[ensembl-dev] Genome Maps, a new HTML5 web-based genome browser

Nacho imedina at cipf.es
Wed Jul 25 19:51:01 BST 2012


I would like to announce Genome Maps to Ensembl developers, it is a young
HTML5 web-based genome browser developed during last months in my lab. I do
think this project may be of interest to many Ensembl users and developers,
any comment or suggestion will be appreciated.

For a quick visit just go to:   http://genomemaps.org/     But let me
comment and explain some features.

I consider that Genome Maps is stable enough to be announce and used by the
community. Actually this is a second release and contains many more
biological features and performance improvements. Genome Maps is built with
open and free technologies like HTML5 and SVG inline, so no plug-in is
needed in modern Internet browsers. We’ve focused on providing the best
user experience possible with a modern drag navigation and many features

One of the goals was to implement a modern genome browser based on modern
web technologies such as HTML5+SVG inline or RESTful web services. Other
goal of this project was to provide to the community with a very fast and
real time genome browser with many features and biological data integrated
on it. Genome Maps has been designed to be very efficient in CPU and
memory; and to be easily embedded in any web application or project.

*Biological data*
Biological data is taken from CellBase project (
http://docs.bioinfo.cipf.es/projects/cellbase) which provide very efficient
RESTful web services API from a homemade database that integrate
information from Ensembl and many other sources like Uniprot, COSMIC,
IntAct, etc

*Main features*
There are many features, even though some of them are not still documented
but they will be in a few days, let me just comment a few of them:
 * Biological features like genome sequence, genes, transcripts, TFBS,
miRNA targets, SNPs, COSMIC mutations, regulatory features, etc are
available through tracks that can be hidden from the menu
 * Data is cached to minimised remote connections. Memory is also under
 * Eleven species available (more are coming)
 * 4 main panels: 'Karyotype', 'Chromosome', 'Region Overview' and
'Detailed information' allow to navigate through genomes.
Keyboard navigation is also available. An auto-complete quick search text
box is also implemented. Users can also drag main panel.
 * All features show a pop-up when mouse is over them with, some of the
features are also clickable and show a rich info window with a lot
information depending on the feature.
 * DAS client implemented, DAS server can be also added to Genome Maps
 * Import local files, through "Plugins > Load " local data can be loaded
 * many others...  and many more coming!

Genome Maps technology is being used in some applications form our lab like
VARIANT (http://variant.bioinfo.cipf.es/).

Notice that, even though, Genome Maps does not pretend to be a replacement
to any other genome browser as all them have very nice features, I do think
this project may be of interest to many bioinformaticians as many of them
are using it right now and embedding it in their applications.

I hope Genome Maps can be useful for you and feel free to contact me if
some features are needed or some bugs are found.

Best regards,


Ignacio Medina Castello
Head of the Computational Biology Unit
Bioinformatics & Genomics Department
Prince Felipe Research Centre (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(Junto Oceanografico)
46012 Valencia, Spain.

Tfn: +34 96 328 96 80 ext: 1016 (+34 96 328 96 81 1016)
Fax: +34 96 328 97 01
Web : http://bioinfo.cipf.es
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