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 on TogoDB.
• Galaxy/gbrowse: two way communication

# 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
• Todd Harris
• Shin Kawano

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
  • Install Galaxy on your computer in 10 minuites and add a tool as well (nakao-san_lecture.zip)

• 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
    • Most of wet biologists cannot make full use of computational services, so it is effective to provide screencasts of a tool usage as well as documents
    • Currently, togoTV has over 150 movies and 250~300 accesses/day (only togoTV main site)
    • the movies are played about 200 times/day in togoTV and some movie servers (e.g. Youtube) although most of contents described in Japanese.
    • The most popular content is Primer3 tutorial, it played 4000 times since its release

• Galaxy Screencast
  •  http://galaxy.psu.edu/screencasts.html

• Biobookmarklet - KazusaWiki? (ja)
  •  http://wiki.kazusa.or.jp/Biobookmarklet

• List up i18n-ed scientific application
  • gbrowse (web)
  • CiteULike (web)
  • ...

Results

• i18n
  • Two reasons
    • To extend end-users with dislaying native language translation of texual messages (using gettext and babel)
    • To display non-ascii charactors (article author names, gene names, ...)
  • Create a repository  http://bitbucket.org/mn3/galaxy-central-i18n/ from the galaxy repository to share the gettext message files and patches
    • Merged.  http://bitbucket.org/galaxy/galaxy-central/changeset/dc62ee52012e/
    • Known issues
      • Static files, cheeter (.tmpl) templates
      • GetText? Messages for Tools
      • 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.
    •  galaxy / galaxy-central / issues / Problems with non-english data — bitbucket.org
    •  galaxy / galaxy-central / issues / Sample sentences of Japanese and Korean — bitbucket.org

• Workflow
  • Introduced the tools developed by DBCLS.  http://testgalaxy.lifesciencedb.jp
    • 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, analyze, 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.
    •  galaxy / galaxy-central / issues / OpenID authentication support — bitbucket.org
  • Known issues
    • login email address management.

• Galaxy/TogoDB
  • In terms of data lifetime, TogoDB and Galaxy are complementary. (and also BioMart)
    • TogoDB is feasible for long lifetime data (dataset, reusable solid data, ...)
    • Galaxy is feasible for short lifetime data (no name data, temporal results, ... )
  • Two way communication (Import data from TogoDB, send data to TogoDB)
    • Import data from TogoDB
    • Send data into TogoDB [todo]

• 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.
• Send data into TogoDB [todo]