Hi,
As part of a project, we have been using a method to select and qualify
free and open source software (QSOS, http://www.qsos.org/) to help
biologists/bioanalysts/bioinformaticiens in (1) listing few genome
browsers that would fit his/her project requirement the better
(weighting of criteria) and (2) select few genome browsers to visualize
their features comparatively in a table or graphical format. With
regards to this project, we would like to incorporate the UCSC genome
browser (version as of April 2009). I have carried out a draft by
filling out our different criteria with regards to the UCSC genome
browser features (enclosed QSOS file). Please feel free to correct or
further comment the draft or the list of criteria, we will be happy to
have your insight and feedback.
Best regards,
Thomas
PS : You can open the QSOS file with the dedicated QSOS Editor tool,
allowing you to edit it or add comments. The easiest way to install the
QSOS tool is by adding a plugin to firefox. From
http://www.qsos.org/?lp_lang_pref=en&page_id=5, download the firefox
extension of the QSOS XUL Editor (section "Sheet Editors"). A confusion
can arise with regard to which firefox extension to install as there are
two different tools available : a Template Editor for editing the
scoring criteria, and the Sheet Editors. Open the file with firefox to
install it if this is not done automatically. Restart Firefox. Under the
firefox's tab "tools", there should be a "QSOS Editor" shortcut that
launches the application. Use File -> open local file to load the .qsos
file. You should then be able to read and modify it.
PS2 : we have been setting up a server
(http://genome.jouy.inra.fr/o3s/set_weighting.php?family=genome-browser)
to visualize the different genome browsers features. To see the features
for the UCSC genome browser, click on "Etape 3" (means "step 3", all the
criterion and commentaries are in english but QSOS has not made the menu
of its tool available in english yet), then check
"UCSC_Genome_Browser-July09_fr" and click on "Etape 4-visualiser".
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
