Search Results for "applied"
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Showing 23 open source projects for "applied"
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FullSSR
SSR detection and primer designing software
Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step. -
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FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013.
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Accent Tool Suite
Accent interfaces and controls systems through goals and policies
Accent (Advanced Component Control Enhancing Network Technologies) is a comprehensive tool suite that interfaces a variety of communications systems and allows these systems to be controlled through goals (high-level user aims) and policies (lower-level system rules). Accent has been applied to the domains of: o Call Control: for telecommunications, particularly call control in Internet telephony o Home Care: for home automation and telecare, particularly for domestic appliances... -
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miARma-Seq
a A suite designed to study mRNAs, miRNAs and circRNAs
miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow. As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together well-established... -
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rePhase
A loudspeaker phase linearization, EQ and filtering tool
rePhase project has moved to https://rephase.org, please go there to download rephase and to get info, support and updates. rePhase is a FIR generation tool for building fully linear-phase active crossovers with arbitrary slopes. It also let you manually compensate for the phase shifts of your loudspeakers and existing crossovers, be it active or passive. Once generated, the FIR can be applied using any hardware (openDRC, miniSHARC, Najda, ...) or software (foobar, convolver, JRiver... -
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rcg-tool
Automatic configuration generation tool for routers
... protocol to be used and which baseline configuration should be applied. This extension for GNS3 allows beginner practitioners to produce valid configuration files that can be further analysed, replicated and even applied to real network equipments. For more experienced students or practitioners this extension allows to speedup the overall network configuration task in large and complex network topologies, since they may overtake some initial and repetitive IP configuration steps. -
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mCarts
A hidden Markov model to predict clustered RNA motif sites
... of in vivo RBP binding sites obtained from high throughput sequencing of RNAs isolated by cross-linking and immunoprecipitation (HITS-CLIP). We applied this algorithm to study two representative RBPs, Nova and Mbnl. Despite the very low information content in individual motif elements, our algorithm made very specific predictions for successful experimental validation. -
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basecv
BCV is DNA base caller with vocabulary
The Base Calling with Vocabulary (BCV) software package is intended for analysis of direct (population) sequencing chromatograms using known vocabulary sequences similar to the target DNA. The current version of BCV can only process chromatogram files obtained on Applied Biosystems capillary sequencing machines (ABIF file format). -
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BrutefirDRC
Apply digital room correction and/or loudness to LogitechMediaServer
A plugin to use the BruteFIR software convolution engine with slimdevices SqueezeCenter clients for Digitial Room Correction. Provides transparent/automatic switching of filters for different sample rates. Filter creation can be done with DRC, Audiolense, acourate or other DRC-software. An optional loudness correction using the digital volume control can be applied. The loudness features uses sox loundess that is based on the ISO 226 curves. -
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
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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.
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Continues Integration system which has been developed for distributed networking execution environment. It started its life serving builds and tests in a commercial environment early days well before continues integration became a standard well-applied best practice in the industry. The code was open-sourced and was used by multiple local development teams known to the author. Later on alternative CI systems, like Jenkins and BuildBot, gained popularity, established big communities and evolved...
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The SNP ratio test can assess significance of enrichment of significant associations in genome-wide association studies. Tests can be applied to pathways such as KEGG/GO, or user-defined pathways to test specific hypotheses. See link below for more.
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ddns.pl - A cgi-bin Perl script to manipulate the content of any number of (BIND) zones on any number of Dynamic DNS (DDNS) server instances.
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A repository linking to eight Bioinformatics Resource Centers (BRCs) sponsored by the NIAID. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of bioterrorism
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TraceTuner
DNA sequencing quality values, base calling and trace processing
Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions... -
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This project contains a perl script which can be used to get the Enterprise Version of the Linux (RHAS2.1/RHEL3/RHEL4/SLES8/SLES9/SLES10) and the applied update/service pack(U1/U2/U8/SP1/SP2) on the system.
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Everybody knows the Perlfect Search distributed under the GNU GPL. This is just a try to put one in a real world. Here in RUssia we need two stuffs: the fuzzy search (applied) AND --- surprise! Cyrillic. That's a major feature and a goal of such project.
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NewsOutlook lets you set rules to receive, in your mailbox, only those Usenet articles and Syndication feeds (rss & atom) you are interested in. Rules can be applied on author and text (regex can be used as well) and are configured with a Web-based front
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OAAQ or Open Ask A Question is a web based virtual reference application for libraries. It is a basic trouble ticket system applied to library reference questions that supports collaborative management of answers in a multi- sector/institution/department
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A simple utility for taking two, presumably related, SQL database creation scripts, and generating SQL 'patches' that can be applied to a live SQL database in order to upgrade it.
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Abbruch is a commandline utility to ease the generation of banned/allowed/special actions to be applied to a list of users sending you email, by generating a .procmailrc file. requires: perl5, procmail
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This project is a qmail-spp plugin that provides simple and powerful white, black, and regexp list management and logging for mail servers using qmail. At any SMTP phase, simple or regexp lists can be applied, logged, and even auto-generated.
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