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Sheri Sanders, Indiana University
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Meg Staton, UTK
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Abdullah Almsaeed, UTK
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Bradford Condon, UTK
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Ming Chen, UTK
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Emily Grau, UConn
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Sumaira Zaman, UConn
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Ethy Cannon, Iowa State University
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Jodi Humann
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Victor Unda, WSU
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Taylor Falk
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Katheryn Buble, WSU
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Shawna Spoor, WSU
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Monica Poelchau
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Sofia Robb, Stowers Institute for Medical Research
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Sean Buehler
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Nic Herndon, University of Connecticut
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Yi Zheng, Boyce Thompson Institute
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Carolyn Caron, USASK
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Reynold Tan, USASK
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Malachy O’Connell, Iowa State University
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Sook Jung, WSU
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Gerard Lazo, ARS, Albany, CA
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Taein Lee
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Connor Wytko, WSU
Sends Regards: Lacey Sanderson
Agenda
Reminders
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Further PAG Events
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Tripal Workshop on Sunday in the California room at 4pm https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4885
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GMOD Workshop on Wednesday in the Pacific Salon 4&5 at 10:30am.
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Tripal Galaxy talk on Tuesday , 5:50pm, California room
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AgBioData Booth -- Check it out if you aren't participating. Booth #407
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AgBioData Meeting -- Monday, 7:00-8:30PM, Pacific Salon 3-4.
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Post funded projects on the Tripal site
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http://tripal.info/projects
What we need:-
A description of the project
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Who does the project serve?
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A description of your team?
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Funded dates.
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Use Cases if available.
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Doesn't need to be funded by a large funding-agency.
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Consider adding your modules into the Tripal GitHub organization.
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Remember to update the status of your modules on the Tripal.info site.
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If you have a new site or major updates to your existing site let us now and we can publish those on the Tripal news feed and twitter accounts.
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Send us your logo if you have shared a module with the community and would like it showcased on the Tripal.info site.
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If you publish on your site please remember to cite Tripal (Sanderson et. al. 2013). A Tripal v3 paper will be submitted this year. (We did not have a Tripal v2 paper).
Discussion Topics (Open Agenda)
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Any ideas to add to the agenda?
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Any new extension modules?
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Knowpuse (Lacey)
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Tripal Fancy Fields (USASK; beta released)
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Single-series Chart Field Type: pulls data from a configurable mview and displays results as a pie, donut, or bar chart, as well as, a simple table formatter. Resulting chart is specific to the Tripal Content Page using configurable filter database column => Field mapping.
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Future Development: Multi-series Chart Field Type, Pedigrees, Quick Search (search box which re-directs to existing search), Hierarchy/Relationship Chart Field.
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Tripal D3.js API (USASK; beta released)
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Call a single javascript function to draw a variety of charts. Highly configurable. All the charts in Tripal Fancy Fields are drawn by this module.
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Already has a wiki started that shows how to use the module and documents options
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README also shows how easy it is to use
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ND Genotypes (USASK; release by the end of January 2018)
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Marker x Germplasm matrix search (complete)
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Tripal 3 Fields: Marker/Variant Genotype pie chart & Marker/Genotype flanking sequence showing all flanking variants (almost done)
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See this module on our KnowPulse poster at PAG: #P0737
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Phenotypes (USASK; release 1.0 coming soon;)
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Data upload & download
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Dynamic quantitative trait chart summarizing the data for a given trait/project combination. This chart keeps site-years separate but averages replicates.
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Version 2.0 will include trait pages and specialized Tripal 3 fields
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Boyce Thompson Institute
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Synteny Viewer
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Circos plots, user's can click the blocks to show collinearity.
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RNA-seq Module
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expression viewer + DEG analysis.
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Main Lab
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Tripal Map
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Replacement for CMAP. Integrates with Chado directly. https://www.rosaceae.org/mapViewer
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Breeding Information Management System
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See the talk in the Tripal Workshop by Dorrie Main. She'll discuss both modules.
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Data templates and loaders for loading non-sequence data: markers, maps, genotypes, contacts, QTLs import into Chado. Data Display Chado Loader
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Search module for faster Chado searches without Views Chado Search
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Legume Federation
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Link Out module (proposed). Allows you to link out to other resources for an entity (e.g. gene -> genome browser, synteny browser, gene pages, etc.)
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Should they genericize this for other folks to use? Seems the answer is "yes".
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Blast UI. Also USask. Working to convert to Tv3 to take advantage of web services.
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overview images of hits on entire genome and local alignments.
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Uses CViTjs for interactive whole genome view. Still beta. Code is here.
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Phylogenetic Tree Viewer.
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GIS Tool is available for placing germplasm on the map of the world
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Vivek at JCVI is working on a Drupal module that queries across InterMine instances.
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LegumeInfo uses InterMine by dumping Chado data into it.
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Allows for cross-site InterMine searching.
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Has an H5ai interface (non-Tripal sepcific) that can be used for providing a web-browser for files stored on the site. http://larsjung.de/h5ai
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Staton Lab
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ElasticSearch module to do cross-site querying
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Integrates with Tripal v3 Data Collections
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RNA-Seq Expression
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mature for Tv2 but being currently updated for Tv3
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Tripal Field Generator
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Helps simplify generation of Tripal fields.
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Entity converter
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For Tripal v3 entities.
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Allows you to transform one entity type to another type.
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Ficklin / Staton Lab
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Tripal Galaxy Module
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Allows for integration of Tripal workflows with Tripal.
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Can annotate the Tripal workflow and then share workflows across Tripal sites.
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Upgrading to Tripal v3. Who has started & how is it going?
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KnowPulse: “cleaning” up our Chado, improving cvterms used & developing Tripal3 fields for our extensive customizations
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PeanutBase
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GrainGenes (non-Chado db interface; migration strategy; also ground-up dbs)
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CSFL development site is in Tv3
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Hardwoods + expression module will be fully upgraded very soon
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Took longer than expected
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Need more documentation!!!
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Issues occurred with storing differently in Chado than what Tripal expects.
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PeanutBase
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upgrade a Tv2 to Tv3 relatively quickly!
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What is Tripal lacking?
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Gene page how to create a single flat gene.
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Is Tripal FAIR? -- We should have a discussion on this.
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Documentation to have a common method for accessioning data.
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What do you dislike about Tripal?
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Debugging
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Give a call stack with an error?
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Fail early and often.
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How to determine where the problem is especially if Drupal.
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where do tripal_set_messages go.
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Long-term sustainability plans for your sites?
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Tripal forms the part of sustainability
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Tripal permits the site to be built with fewer people.
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Have folks to build into their grants funding for people to curate data to work closely with the database.
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Make data accessioned elsewhere if funding slows. To guarantee that the data has more permanence.
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Get DOIs for dataset.
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Training and outreach… what do you need?
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regular online codefest to target coding issues.r Tripal Therapy.
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Training topics:
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How to write a Tripal Module to define a content and add some fields.
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Web Services
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Setting up Site-wide searching.
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Intro to Chado -- where to put stuff.
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Visualization tools for Chado.
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How to use the Natural Diversity module (or not use it).
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There are programs to get transcripts off of videos to make searches.
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Camtasia -- make Training videos. rather than
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API to pass files to Galaxy workflow (Nic).
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TODO: a future user's meeting or hackathon meeting today.
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How to let folks evolve the documentation
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Documentation for users and developers.
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Hackathon Afternoon ideas
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Site debugging (before/after lunch)
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Tripal v3 site development. (after lunch)
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How to store data in Chado. (https://iastate.zoom.us/j/8031935609)
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Explore CVTerm module.
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Making Tripal FAIR discussion.
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Documentation standards