Search Results for "throughput" - Page 17

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.

...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

...It can be inserted into any normal pipeline between two processes to give a visual indication of how quickly data is passing through, how long it has taken, how near to completion it is, and an estimate of how long it will be until completion. Additional support is available for multiple instances working in tandem, to given a visual indicator of relative throughput in a complex pipeline The README explains how to compile and install pv for cygwin. Know issues: pv can't lock mintty terminal. However it works when running pv from cmd.exe

A tool for structural variation discovery on genomes using high throughput sequencing technologies.

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...

OpenBandAid is a collection of tools which can help you fine tune different network parameters, to achieve maximum network throughput and performance. It currently includes a Bandwidth-Delay Product (BDP) and Packet Loss Analysis calculators with plans to expand it.

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.

ngsdataqeval is a Python tool to evaluate the quality of high-throughput sequencing data, used by Next Generation Sequencing. Unlike other tools that analyze raw data, this is designed to evaluate the quality of the processed reads after mapping to a reference genome. The evaluation is performed in a genomic region defined by the user, and it provides some statistics computed from the reads that map to that region (ie. a single gene).

Cpipe copies its standard input to its standard output while measuring the time it takes to read an input buffer and write an output buffer. Statistics of average throughput and the total amount of bytes copied are printed to the standard error output.

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.

lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.

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/

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.

QiSampler is an R script used as a command-line bioinformatics tool that evaluates the prioritization done by scoring schemes and experimental parameters of high throughput biological datasets.

CB-Commander is a plugin based tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface.

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.

HiC is high-throughput sequencing technology applied to chromatin conformation techniques. This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.

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

Text Searcher is a high performance text scanning/matching tool that can be directly used in public websites for the purposes of autofill on a text box.

iMethy for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing

SRMA is a post-alignment micro re-aligner for next-generation high throughput sequencing data.

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.

A simple, portable tool for measuring SMTP server delay, delay variation and throughput.

A tool for monitoring and reporting on various aspects of a Linux System, with performance and stability being the emphasis.

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.