Search Results for "throughput" - Page 15
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Showing 502 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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Bioimage Analysis (the Robatzek Group)
High Content and High-throughput Image Processing in Plants
High Content and High-throughput Image Processing in Plants. -
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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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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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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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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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elise-ebay
Simulate ebay ecosystem - N clients bid on M items
...Makes heavy use of generics for entities, keepers, factories, & DAOs. Performance Peaks - impl1: 1.6 M bids/sec - impl2: 2.5 M bids/sec - impl3: 2.,6 M+ bids/sec Throughput increased and jitter reduced by setting init capacity of maps to 1k. see README MEMORY MODEL -
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Domainhound
High-throughput parsing of hmmer3 output on sequence files
...Provides a phylogenetic table showing the number of occurrences of domain hits in input species. Identifies the highest scoring domain in case of overlaps. Useful for classifying protein sequences based on domain content with high throughput. -
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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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CygwinMirrorTest
Cygwin Mirror Speed Test
.... :) ] This utility tests the speed of local Cygwin mirrors, to determine which will be fastest for you to use. It first checks for latency. Anything too slow it will skip. It then tests for throughput by downloading a file (setup.ini from the Cygwin mirror being tested) *** INSTALLATION *** Installation is simple. Download the perl script, and run it. This script will run on almost any Unix machine, or on Windows machines with Cygwin installed. The only requirements are: Executables: perl, wget, sed standard shell commands: cat, grep, cut, sort, uniq) Perl modules: Time::HiRes, Net::Ping If you are using Cygwin, you may need to install perl, wget, and sed. ... -
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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. ... -
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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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estMOI
estimating Multiplicity Of Infection using short read sequence data
estMOI is intended to estimate Multiplicity of Infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data as follows: INPUT files: estMOI requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. 1. Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. 2. ... -
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Mi-perf
Miperf is an automated enhancement of iperf tool
iperf is a tool that can create TCP&UDP data streams and measure the throughput of a network that is carrying them. basically to do this iperf testing, we need 2 machines to act as server and client. we run a command -s in server side and then launch a client connection to a server by typing a command -c in client side. before that we need to enter the webgui of the wifi AP to do some configurations such as, change the frequency mode and channel. so we need to repeat the same process/steps for next test cases.imagine if we have hundred test cases, how much time we have to spend for this testing. ... -
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ConoSorter
A Large-scale Cone Snail Transcriptome/Proteome Analysis Program
ConoSorter is a high-throughput standalone program that implements regular expressions and profile Hidden Markov Models (pHMMs) for large-scale identification and classification of precursor conopeptides into gene superfamilies and classes based on the ER signal, pro-, and mature conopeptide regions generated from raw next-generation transcriptomic or proteomic data. -
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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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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.
