Search Results for "taxonomy" - Page 2
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Showing 71 open source projects for "taxonomy"
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Go Patterns
Curated list of Go design patterns, recipes and idioms
...Creational, structural, behavioral pattern examples in Go. Explanatory commentary and sample code snippets. Concurrency idioms (e.g. bounded parallelism, fan-in/fan-out). Organized taxonomy for Go idioms. -
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HitKeeper is a database application for use in BioInformatics. It deals with "hits" (predicted features) on biological sequences (protein, DNA), handles incremental updates effectively, supports taxonomy, and provides original query tools.
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MT-MT-Toolbox
Metagenomics version of MTToolbox
MT-Toolbox is a pipeline of tools used for analyzing molecule tagged MiSeq reads. The metagenomics version of MT-Toolbox is a plugin that includes operations for OTU building, OTU taxonomy assignments, and OTU contaminant filtering. These features are not included in the basic version because they only apply to microbial 16S profiling experiments. The standard version of MT-Toolbox can be applied to any amplicon sequencing project where molecule tags are incorporated. For more information on MT-MT-Toolbox and basic features included in MT-Toolbox please refer to the MT-Toolbox webpage (link below). ... -
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IM-TORNADO
Illinois Mayo Taxonomy Operations for RNA Database Operations
IM-TORNADO HAS MOVED TO GITHUB: https://github.com/pjeraldo/imtornado2 Pipeline for analysis of paired-end 16S rDNA amplicon data. -
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...Chronos is a highly sensitive and efficient multiple whole genome aligner in a population. Apollo is a structural variant caller in a population. Poseidon is a highly sensitive and efficient taxonomy classifier. All algorithms are developed since Feb. 6. 2015 by Euncheon Lim in Prof. Weigel's Lab in Max-Planck Institute for Developmental Biology.
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Gleez CMS
A Light, Simple, Flexible Content Management System
...Built on the PHP programming language and the MySQL database, Gleez delivers superb performance on any size application. Gleez uses the MPTT system for classifying content, which is known as taxonomy and is implemented in the core. You can define your own vocabularies (groups of taxonomy terms), and add terms to each vocabulary. Users, Roles, and Permissions. Users on your site can be assigned permissions via roles. -
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Taxy is a tool for browsing and quering data organized as a taxonomy. Through the use of plugins it allows to connect to different data sources, such as the NCBI species taxonomy or the catalogue of biomedical services of the EU project ACGT.
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A General Theory of Reactivity
A General Theory of Reactivity
A General Theory of Reactivity, or GTor, is an experimental specification and conceptual framework for understanding reactive programming primitives. Rather than introducing one application, it attempts to organize values, promises, streams, observables, tasks, generators, and related concepts into a common model. The theory distinguishes singular from plural data and spatial values from temporal ones. It also examines dual relationships such as getters and setters, readers and writers, and... -
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QuickApps CMS
The open source CMS powered by CakePHP v2 Framework
QuickApps CMS is a free open source CMS released under GPL license and inspired by most of the popular cms. Powered by CakePHP v2 MVC framework makes this CMS the perfect development platform. A robust application fully expandable and capable of manage virtually any website, from very simplistic websites, as well as very complex web sites. Easy for both developers and users to work with. -
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mirUtils
miRNA alignment quantitation based on miRBase annotations
mirUtils provides quantitation of aligned microRNA sequences based on miRBase annotations. Starting from a miRBase-aligned BAM/SAM file, mirUtils reports counts and quality metrics for several taxonomy levels, including miRNA precursor hairpins, hairpin groups and families, mature miRNA loci, mature sequences, and genomic clusters, as well as per-hairpin-position alignment start and base coverage details. -
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“Arabic Wikipedia into Named Entity Taxonomy” is a dataset consists of 4000 of Arabic Wikipedia articles that classified into coarse-grained NE taxonomy. This dataset can be used in document classification tasks in relation to NER. To use this corpus, please cite the following publication: F. Alotaibi and M. Lee, "Mapping Arabic Wikipedia into the Named Entities Taxonomy", In Proceedings of COLING 2012: Posters, p43-52, IIT, Mumbai, India, December 8-15. 2012. ...
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Coulson Plot Generator
Graphics generator for pie diagram matrix from spreadsheets
For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG. -
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Arron-IMSA
Integrated Metagenomic Sequence Analysis for Next Gen Datasets
...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). IMSA also outputs the specific sequence reads assigned to a taxon of interest for downstream analysis. -
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Fine-grained Arabic Named Entity Corpora
Fine-grained Arabic Named Entity Corpora
The gold-standard and automatically-developed fine-grained Arabic named entity corpora are resources created by annotating Named Entities into 50 fine-grained classes. The annotation uses two-levels taxonomy in which an entity has been annotated into coarse- and fine-grained classes. A) Manually gold-standard: 1) WikiFANE_Gold: Gold standard Wikipedia-based Fine-grained Arabic Named Entity Corpus, ~500K tokens and 2) NewsFANE_Gold: Gold standard Newswire-based Fine-grained Arabic Named Entity Corpus, ~170K tokens. Those corpora have been manually annotated from the Arabic Wikipedia and Newswire sources respectively. ... -
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TopiaryExplorer has moved to GitHub. Find the new project info page here: https://github.com/qiime/Topiary-Explorer. If you need help or would like to add a bug/feature request, please do so there.
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Vanator-CVR
A metagenomics & virus discovery pipeline
Vanator (Virus Alignment, de Novo Assembly and Taxonomy On Reads) is a Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. The philosophy behind Vanator is described by Jarrett et al (2013) http://www.ncbi.nlm.nih.gov/pubmed/23296970 -
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Constellio Enterprise Search engine
Open source Search Engine and Enterprise Search
Constellio is an enterprise search engine that allows companies to search all their organization's information through a single interface (Web, CRM, ERP, ECM, Mail etc.). Constellio is Based on Apache Solr and Google Search Appliance's connector. Constellio has a powerful web crawler. -
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TaxoAssignement
Taxonomic assignement of sequences
TANGO is one of the most accurate tools for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy -
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u/sbmv2012
Taxonomy assignment of metazoans using a python based pipeline
The aim of this project is to create an automated pipeline for taxonomic assignment of DNA sequences obtained from environmental samples. We develop a series of python scripts to process the raw sequence data obtained from benthic environmental samples and to taxonomical assignment of these sequences and finally to integrate all data in a relational database. -
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DeltaQt
Parser for DELTA files (Qt, C++)
DeltaQt is part of the FreeDelta project and aims to implement a parser for DELTA (DEscription Language for TAxonomy) files using the Qt core framework. DeltaQt is a library intended to be incorporated into other applications that require the ability to parse DELTA files. -
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The ExcelXbrlGen tool is a Data Modeler developed in order to facilitate creation of XBRL taxonomies according to the draft EuroFiling architecture out of the Data Points Model (DPM) in MS Excel format as an Excel add-in.
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Dynamic multi-channel multi-taxonomy W3c standard compliant Content Management System with distributed editing and streaming support developed with XML/XSL and Java technologies (based upon HippoCMS).
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Data mining tool for sequences (e.g. trajectories on a map, visited web pages, etc.) that creates a succinct description of the sequences, given a taxonomy (e.g. regions and sub-regions in the map, categories and sub-categories of pages, etc.).
