Search Results for "throughput" - Page 13
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Showing 350 open source projects for "throughput"
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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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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... -
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throughput
A repository for replicable experiments with human-robot systems
The Throughput repository aims to provide a mechanism for sharing complete experimental papers for human-robot systems. Each experimental paper consists of 5 parts: Description (e.g. link to a journal paper), data sets, code (and/or executables), hardware identifiers, and method (e.g. experiment protocol). That is, each experimental paper is a sufficient description of an experiment that has both a robot and a human component, for the purpose of allowing replication of the experiment. -
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HypoPhen
A hypocotyl phenotyping software
This is a semi-automatic high-throughput hypocotyl phenotyping software. It takes as input time-lapsed images of hypocotyls and measures their elongation and bending -
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PortFusion
Distributed reverse / forward proxy and tunneling solution for TCP.
...A single package that makes the most of each platform by tapping into their unique capabilities, combining this power with an intuitive interface, beautiful design and Haskell's excellent support for unprecedented levels of concurrency and parallelism. It strives for the smallest source code size (< 500 lines) while delivering maximum throughput with near zero overhead. -
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GWT Uploader
GWT library that encapsulates the browser's file upload capabilities.
...Using GWT Uploader allows for enhanced file upload dialogs (multiple uploads, drag and drop, queues, parallel streams, etc.) and interactive interfaces (upload progress indicators, real-time throughput display, etc.) within GWT applications using pure Java code that provides a consistent experience across all browsers. If the browser is capable of handling file uploads using a modern HTML5 approach, the upload is handled using pure DOM elements and Javascript events. In the case that the browser does not support the modern approach (most notably IE 9 and earlier), the GWT Uploader component instead transparently handles the uploads via the Flash-based SWFUpload library. -
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Head-Body String Matching
scalable string pattern matching with head-body partitioning
Scalable dictionary-based string pattern matching based on the head-body partitioning technique. Aims to handle very large dictionaries and achieve attack resilient multi-core scalable throughput performance. Prototype/experimental project. -
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jTrcezer
NS-2 Trace file analyzer, graph creator for wired and wireless sims
...Wired, old wireless and new wireless are already supported but jTrcezer was developed in order to be easy for users to make changes or/and add new trace formats. The final results of the analyzing process are 2D charts for throughput,load,jitter,sent-forwarded-dropped packets and endtoend delay. Also jTrcezer support two different modes for these charts, As-Is and Time Average mode. This application uses jFreechart 1.0.13 library -
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R-SAP
RNA-Seq analysis pipeline
R-SAP is a user-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. R-SAP accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values. -
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colonyzer image analysis software
Image analysis estimating cell density in arrayed microbial cultures
...Specialises in detection of extremely low cell densities. Forms part of the Quantitative Fitness Analysis (QFA) workflow: http://research.ncl.ac.uk/qfa/ Suitable for high-throughput, genome-wide analysis of culture libraries when combined with the following qfa R package: http://qfa.r-forge.r-project.org/ This is the version presented, used and demonstrated in the following manuscripts: Lawless et al. 2010 http://dx.doi.org/10.1186/1471-2105-11-287 Addinall et al. 2011 http://dx.doi.org/10.1371/journal.pgen.1001362 Chang et al. 2011 http://dx.doi.org/10.1534/g3.111.000216 Banks et al. 2012 http://dx.doi.org/10.3791/4018 Development has been moved to github, where Colonyzer has undergone several recent improvements, particuarly making installation easier and analysis faster: https://github.com/CnrLwlss/Colonyzer -
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Java EE Two-Phase Commit Testkit
A Portable Thin Client & Server Pair for XA / 2PC Testing
A portable testing tool to validate the configuration of XA and two-phase commit for Java EE 6 Containers. The tool permits the stress-testing, performance characterization and correct transaction semantics of distributed transactions across Three XA resource managers by Exception Injection. The thin-client can be run from the command-line or inside the IDE. The server side component includes EJB packaging and some simple Web servlet support for retrieving diagnostic and performance data... -
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FluxY
FluxY – a processing tool set for stable isotope label MS data
FluxY is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data used for metabolic flux analysis. To get started simply download and unzip the FluxY.zip file and follow the getting started document in the Instructions folder. -
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Screensaver is a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays. It is a Java/JSF/Hibernate/Spring web application that is actively being developed and used at Harvard Medical School. Note: The Screensaver project has moved to GitHub at https://github.com/hmsiccbl/screensaver.
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Assembler for mate pair/paired-end reads from high throughput sequencing platforms, e.g. Illumina and SOLiD. For the latest version, please visit: http://www.physics.rutgers.edu/~anirvans/SOPRA/
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BioPathXplore is a Bioinformatics Pathway eXploration tool for the visualization and exploration of biological pathways through the integration of KEGG pathways and high throughput data, using Petri nets.
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Pamvotis is a Wireless LAN Simulator for all the current physical layer extentions of the IEEE 802.11 (IEEE 802.11 a/b/g) standard and for the IEEE 802.11e Draft for Quality of Service in WLANs.
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SyMBA is a Data Archive and Integrator that is based on the Functional Genomics Object Model (http://fuge.sf.net) and which archives, stores, and retrieves raw high-throughput data. See http://symba.sf.net and http://www.cisban.ac.uk
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iMethy for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing
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The Informatics project is an open-source environment that provides a lasting, extensible, platform-agnostic and distributed infrastructure enabling high-throughput informatics, efficient data management, robust genomics analysis and provenance.
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This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. "Novel computational methods for increasing PCR primer design effectiveness in directed sequencing". BMC Bioinformatics 2008, 9:191.
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cangsdb
a stand-alone web-based database tool for processing, managing and ana
CANGS DB is a user-friendly and stand-alone database tool for processing, analyzing and managing the high throughput sequencing data from 454 amplicon resequencing projects. CANGSDB is very easy to use; it could be installed and used on any UNIX based computer to handle individual as well as multiple sequencing projects. It provides full-fledged flexibility with various options in raw sequence processing and analysis. CANGS DB provides a very powerful data retrieval interface, which enables researchers to retrieve sample information and primers and barcodes information from any individual data set or from a combination of data set. ... -
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NoiseMaker is a program that creates in silico simulated high throughput screening data sets for use in testing and selecting appropriate statistical techniques for quality determination and hit identification.
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oTWLAN is a tool to simulate ad-hoc networks. The project facilitates throughput/delay performance study through a GUI based user interface. oTWLAN supports relaying, priority handling of user traffic and the data rates 100k, 1M and 10Mbps.
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16s Ribosomal DNA analysis software. It includes a modified version of the Ribosomal Database Project's classification algorithm, as well as chimera detection. It is geared toward high-throughput classification of shorter, next-gen sequence data.
