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[gofriends] OmicBrowse open-source programs updated

Tetsuro TOYODA toyop at
Wed Jul 18 15:23:01 PDT 2007

Dear colleagues,

OmicBrowse source programs and installation package for LINUX are updated
and available from SourceForge,

Added new functions are
1) Access controls over secure datasets
2) Changing the browser's window size
3) human, mouse, rat, C.elegans, Arabidopsis and rice genome annotations

Please see a demonstration page:

OmicBrowse is a genome browser displaying an integrated view of multiple
omics annotations filtered with ontologies including GO. It consists of a
Flash client which retrieves XML data from a server composed of Java
servlets. Administrators can configure the server to subscribe to other
OmicBrowse servers and to return a response of merged data thereof, so the
user can search multiple datasets across every server simultaneously and

Users can also integrate in-house private-data, along with various genomic
annotations from public internet servers. OmicBrowse also assists users to
share views by e-mail, to print out views, to register frequently-viewed
chromosomal intervals, and to define groups of often browsed datasets as
menu items.

This system has another unique feature in that it allows administrators to
have fine grained control over secure datasets. They can assign restrictions
to any datasets so that only authorized users can access them, which is very
useful for large-scale genome analysis projects that may consist of
collaborators from various laboratories.

OmicBrowse is developed by RIKEN in Japan and is released under the GPL.

For more details, please see

Tetsuro Toyoda, Yoshiki Mochizuki, Keith Player, Naohiko Heida, Norio
Kobayashi and Yoshiyuki Sakaki "OmicBrowse: a browser of multidimensional
omics annotations," Bioinformatics, 23, 524-526 (2007)

Tetsuro Toyoda, Ph.D.

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