Version 28 (modified by mn, 15 years ago)

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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

Results

  • 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 ?

  • TogoDB/Galaxy companion
    • In terms of data lifetime, TogoDB and Galaxy are complementary.
      • TogoDB is feasible for long lifetime data (named dataset, reusable solid data, ...).
      • Galaxy is feasible for short lifetime data (no name data, temporal results, ...).
    • 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.

Attachments