the host background. IMSA assigns a score to each node of the taxonomy based on read frequency, and can output this as a taxonomy report suitable for cluster analysis or as a taxonomy map (TaxMap). ... -
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AS-peak
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus identification of RNA-protein binding sites from high throughput sequencing data presents unique challenges. While peak identification in CHIP-Seq data has been extensively explored, there are few bioinformatics tools tailored to peak calling on the analogous datasets for RNA-binding proteins. Here we describe ASPeak, an implementation of an algorithm that we previously applied to detect peaks in Exon Junction Complex (EJC) RNA immunoprecipitation in tandem (RIPiT) experiments. ... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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UNVedu
streaming of MKV (Matroska) video for research and development
...We propose Java-based media streaming over IP utilizing the Matroska (MKV) container, which is rapidly gaining popularity within online user communities. Fast and accurate access to individual MKV elements is ensured by a hinting mechanism tailored to the container. The achieved throughput and continuous playback capability has been examined under RTSP/TCP with UDP transmission over Wi-Fi, which is setup via a single port or via multiple ports. New avenues for media traffic differentiation with the proposed framework are highlighted. The project is suitable for research and advanced graduate courses on video streaming systems over the Internet Protocol. ... -
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HErCoOl
High-throughput Error Correction by Oligomers
Error correction software for next-generation sequencing data based on k-mer spectrum. -
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eRNA
A RNA data analysis tool
eRNA: A RNA data analysis tool for high-throughput RNA sequencing experiments -
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BriPy
A BRIC-seq data analysis package written in Python.
...It employs metabolic labeling by BrU of newly synthesized RNAs to chase chronological decreases of BrU-labeled RNA (Pulse-chase labeling), followed by immunoprecipitation with antibody for BrU, construction of cRNA library for High-throughput sequencing and computational data analysis. -What is BriPy? BriPy package is a BRIC-seq data analysis tool written in Python. It can calculate RNA half-life for each transcript and draw graphs describing the kinetics of RNA decay. In the future, it will provide several useful modules(e.g. calculating RPKM of each transcript from BAM file or ELAND output file). ... -
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LimiNet
Network emulation tool.
LimiNet is a network emulation tool based on Debian Linux. The main purpose of the project is to provide an emulation tool which offers: - Emulation of throughput, delay, jitter and packet loss - Fixed settings of the network parameters. Once defined parameters of network should be working all the time - Dynamic settings allow to change the parameters of the network while the communication is running, i.e. TCP connection works - Scenarios should allow to automatically change the network properties in the defined time moments. ... -
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The goal of this project is to combine different sources of information as well as methods to help in the process of gap closing / genome finishing in high throughput sequencing.
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LoadMonger
Java based load testing tool for HTTP applications.
Load - the demand on the operating resources of a system (as a telephone exchange or a web service) Monger - a dealer in or trader of a commodity LoadMonger - a command line Java based tool that provides a balance between ease of use and flexibility to define reasonably complex load patterns and can generate loads comparable with Apache bench, but with the ability to define more sophisticated load patterns and sophisticated data compilation via log files that can be merged on test end... -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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JdonFramework
a Domain Driven Design + CQRS + EventSource java framework
...INTRODUCTION --------------------------------------------- JdonFramework is a java framework to build your Domain Driven Design + CQRS + EventSource applications with asynchronous concurrency and higher throughput. 2. GETTING STARTED ------------------ In the "example" directory there are several examples for web application. You can run runTest.bat in this directory to see how to play JdonFramework in Application. In the "doc" directory there are all documents about how to use. Source Project : https://github.com/banq/jdonframework -
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TFAST
Software for analysis of afSELEX-seq data
Transcription Factor Analysis using SELEX with High-Throughput Sequencing (TFAST) is software developed by the Mobley lab at the University of Michigan designed to assist with transcription factor binding site discovery using data generated from aptamer-free SELEX-seq (afSELEX-seq). -
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A simple lightweight system for genomic annotation written in Java. SHAP uses the Spring application framework, Hibernate for persistence and full-text searching of results and DRMAA for Grid computing.
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rmisockfactory
Collection of RMI Socket Factories
This project contains a collection of RMI socket factories -- for instance gzip-encoded data sent over the wire, NIO-based communication etc. -
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...See here: https://github.com/ziplet/ziplet A J2EE servlet filter which compresses data written to the response. It supports several algorithms (gzip, deflate, etc.) and emphasizes minimal memory usage and high throughput. Also provides detailed performance stats. Feel free to fork pjl-comp-filter on Github: https://github.com/ziplet/ziplet
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Kayacc
A Compiler Development Toolkit
Kayacc is an alternate name for the TOMBO project. I am in the process of updating the Tombo project page with version 2.1.0. Please download Tombo2.1.0.tar.gz from the Files tab. Tombo is a compiler generation toolkit for constructing compilers and interpreters. It includes a BNF compiler that generates parsers for context free grammars, and a class library to support compiler development. The class library supports symbol tables, Unicode text manipulation, reserved word mappings,... -
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DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
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NoCTweak
a Parameterizable Simulator for Early Exploration of Networks On-Chip
A networks-on-chip (NoC) simulator allows designers to early estimate performance (latency and throughput), energy efficiency (average/peak power, average energy per packet) and area of several networks on-chip configurations at different CMOS nodes. This tool is a cycle-accurate simulator and is open-source using SystemC, a C++ plugin, which is used to quickly model complex systems at a higher level but less details than RTL. NoCTweak was developed by Dr.
