Victor Unda, (WSU)
Chun-Huai Cheng (WSU)
Nic Herndon (UConn)
Michael Wynne (UConn)
Lacey-Anne Sanderson (Univ. of Sask)
Jobil Joseph (UConn)
Ethy Cannon (Iowa State)
Stephen Ficklin (WSU)
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Thanks to those who participated at our PAG Meeting and Hackathon!
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55-65 attendees at our Tripal Workshop at PAG
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20 people at the Hackathon
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30 people at the Tripal User's Meeting.
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Is anyone going to the Plant Biology 2017 annual meeting in Honolulu? Would a Tripal User's meeting be good at this meeting? Maybe a hackathon similar to PAG?
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Stress Testing
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Lacey is storing ~5 billion of records for natural diversity with fast response times but at the expense of data storage.
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Using materialized views and indexes to get this performance.
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At the expense of data storage (over 2TB to store).
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Is there a plan for storage expansion?
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Will that be a bottleneck?
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Option is to store materialized views in a non-SQL option. But will keep data in Chado as a "warehouse" for data integrity.
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Tripal v3 beta: planning for next week. Feb 10th.
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Will have a migration/upgrade path available
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Will use drupal updates from here on out to support further updating.
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API for Tripal v3 will be stable but documentation for it is not yet ready.
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Perhaps do a training meeting if interested on Tv3 API.
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What components have to be manually upgraded to Tripal v3 if customized? (Nic)... If you have a Tripal v2 site what do you need to manually adjusted.
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Initially there's nothing you manual upgrade.
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Switch nid_is to entity_ids in custom searches and materialized views
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Custom code that attaches custom panes/fields to the node.
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Move old Tv2 templates to GUI-based layouts.
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Tripal v2.1 stable -- delayed by need for testing.
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Currently working on Unit/Functional tests to help make releases go faster.
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Proposed changes to the Tripal Job Launcher (Ethy)
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Add TJL parameter ‘max_jobs’ and function tripal_max_jobs_exceeded().
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This is meant as protection when turning on parallel mode to ensure that the system is not overrun with jobs
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Add TJL parameter ‘single’ to mean only one queued job should be executed each time the TJL executes.
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--parallel=1 --single=1 ensures that each job will be executed in parallel.
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Add timestamps to messages.
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ACTION ITEM: Ethy to submit pull request :-)
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Report on GO loading problems (Ethy)
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Error is due to a cyclical cvterm_relationship which is not in the GO obo file.
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Didn’t seem to be in the original file?
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Guessing this is left over from loading an older GO obo file; cvterm_relationships are not cleared when a new version is loaded and the new obo file added a relationship that caused the cycle.
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Stephen has had this happen on a fresh install
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Could this be related to this? https://github.com/erasche/chado-schema-builder/pull/3 (Anthony Bretaudeau)
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ACTION ITEM: Stephen to look into this
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ACTION ITEM: Ethy to send the particular terms that she suspects
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Google Summer of Code 2017
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Email from Robin Haw states:
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Our team name since 2011 has been Open Genome Informatics. Since 2011, the Open Genome Informatics team has served as an "umbrella organization" to a variety of open bioinformatics projects, including GMOD and its software projects -- GBrowse, JBrowse, etc.; Galaxy; PortEco; Reactome; SeqWare; WormBase; DockStore and others.
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If you have a project idea for which you would like to mentor a student, please contact Robin Haw, cc’ing Scott Cain and Marc Gillespie
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If you don't have their email's Stephen can forward them to you.. just ask.
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Just don’t want to paste them here since our notes go online
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Application Due Feb 9th!... email Robin this week with a project idea.
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Stephen participated last year and had a very good experience with a student from India.
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Get rid of gmod-tripal, gmod-tripal-devel. Use only gmod-tripal-announce to make meeting, outreach and new version announcements.
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There was concern that “what do you think” questions might feel out of place on the issue queue on github
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Suggestion was to use biostars
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Also suggestion to use custom issue tags to make it obvious we want these questions on github to make it more inclusive
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Upcoming Training Topics
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Using the Tripal API
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How to write your own module. (An interest for Nic/TreeGenes)
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Using the bulk loader
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How to make your custom modules generic enough for sharing with others.
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There are some notes on this in the PAG Hackathon Notes.
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ACTION ITEM: Lacey to make this into a full document
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Where does Drupal end and Tripal begin?
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Using Views to create custom searches.
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How others have created custom search pages. (Ethy -- late March is better.)
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Other ideas?
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ACTION ITEM: Stephen send out doodle poll for training.
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Round table: Anyone with new modules, a new site, anyone needing help with any particular topic?
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Maybe a CyVerse question - can data uploaded to TACC with Tripal Workflows (using Galaxy API), be accessed without Tripal (e.g., using Agave API), and vice versa? (Nic)
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ACTION ITEM: Find out how much interaction there is between the Galaxy and Agave API.
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Currently an option is to store your files at TACC and then tell Tripal Workflows that is where it is.
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Stephen recommends storing data physically close to the Galaxy instance that you intend your users to use with Tripal Workflows.
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For example, if using the public galaxy then store your data at CyVerse
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If you are looking at having a public dataset available separately from your Tripal site, you may want to talk to the Legume Federation (Ethy) to see how they are doing it
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They’ve put a lot of thought into how to store the metadata associated with a file
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Reminders
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Anyone can put Tripal related repositories on the Tripal Github organization
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We would love to add you to this organization to make it easier to see what modules are available and what progress is occurring on various modules
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If you are listed as private, please consider making yourself public to show amazing our community is and how many active members we have
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We can organize people into teams to ensure that your module is still attributed to your group if you put it under the Tripal organization
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Please remember to add your modules to the tripal.info site (let us know if you need an account).
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There is page in every Tripal site that pulls from this site and shows admin what extension modules are available
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To make your module visible, please add it to this site
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Let us know if you want your site featured on the Tripal.info site.
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Only sites we have specific permission to highlight will be shown on here
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