-
Notifications
You must be signed in to change notification settings - Fork 10
Release Notes and Roadmap
Web design updates. CellBase host and OpenCGA host are now configurables. On max zoom, codon information is shown when the mouse is on the exon coding region.
Indexed DB is now used to store tracks information.
The most important feature is that Genome Maps can now visualize BAM and VCF file formats.
Just a couple of minor bugfixes
Sidebar menu with active and available tracks, new and improved Search panel and Region History Track filtering is now possible, i.e. users can open two tracks with genes for different biotypes A region can be specified, so far only a position was possible Track order can be changed from Active panel Users can now select a region in Chromosome and Region panels URL accepts more query parameteres: zoom, gene, snp; i.e. http://genomemaps.org/?gene=brca2 or http://genomemaps.org/?gene=brca2&zoom=50 New theme Bug fixes and some performance improvements
Genome Maps is licensed under GPLv2 license. New mirror is available under Amazon AWS in USA region to provide a better user experience, it is available at http://usa.genomemaps.org/ Minor corrections and improvements.
Mouse now tracks the genomic position. Genome Maps fits to the window size automatically. Quick search field auto-completion with CellBase information.
Key movement fix. Now keys are only enabled when the mouse is over the detailed information panel. Chromosome panel rewrite. Karyotype panel rewrite. Binary search tree added to calculate the features draw position.
Data Sources and Data Adapters schema implemented. GFF3 File format is now supported. QTip 2 library added for fast information.
Core code rewrite. JavaScript cache implemented, server calls have been reduced. SVG help class now receives SVG standard parameters.
This is a minor released with just 2 bugs fixed:
- A mistake in server configuration prevents the server from sending GZipped JSON and TXT data
- Some cytobands are wrongly displayed in purple
- Some minor bugfixes and performance improvements
Main changes since v1.0.0 are detailed briefly:
- 4 new species added: Canis familiaris, Sus scrofa, Anopheles gambiae and Plasmodium falciparum
- RegionOverviewPanel: new panel with a higher zoom to see the context area
- New panels are now integrated into Genome Maps application, no more new windows
- Zoom levels have been increased from 12 to 20
- Keyboard navigation is now possible
- MenuBar has been redesigned to better accommodate new options and features
- Ensembl ID is now shown when Gene Name is now available
- InfoWidgets windows with the info of Gene, Transcripts, SNPs, … have been enriched with more information
- A 3D view of proteins is shown when available in PDB database
- VcfInfoWidget window shows now the Consequence type calculated from VARIANT application (http://docs.bioinfo.cipf.es/projects/variant)
- Histogram performance has been dramatically improved
- Google Chrome Extension has been developed
- Some minor bugfixes and performance improvements
First stable release, more noticeable features:
- Real time navigation (similar to Google Maps): biological database, Java RESTful WEB Services and data model have been extremely optimized
- Genome browser implemented using modern HTML5 technology with Javascript
- Tracks: many biological databases have been integrated into a homemade project called CellBase:“http://docs.bioinfo.cipf.es/projects/cellbase” with information about: genes, transcripts, proteins, SNPs, mutations, phenotypic SNPs, miRNA targets, conserved regions, TFBS, … All this information is export through RESTful WEB services to Genome Maps and other applications
- 7 species available: Homo sapiens, Mus musculus o Rattus norvegicus among others
- Navigation bar allows user to browse the genomes selecting a chromosome or a region
- 12 zoom levels available
- Search is available for genes, SNPs, miRNA, …
- Sequence allows to explore the Genome sequence
- DAS server data can be browsed as a DAS client has been implmented, some DAS servers are offered and others can be added
- Data import: users can load their GFF, BED and VCF files, tests show that Google Chrome display up to 300,000 variants easily
- Plugin framework developed: many functionalities will be implemented through plugins
- Developer oriented Javascript API: to make easily embeddable for bioinformatics developers all functionalities are available through Javascript API
var gm = new GenomeMaps(); gm.draw();
- Users can store their data in our server, 1GB of space is provided freely
- Server architecture implemnted in HA (high-availability): MySQL Cluster and Java RESTful WEB servers have not single point of failure
- Some InfoWidgets/ implementes to visualize features information: GeneInfoWidgets with information about genes or SnpInfoWidgets with information about SNPs
- Many others minor features