Search Results for "throughput" - Page 14
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Showing 432 open source projects for "throughput"
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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. ... -
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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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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. -
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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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...However I will be happy to answer any queries or provide support and comments if you are interested in extending this algorithm. The method is fully described in Deshpande, V., Fung, E. D., Pham, S., & Bafna, V. (2013). Cerulean: A hybrid assembly using high throughput short and long reads. arXiv preprint arXiv:1307.7933. http://arxiv.org/abs/1307.7933
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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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ParaSim
Parallelized calculation of molecular similarities
...ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently queried datasets as persistant objects in memory for short response times. ParaSim calculates chemical similarities based on binary structural fingerprints. ... -
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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. -
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GenOO-HTS
A Modern Perl Framework for High Throughput Sequencing analysis
GenOO-HTS [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead and complexity of managing the data and the biological entities at hand. ... -
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MspJI-seq_pipeline1.0
an pipeline for MspJI-digesting sequencing in DNA methylation study
...Modification-dependent restriction endonuclease MspJI digestion coupled with next generation sequencing could estimate the methylation state of "CNNR" Cytosine location in the genome by mapping high throughput reads to the reference sequences. MspJI-seq_pipeline1.0 is designed to be a general-purpose mapping program to handle these special characteristics of MspJI-seq. Its alignment is based on the open source program SOAP (Short Oligo Alignment Program), and mCNNR sites recognition is performed by regular expression in perl. -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
IMPORTANT: Since publication of the AMBIENT method in BMC Sys Bio, several updates have been made. If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have...
