= 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. * [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] * 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. * [http://bitbucket.org/galaxy/galaxy-central/issue/14/openid-authentication-support 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]