Fast, embeddable genome visualization. Biodalliance is a fast, interactive, genome visualization tool that's easy to embed. Dalliance 0.13 is released with BAM and gene rendering improvements. Discuss Dalliance at BOSC 2014. Dalliance 0.12 is released with support for plain BED, WIG, and VCF files, and substantial performance improvements. Last update 06 September 2016.
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Home :: Biodalliance | biodalliance.org Reviews
https://biodalliance.org
Fast, embeddable genome visualization. Biodalliance is a fast, interactive, genome visualization tool that's easy to embed. Dalliance 0.13 is released with BAM and gene rendering improvements. Discuss Dalliance at BOSC 2014. Dalliance 0.12 is released with support for plain BED, WIG, and VCF files, and substantial performance improvements. Last update 06 September 2016.
biodalliance.org
Older news
http://www.biodalliance.org/oldnews.html
Dalliance 0.11 is released with VCF support, a new track editor, and many other improvements. See the release notes. Dalliance 0.10 is released with mostly-complete support for UCSC-style track hubs. And substantial user-interface improvements. See the release notes. Dalliance 0.9.0 is released with new back-ends and many fixes and improvements. See the release notes. If you didn't make it to BOSC, see our presentation here. Meet Biodalliance developers at BOSC 2013.
Release notes
http://www.biodalliance.org/notes.html
Version 0.13 (3 Feb 2014). BAM rendering improvements (thanks to Yifei Men). Improved guideline when viewing base-pair resolution data (thanks to Daniel Rice). BAM index-index support (thanks to Dan Vanderkam). Amino acid translations of genes (thanks to Yifei Men). Added support for exporting bitmap (PNG) images. BAM and navigation bug fixes. Better placement of feature labels. Version 0.12 (8 May 2014). Support for textual file formats: BED, WIG, and VCF. Version 0.11.0 (2 February 2014). Numberous bug...
Configuring a source
http://www.biodalliance.org/config-source.html
General options when configuring a tier. The name of the track, as shown in the tier-identification tab. A longer description of the content, shown when clicking on the tier-identification tab. Currently only plain text supported - should probably allow a subset of HTML as well (TBD). The source is disabled by default (can be manually re-enabled from the track selector). URI of a DAS Stylesheet. Array of JSON-encoded style rules. Remap the data for this source using a mapping specified in the global.
Getting started
http://www.biodalliance.org/started.html
Dalliance is a track-oriented genome viewer similar to Ensembl. However, it is a little different in operation because it uses recent extensions to web standards ("HTML 5") to offer a higher level of interactivity than most previous genome viewers. You can add your own data using either DAS. Or direct access to a range of standard genomic file formats. Before reading on, you might want to click here. To open a genome viewer in a new window. Hosted at the EBI. Or the arrow keys on your keyboard. If you zo...
Stylesheets for Dalliance
http://www.biodalliance.org/stylesheets.html
Dalliance aims to implement the full DAS Stylesheet. Language, including all glyph types. There are also a number of extensions:. Label matching (since 0.7). Features can be filtered by label if you add a label attribute to the. Regexp matching (since 0.7). The id, method, and label fields of the. Element can take regular expression arguments as well as exact matches, e.g.:. Orientation matching (since 0.11). Features can be filtered by orientation, e.g.:. POINTS glyph (since 0.9). SIZE (since 0.10).
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Introducing pileup.js, a Browser-based Genome Viewer · Hammer Lab
http://www.hammerlab.org/2015/06/19/introducing-pileup-js-a-browser-based-genome-viewer
We're a lab within the Icahn Institute. Introducing pileup.js, a Browser-based Genome Viewer. Over the past few months, we’ve developed pileup.js. A new genome viewer designed for embedding within web applications. Try the demo. While it’s still in the early stages of development, it can already load and visualize data from a variety of sources:. Pileup.js showing the reference genome, variants, genes and a pileup view of alignments). We use node-style modules via. We use Facebook’s FlowType. Features to...
Institute of Cardiovascular Regeneration Webtool Repository
http://www.c-it-loci.uni-frankfurt.de/help
C-It-Loci: A knowledge database for tissue-enriched loci. Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main. Studies Used in Project. Osition , which is a region in which pairs of adjacent homologous protein-coding genes shared between one or more species. Regions defined by the database for ultra-conserved non-coding elements (UCNEs) called UCNEbase ( http:/ ccg.vital-it.ch/UCNEbase/. It is advised to use C-It-Loci's advanced search. However, in many cases, simplified sea...
Michael Paulini
http://blog.wormbase.org/author/mpaulini
WormBase - The Blog. The Official Blog of WormBase. August 3, 2015. We are pleased to announce the third release of WormBase ParaSite, the home for parasitic worm draft genomes and genomic data in WormBase. This release includes two new annotated genomes, taking the total number of nematode and flatworm genomes in WormBase ParaSite to 99, representing 90 species. The new genomes are:. Http:/ parasite.wormbase.org/api/. And an improved BLAST search. And Hymenolepis microstoma ( as example. July 27, 2015.
Introducing CycleDash 0.0.0 · Hammer Lab
http://www.hammerlab.org/2015/01/28/introducing-cycledash-0-0-0
We're a lab within the Icahn Institute. Introducing CycleDash 0.0.0. When iterating on a variant caller. It’s helpful to be able to rapidly identify the most interesting variants called and to visually inspect the evidence used by the caller to make each call. CycleDash. Is our variant call analysis application, used to inspect, query, compare, and export variant calls imported from VCF files. The variants are then available for inspection through the web interface. What’s in 0.0.0. Download functionalit...
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Home :: Biodalliance
Fast, embeddable genome visualization. Biodalliance is a fast, interactive, genome visualization tool that's easy to embed. Dalliance 0.13 is released with BAM and gene rendering improvements. Discuss Dalliance at BOSC 2014. Dalliance 0.12 is released with support for plain BED, WIG, and VCF files, and substantial performance improvements. Last update 06 September 2016.
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