Lacey Sanderson (University of Saskatchewan)
Stephen Ficklin, Chun-Huai Cheng, Connor Wytko (WSU)
Christopher Childers, Vijaya Tsavatapalli, Monica Poelchau (USDA/ARS/NAL)
Sudhansu Dash (NCGR)
Nate Henry (U Tenn)
Steven Cannon (ARS - Ames)
Valentin Guignon (Bioversity International)
Ethy Cannon (Iowa State University)
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Report from last meeting:
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Issues from last week’s meeting were added to the issue queue for Tripal. Drupal.org (Thanks Lacey for adding all of those). See list of issues at the bottom of last month’s meeting notes: http://tripal.info/meetings/developers/2015-06-02-160000
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Overview and update of the Legume Federation (By Ethy)
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Effort to get legume databases to communicate and share data, services and software.
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Attendees: SoyBase, PeanutBase, LegumeInfo, Medicago Genome (JCVI), iPlant.
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Other groups: Noble Foundation (Alfalfa), and hope that other groups will join in.
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Development efforts will be focus on Tripal development (e.g. phylotree out of NCGR, blast with U Sask Lacey S).
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Want to redo CMAP in JavaScript and D3.
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Want to integrate InterMine.
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Araport has some Drupal/Tripal modules that may be of interest to others.
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QTL meta-data. And some ontologies
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Tripal is an integral part of the effort
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Kick-off meeting a few weeks ago. Will have a web page soon.
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May have weekly phone calls.
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Things of importance:
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Tripal REST services for inter-site communication and
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cross-site querying.
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Establish at iPlant a repository of legume blast databases and potentially a blast service (web service, not a user interface) for transcriptomes, genome assemblies, etc.
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What an iPlant repository for GBrowse and JBrowse tracks. Put everything you need for a browser instance there. With potentially for streaming (not on site).
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Chado / Tripal Stress Testing
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Issue arose from the USDA organized Databases group’s July meeting.
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Many have criticized Chado for not being able to support large data and use this as a reason not to use it.
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Foreseeable problem for i5K (but all of us as well)
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When is there too much data for Chado as it is currently designed.
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Form committee to:
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Identify use cases for testing.
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Generate fake data for each use case.
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Identify computational resources that can handle the testing.
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Publish results to help others plan for future
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Use results to guide future direction of Tripal/Chado.
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Postgres 9.4 has new functionality for integrating with noSQL data. Has been shown to be faster to MongoDB ( http://www.enterprisedb.com/postgres-plus-edb-blog/marc-linster/postgres-outperforms-mongodb-and-ushers-new-developer-reality ).
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Status of Tripal Web Services
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Chado-centric access has prototype. Available for browsing on the Tripal 2.x demo site: http://demo.tripal.info/2.x/web_services
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Designed centered on controlled vocabularies.
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Slowed by difficulties hiring.
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Testing design and on two test cases:
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genomics
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germplasm (breeding)
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Will have a meeting in August (perhaps second half of august) to submit design to the community and test cases for feedback.
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Trying to have an implementation available by October/November.
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iPlant AGAVE API uses Hypermedia Transport Language (HAL)
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Furthermore, Drupal 8 uses HAL: https://drupalize.me/blog/201401/introduction-restful-web-services-drupal-8
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Search-all functionality, Especially across multiple sites
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Action item:
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sitewide indexing for searching. Should come up with a recommended method and put formal documentation online on tripal.org.
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Setup a separate meeting to discuss a site-wide searching method.
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Setup a separate meeting for stress testing of Chado.
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ASPB, Legume Meetings in Niagra Canada. Will anyone attend?