Satellite meeting for Galaxy


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

The URL of Galaxy is:

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.


  • Mitsuteru Nakao


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


  • 18th March, 2009


  • Chura Hall (3F)


  • James Taylor
  • Greg von Kuster
  • Mitsuteru Nakao
  • Takashi Hatakeyama
  • Atsuko Yamaguchi
  • Kozo Nishida
  • Hong-woo Chun
  • Yasunori Yamamoto
  • Todd Harris
  • Shin Kawano


  • 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 (
  • Atsuko Yamaguchi
    • Activities of DBCLS related to Galaxy
  • Hong-Woo Chun
    • GALAXY: Expression of terms that are NOT Ascii characters and symbols.


  • TogoTV
    • 統合TV - galaxy1en
      • 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
  • List up i18n-ed scientific application
    • gbrowse (web)
    • CiteULike (web)
    • ...


  • Workflow
    • Introduced the tools developed by DBCLS.
      • 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
    • Web based tool manage system / central tool repository ?

  • 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)


  • [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]