Search Results for "throughput"

...Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data

Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).

An open-source software aimed at high-throughput generation of molecular interaction fields (MIFs)

This SourceForge page is outdated! HTSeq has been moved to github: https://github.com/simon-anders/htseq General information and documentation on HTSeq; http://www-huber.embl.de/users/anders/HTSeq

iMS2Flux is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data targeting metabolic flux analysis. To get started simply download and unzip the iMS2Flux.zip file and follow the getting started document for your OS. Current version 7.2.1 (last updated 9/30/2014) - Completes support and correction functionality for a new user specified generic data class.

Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. We process around 1500 samples/year resulting in hundreds of millions of sequencing reads, requiring automation and posing new challenges in data storage, monitoring of sample process and computational tools for analyses. ...

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.

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. ...

...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

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.

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.

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

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.

The Vyper Dynamic Server framework is a pure-java library for use in the creation of backend / server platforms. VDS is specifically tailored for financial applications, and suited for many high-throughput, asynchronous and distributed environments.

ciperf is used to calculate the -b and -l values for iperf in order to produce a chosen udp packet throughput (overhead = 51 bytes) in respect to some variables which may change the calculation of the parameters (e.g. computers, links, ...).

ArrayPipeLine is a web-based Laboratory Information Management system, using MySQL, Perl CGI and R. It enables high-throughput analysis of microarray data, providing automation of data handling, and rapid creation and implementation of analysis pipelines

Open Screening Environment is a open source system for management of High Throughput Screening related experiments. The platform consists of new research tools that will enhance significantly management and analysis of HTS data. More information can be f

XAS is a software with graphical user interface to performan analysis of data generated by a high-throughput expression cloning technology using gene expression microarrays.

Project MOVED to Codehaus New location is http://esper.codehaus.org The Esper project aims to provide a general-purpose event processing facility in Java for complex event processing of real-time, high throughput data streams.

Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.

A Java-based mesoscopic, intermodal traffic simulator (MITS), providing a tool to evaluate scenarios (consisting of a road/rail/waterway network topology and load allocation) in terms of throughput, average speeds/travel times, congestion prediction.