= Satellite meeting for Galaxy =

== Topics ==

Galaxy is an interactive platform to process biological data using various tools.

The URL of Galaxy is: http://main.g2.bx.psu.edu/

This meeting provides an opportunity to discuss the following topics on Galaxy. 

 * Internationalization (i18n):  UTF-8 encoding support, etc.
 * Workflow:  Future plan, accessibility to workflows through API, etc.
 * Authentification: remote_user login: OpenID support, email address management etc.
 * TogoDB/Galaxy companion: To browse, search and share a Galaxy history item at TogoDB.

# Please add a new topic to this list.

== Chairperson ==

 * Mitsuteru Nakao

== Targets ==

 * Developers of Galaxy and its related software
 * End-users of tools for biological data

== Date ==

 * 18th March, 2009

== Room ==

 * Chura Hall (3F)

== Attendees ==

 * James Taylor
 * Greg von Kuster 
 * Mitsuteru Nakao
 * Takashi Hatakeyama
 * Atsuko Yamaguchi
 * Kozo Nishida
 * Hong-woo Chun
 * Yasunori Yamamoto

== Presentations ==

 * James Taylor (in the Symposium on 16th March)
  * Integrated reproducible analysis with Galaxy 
  * Attachments (PPT or PDF slides etc.) 

 * Mitsuteru Nakao 
  *  Current state of Galaxy i18n

 * Atsuko Yamaguchi
  * Activities of DBCLS related to Galaxy

 * Hong-Woo Chun
  * GALAXY: Expression of terms that are NOT Ascii characters and symbols.


== Notes ==
 * How to join developing Galaxy (Japanese)
   * http://d.hatena.ne.jp/kozo-ni/20090317#1237263807
 * TogoTV
   * 統合TV - galaxy1en http://togotv.dbcls.jp/movie/090312galaxy1en_f.html
 * Biobookmarklet - KazusaWiki (ja)
   * http://wiki.kazusa.or.jp/Biobookmarklet


== Results ==
 * i18n
   * Create a repository http://bitbucket.org/mn3/galaxy-central-i18n/ from the galaxy repository to share the gettext message files and patches. 
   * Known issues
     * Static files, cheeter (.tmpl) templates
     * Messages for Tool
     * Use URL lang parameter (lang=en)
     * Use Accept-Language HTTP request header (HTTP_ACCEPT_LANGUAGE)
     * Use pybabel with mako.ext.babelplugin:extract
   * Set UTF-8 to display non-ascii characters at the history and middle pane.
     * [http://bitbucket.org/galaxy/galaxy-central/issue/13/problems-with-non-english-data galaxy / galaxy-central / issues / Problems with non-english data — bitbucket.org]
     * [http://bitbucket.org/galaxy/galaxy-central/issue/15/sample-sentences-of-japanese-and-korean galaxy / galaxy-central / issues / Sample sentences of Japanese and Korean — bitbucket.org]
   * List up i18n-ed scientific application
     * gbrowse (web)
     * CiteULike (web)
     * 

 * Workflow
   * Introduced the tools developed by DBCLS. http://testgalaxy.lifesciencedb.jp
     * OpenID login via mod_openid_auth
     * TogoWS tool
     * Search tool of MEDLINE related PNE articles that are written by Japanese
     * Bookmakrlet tool, to display a protein 3D view of an PDB ID in a galaxy history data. Such function can be replaced by the semantic column function in future. 
   * RSS feed for a workflow to know the result updated. (c.f PubMed article alert)
   * Added View, analysis, workflow and libraries on http://test.g2.bx.psu.edu
   * Web based tool manage system / central tool repository ?
 
 * Authentification
   * Introduced the OpenID Galaxy at http://testgalaxy.lifesciencedb.jp.
   * login email address management.
   * [http://bitbucket.org/galaxy/galaxy-central/issue/14/openid-authentication-support galaxy / galaxy-central / issues / OpenID authentication support — bitbucket.org]
 
 * TogoDB/Galaxy companion
   * Export a history item into TogoDB is likely to implement as a tool.
   * Import a history item from TogoDB is likely to use the URL based GetData.

 * Galaxy/gbrowse 
   * Two way communication (Import data from wormbase, send data to wormbase)


== TODOs ==
 * [nakao] Provide  a workflow scenario to use the TogoDB/Galaxy companion. 
 * [atsuko] present a workflow that we want to use through RSS feed.