Version 29 (modified by mn, 16 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
- Todd Harris
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)
- TogoTV
- 統合TV - galaxy1en http://togotv.dbcls.jp/movie/090312galaxy1en_f.html
- Biobookmarklet - KazusaWiki? (ja)
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
- 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.
- 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 ?
- Introduced the tools developed by DBCLS. http://testgalaxy.lifesciencedb.jp
- Authentification
- Introduced the OpenID Galaxy at http://testgalaxy.lifesciencedb.jp.
- login email address management.
- galaxy / galaxy-central / issues / OpenID authentication support — bitbucket.org
- TogoDB/Galaxy companion
- In terms of data lifetime, TogoDB and Galaxy are complementary. (and also BioMart)
- TogoDB is feasible for long lifetime dataset, reusable solid data, ...
- Galaxy is feasible for short lifetime no name data, temporal results, ...
- [plan] Two way communication (Import data from TogoDB, send data to TogoDB).
- In terms of data lifetime, TogoDB and Galaxy are complementary. (and also BioMart)
- 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
- nakao-san_lecture.zip (21.3 MB) - added by ogishima 16 years ago.