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

[Nacho]

Hello,

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
included.

*Goals*
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
control.
 * 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,

Nacho

-----------------------------------------------------------
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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