extensions

Communication

1. Official Design Spec

   1. Google Doc

   2. Slack Channel for discussion - There is a #tripal4 channel.
      https://join.slack.com/t/tripal-project/shared_invite/enQtNDExNDU1NzUxOTI3LTNlOTg1MTNjZGQ1NjRmNGQxMWRjOGVjN2IwMjQyOTc2ODZlYWM2OTQxM2Y1ZWM1MmFkNWJhOGEwN2RkZjdkNGU

   3. Ficklin: share a template.   

2. Value of diagraming (UML type)

   1. Communications, process, flow control

   2. yED as a platform that is shareable/editable

Proof of Concept

1. Use Case

   1. Entities and Fields

      1. Gene Page

      2. Germplasm Page

      3. We want to maintain the controlled vocabulary infrastructure of Tripal v3 share th

      4. How well do Drupal + PHP get along with Python Library.

   2. Speed

      1. Variant Queries

         1. Needed for testing speed of large data

         2. Genotype matrix?

   3. Python - PHP interface: how/will this work?

2. Approaches

   1. Service Layer

      1. GraphQL: https://graphql.org/

      2. How do we integrate objects with services.

      3. Advantages

         1. Upgrades

         2. Scale

         3. Allow others to call your services.

   2. Python Layer

Requirements

1. Strict Object Oriented.

   1. Entities and Field

   2. ChadoRecord

   3. ChadoSchema

   4. TripalImporter (for importing and loading files into Chado).

2. How do we know when we're doing the right thing in terms of the API design?

Concerns

• Will lose some functionality if decoupled from Drupal

• Services approach could limit sharing because there is no shared framework

• Services may be more challenging to adopt than a library

• A library may still have the drawbacks of a monolithic entity ... a set of libraries?

• Could a service also be useable as a library

• How will Python and PHP play together?

Action Items

1. Define how the service layer might look.  -- Ethy's group will look into how this could be done.

2. Document an inventory of those classes, how they could be pulled out of Drupal. -- Stephen's group.

3. Python API function and call those in PHP -- Ethy.

4. Post a design spec template -- Stephen

5. Recurring meeting

   1. Next discussion:  Ethy and Andrew talk about services.  Nov 6th. First Tuesday of the month. Same time.

Everyone:  simple diagram of what your preference would be for "Tripal Stack".  -- Anthony, Stephen, Andrew, Lacey

Upgrade from 2.x

Upgrade from 1.x

Change Log

1. A new extension importer is available under the Tripal -> Extensions -> Import Extensions menu. It finds available extensions for Tripal and makes it easier to install them.
2. Major slowness and memory leak problems have been resolved.
3. Improved record deletion functionality.
4. Support for d3 Javascript library has been aded to the Tripal Core module.
5. A new d3 barchar on the feature admin page provides an overview of features in the database.
6. Added new API functions and improved documentation for others.
   • Now contains autocomplete API functions for contacts, organisms and analyses
   • Bulk loader API function for programatically adding a bulk laoder
   • Improvements to the Chado Node API functions, especially for inserting properties, database cross-references and relationships.
   • New functions for adding indexes to tables (i.e. custom tables in Chado)
   • Add Tripal Variables API, which consists of functions for associating non-biological data with data records in Chado.
   • New functions to the Tripal Files API
7. The GFF3 loader now creates protein sequences for transcripts with CDS if proteins are not present in the GFF3 file. This is consistent with the behavior of the Perl-based GMOD GFF3 loader.
8. The feature browser has been noted as deprecated but is still available to give time to phase it out.
9. Fixed a myriad of bugs.
10. Fixed typos in the example module and added missing functions.

Tripal TEST

View the Tripal talk at the GMOD workshop of PAG XX, San Diego. Jan 2012.

Agenda

• Quick Items

  • blend4php is released. https://github.com/galaxyproject/blend4php

  • TripalProject twitter account is now active.  https://twitter.com/TripalProject

  • Tripal v2.1-beta3 released July 1st.  http://tripal.info/node/310. Only testing needed before full stable release.

  • One-on-one meetings with stakeholders to discuss Tripal experience.

  • Comparison chart for site-wide indexing solutions.

  • Tripal.info site updated a bit (Twitter feed, new site images, updated documentation)

• Tripal v3 and REST API

  • The demonstration shows alpha functionality.  Things can still change, there are still bugs/mistakes in some places. Please offer suggestions!

  • Key Points:

    • Data back-end agnostic

      • Full support for Chado

      • Working on Neo4j support (via another project)

      • API for integration of other back-ends coming in the future….

    • Fully Backwards Compatible.

    • Ontology Driven

      • Integrates with semantic web for data exchange via web services

    • Full support of Drupal Entities

      • Allows for full web-based configuration of fields (less template editing!)

    • Style agnostic

      • Considering no default sidebar.

    • Exposed data is consistent between pages, web services (and other future methods i.e. downloads).

  • References:

    • JSON-LD:  http://json-ld.org/

    • W3C Hydra Vocabulary:  

      • https://www.w3.org/community/hydra/

      • http://www.hydra-cg.com/spec/latest/core/

  • REST API TODO:

    • How to integrate other custom REST APIs?

    • Support for more complex filters (e.g. with and/or conjunctions)

    • Mapping of CV terms to remaining Chado fields

• Natural Diversity Issues

Quick Announcements

• Tripal Workshop at PAG

  • Sunday January 15th 2017 from 4pm-6:10pm in San Diego, CA

  • Abstracts can be submitted by email in MS Word or PDF to pag-abstracts@tripal.info by Friday October 14th.  

• Module Releases

  • Tripal JBrowse API: exposes your chado features table as a JBrowse compatible REST API

    • Credit to Sascha Steinbiss (wrote the SQL queries that make it it work in the parent project by Eric Rasche, kind enough to re-license to make PHP port possible), Nick Booher (ported to PHP)

  • Tripal Download API: provides a framework for downloading Tripal/Chado data

    • Credit to Lacey-anne Sanderson

  • Tripal Docker image: Docker image was updated to Tripal 2.x

    • Credit to Eric Rache and Anthony Bretaudeau

  • Chado 1.31 Database Dumps: there are no pre-built chado database dumps available for v1.31

    • Credit to Eric Rache and Anthony Bretaudeau

    • https://github.com/erasche/chado-schema-builder

  • Python Tripal Data Loader: a python module that allows you to load data into a Tripal instance from command line (or python code).

    • Credit to Anthony Bretaudeau

  • Tripal Jobs REST API: a simple REST API exposing job information and an interface for non-PHP scripts to submit Tripal jobs.

    • Credit to Anthony Bretaudeau

  • Python Chado Tools: a small set of tools for interacting with chado from python

    • Credit to Anthony Bretaudeau and Eric Rache

  • blend4php: A PHP library for Galaxy integration. Currently being used for creation of a new Tripal Galaxy module.

    • Credit to Connor Wytko, Brian Soto, Stephen Ficklin

  • Others?

• Coming Soon:

  • Tripal Expression Module: visual representation of gene expression.

    • Credit to Staton Lab @ Utenn

  • Tripal Elastic Search Module: Provides site-wide searching using Elastic Search

    • Credit to Staton Lab @ Utenn

  • ND Genotypes: Provides an interface and more efficient data storage model for genotype calls

    • Credit to Lacey Sanderson @ UofS

  • Raw Phenotypes: Provides an upload/download interface for raw phenotypic data

    • Credit to Lacey Sanderson @ UofS

  • Tripal Map Module (replacement for CMAP)

    • Credit to Main Lab @ WSU

  • Main Lab Tripal and Main Lab Search

    • Credit to Main Lab @WSU

  • Multi-Chado:  Support for multiple instances of Chado within one Tripal instance

    • Credit to Valentin

  • Updates to Tripal Blast, GO, InterPro:  

    • Credit… fixes courtesy of Anthony Bretaudeau (INRA)

  • Ontology search module: for finding children, siblings, and/or parents for trait searching (i.e. QTLs). Use ontologies to expand searches

    • Credit:  Ethy Cannon

  • Network Module: visualize interaction or co-expression networks

    • Credit:  Ficklin Lab

  • Tripal Galaxy Module: Integration of Galaxy and Tripal.

    • Credit Ficklin Lab

  • Breeding API: Breeding API implementation for Drupal (currently being rewritten)

    • Credit: to Valentin

• Please fill out the GMOD JBrowse & Help Desk Survey!

  • GMOD has given Tripal, as well as many of you, support over the years… Please help us show the funding agencies how important they are!

  • https://goo.gl/forms/1bKIuAMjGKrS0hUi1

• A Big Thank you to everyone who has contributed bug fixes and features! For anyone else who wants to contribute to core Tripal development, we welcome pull requests and would Love to hear from you :-)

Agenda

• Tripal Hackathon and/or Developer/User Meeting before PAG (Lacey)

  • We are looking for feedback from the community on interest in attending a Hackathon and/or Meeting for Tripal on the Thursday and/or Friday before PAG

  • http://doodle.com/poll/qqkwm3x4zrsqqinz

  • Possibly come up with a list of topics for "hackathon"

  • Possibly start early (8am) on Friday… 8-2pm

• Tripal Download API Views Support (Lacey)

  • This API currently provides generic support for custom downloads

    • You register a Download Type using hook_register_trpdownload_type() and a URL that will trigger download using hook_menu()

    • The API provides a generic download page with ajax progress bar that calls your custom download function to create the file.

  • I would like some input on what would be the most useful/performant/flexible with respect to views integration:

    • A) Most flexibility: Use the API to get the views query but you handle executing it, processing results and generating the file yourself.

      • Ensures that the user downloads the same results they saw but allows you full control to manipulate the views results while generating the file.

      • Requires more developer effort to get it going.

    • B) Most Functionality: The API programmatically executes the view, iterates through the results and generates the file. All you need to do is tell it how to transform a single query row into a string to write to the file.

      • Could be too restrictive depending on how much processing is needed to generate your file.

      • Do you need access to more than one row at a time?

      • Additional functions could be made available to customize the header and footer of your file.

    • C) Any other ideas?

      • Even programmers don’t want to write yet another fasta bed gff bam file formatter / writer

      • Implement a) but some support for b)

• Tripal Related Job openings

  • Ficklin Lab (WSU): https://www.wsujobs.com/postings/27783

  • Main Lab (WSU): https://www.wsujobs.com/postings/27523

  • Staton Lab (U Tenn): http://job-openings.monster.com/monster/55d052bf-0dfb-484a-a02a-780384e0b3e7?mescoid=1900305001001&jobPosition=5#

  • Others?

• Google Summer of Code Report

• Neo4j implementation of Chado

  • SciGraph https://github.com/SciGraph/SciGraph

  • Faldo https://github.com/JervenBolleman/FALDO

• Tripal 3 update

• Questions

  • Anyone used Tripal with Drupal 7.50 or Drupal 7.51? (Nick Booher)

  • Tripal 2.1 final release date?

  • Any questions on the Tripal Docker image?

• Action Items

  • Stephen: send out information about Sequence Retrieval Tool build in Chado.  Add documentation to User's Guide (perhaps break out into a separate module)

  • Stephen:  Test Drupal 7.50 or 7.51

  • Stephen & Lacey:  Set a target date for 2.1 release.

  • Add Tripal Docker to User's Guide.

Agenda

• Official Tripal Help Desk Hire

• Hackathon at PAG: Jan 12-13, 2017

  • Will be two days.  Jan 12th is a typical hackathon.  Jan 13th is a round table discussion meeting.  Friday will only be half a day.  

  • What are some desired topics on the hackathon?

    • Tripal Download API

    • Help each other implement each other's modules or generalize them to make more shareable.Nic Herndon @ UConn - plan to attend, might be about 15 minutes late

    • Lacey Sanderson @ USask

    • Stephen Ficklin, Katheryn Buble, WSU

    • Ming Chen @ UTK

    • Andrew Farmer, NCGR

    • Ethy Cannon, ISU

    • Steven Cannon, ARS - Ames

    • Deepak Unni - University of Missouri (Apollo dev team)

    • Eric Rasche, CPT, TAMU

    •  

    • Sends Regards

    • Gerard Lazo, ARS - Albany, CA

    •  

    • SNPs and noSQL storage (Ethy)

      • Tripal 3 notes for how to do this.

• Filter similar to Zappos.com (Nic Herndon)

  • Drupal Faceted Search uses Drupal Search API.  It integrates with ElasticSearch, ApacheSolr or Default Drupal Database.

  • ElasticSearch (Check with Valentin or Ming)

• Training Meeting Dec 2nd

• Legume Federation meeting Jan 13, 12:30 - 4:40 (quite a bit of Tripal discussion)

  • Half presentation / half discussion

  • Presentations will include show and tell of some Tripal related items.  Including phylotree implementation.  BLAST module (Ethy/Lacey).  Integration with Intermine and data store (H5AI; http://LegumeInfo.org/data). Integration with Cyverse (FTP style access) and mirror on Cyverse.

    • MetaData standards are a current challenge.

      • Provenance,  renaming, vocabularies to describe.

      • Still want navigation and directory structure to be intuitive.

      • Store on system for active work with files.

• Main Lab (Sook)

  • Released 3 related modules:

    • Tripal Chado Loader:  comes with Excel templates for importing contacts, markers, map positions, QTLs, genotype, phenotpyes. Can generate the template for your needs and imports that data.

    • Tripal Mainlab Data Display:  provides Drupal theming templates to make a site look like and support data storage similar to GDR/CottonGen.

    • Tripal Mainlab Search Module: advanced search modules for genes, transcripts. markers, genotypes, QTL, MTL, image, germplasm, etc.

      • Based on materialized views.  If your data store is different you can modify the MViews to use the search module.

  • All three described on Tripal.info site with links to GitHub.

  • TripalMap module:

    • Javascript replacement of CMAP, integrates directly with Chado.

    • Will be presenting at PAG within CSFL website.

    • Released a few weeks after PAG.

    • Available on Tripal.info site with link to GitHub (code isn't yet posted, but coming soon).

• Andrew Farmer

  • Tripal Phylotree module replacement. Released next week!

  • Visualized tree, sequence alignment, can subset tree to taxa of interest.

  • Integrates with Chado/Tripal by using Tripal API calls.  

  • Can be used for any species of interest.

  • Need to test compatibility with default phylogeny module with Tripal 2.1

• Lacey

  • Getting close to releasing raw phenotype module.   Perhaps in the next few weeks.

    • Loaders and visualization of the data loaders and downloads for Excel (R-friendly format also available)

    • Loader is specific to the module to ensure data integrity constraints but allow flexibility to support user's specific needs.

    • Traits are stored in Chado… stores data from the field in custom tables that integrates with Chado which are created at time of installation.

  • Also working on Genotype functionality (maybe by PAG).  Handless 500M data points with quick responses!  Requires some database tuning, but tuning is built into the module.  Next test is 5B data points.  

• CMap II (LegFed effort)

  • Prototype stage; aiming for “mature prototype” by PAG

  • Bokeh (python/javascript visualization library; http://bokeh.pydata.org/en/latest/)

  • Aiming for a standalone application, not dependent on Chado or Tripal, but capable of taking data from them or via REST methods

  • Will pull from REST web services for Tripal v3.

1. Thanks to those who participated at our PAG Meeting and Hackathon!

   1. 55-65 attendees at our Tripal Workshop at PAG

   2. 20 people at the Hackathon

   3. 30 people at the Tripal User's Meeting.

2. 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?

3. Stress Testing

   1. Lacey is storing ~5 billion of records for natural diversity with fast response times but at the expense of data storage.

      1. Using materialized views and indexes to get this performance.

      2. At the expense of data storage (over 2TB to store).

      3. Is there a plan for storage expansion?

      4. Will that be a bottleneck?

      5. Option is to store materialized views in a non-SQL option. But will keep data in Chado as a "warehouse" for data integrity.

4. Tripal v3 beta: planning for next week.  Feb 10th.

   1. Will have a migration/upgrade path available

   2. Will use drupal updates from here on out to support further updating.

   3. API for Tripal v3 will be stable but documentation for it is not yet ready.  

      1. Perhaps do a training meeting if interested on Tv3 API.

   4. 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.

      1. Initially there's nothing you manual upgrade.

      2. Switch nid_is to entity_ids in custom searches and materialized views

      3. Custom code that attaches custom panes/fields to the node.

      4. Move old Tv2 templates to GUI-based layouts.

5. Tripal v2.1 stable -- delayed by need for testing.

1. 1. Currently working on Unit/Functional tests to help make releases go faster.

2. Proposed changes to the Tripal Job Launcher (Ethy)

   1. Add TJL parameter ‘max_jobs’ and function tripal_max_jobs_exceeded().

      1. This is meant as protection when turning on parallel mode to ensure that the system is not overrun with jobs

   2. Add TJL parameter ‘single’ to mean only one queued job should be executed each time the TJL executes.

--parallel=1 --single=1  ensures that each job will be executed in parallel.

3. 3. Add timestamps to messages.

   4. ACTION ITEM: Ethy to submit pull request :-)

4. Report on GO loading problems (Ethy)

   1. Error is due to a cyclical cvterm_relationship which is not in the GO obo file.

      1. Didn’t seem to be in the original file?

   2. 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.

      1. Stephen has had this happen on a fresh install

   3. Could this be related to this? https://github.com/erasche/chado-schema-builder/pull/3 (Anthony Bretaudeau)

   4. ACTION ITEM: Stephen to look into this

   5. ACTION ITEM: Ethy to send the particular terms that she suspects

5. Google Summer of Code 2017

   1. Email from Robin Haw states:

      1. 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.

   2. http://gmod.org/wiki/GSoC

   3. 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

      1. If you don't have their email's Stephen can forward them to you.. just ask.

      2. Just don’t want to paste them here since our notes go online

   4. Application Due Feb 9th!... email Robin this week with a project idea.

   5. Stephen participated last year and had a very good experience with a student from India.

      1. https://summerofcode.withgoogle.com/archive/2016/projects/5902985066446848/

      2. Mailing List

   6. Get rid of gmod-tripal, gmod-tripal-devel.  Use only gmod-tripal-announce to make meeting, outreach and new version announcements.

   7. There was concern that “what do you think” questions might feel out of place on the issue queue on github

      1. Suggestion was to use biostars

      2. Also suggestion to use custom issue tags to make it obvious we want these questions on github to make it more inclusive

6. Upcoming Training Topics

   1. Using the Tripal API

   2. How to write your own module.  (An interest for Nic/TreeGenes)

   3. Using the bulk loader

   4. How to make your custom modules generic enough for sharing with others.

      1. There are some notes on this in the PAG Hackathon Notes.

      2. ACTION ITEM: Lacey to make this into a full document

   5. Where does Drupal end and Tripal begin?

   6. Using Views to create custom searches.

   7. How others have created custom search pages.  (Ethy -- late March is better.)

   8. Other ideas?

   9. ACTION ITEM: Stephen send out doodle poll for training.

7. Round table:  Anyone with new modules, a new site, anyone needing help with any particular topic?

   1. 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)

      1. ACTION ITEM:  Find out how much interaction there is between the Galaxy and Agave API.

      2. Currently an option is to store your files at TACC and then tell Tripal Workflows that is where it is.

      3. Stephen recommends storing data physically close to the Galaxy instance that you intend your users to use with Tripal Workflows.

         1. For example, if using the public galaxy then store your data at CyVerse

      4. 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

         1. They’ve put a lot of thought into how to store the metadata associated with a file

8. Reminders

   1. Anyone can put Tripal related repositories on the Tripal Github organization

      1. 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

      2. If you are listed as private, please consider making yourself public to show amazing our community is and how many active members we have

      3. 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

   2. Please remember to add your modules to the tripal.info site (let us know if you need an account).

      1. There is page in every Tripal site that pulls from this site and shows admin what extension modules are available

      2. To make your module visible, please add it to this site

   3. Let us know if you want your site featured on the Tripal.info site.

      1. Only sites we have specific permission to highlight will be shown on here

This is our every-other month open agenda meeting.  There is no formal agenda (aside from a few announcements) in order to allow attendees to bring up topics of interest to them.

1. Announcements

   1. Tripal v2.1 release:  April 1st.  

   2. Ethy… will have tested your changes to the Tripal Job Launcher by then for integration.

   3. Tripal v3 stable release expected in May.

      1. User access/authentication for Web Services

      2. Improved query abilities for Web Services

      3. Upgrade testing of some existing sites that we've reached out to.

      4. Fix some hard-coding in the Storage API to allow multiple-storage backends

      5. Complete online documentation: User's Guide and Developer's Handbook.

         1. Migration documentation up this month! (March).

      6. Fix bugs and unwanted or poor behavior.

      7. Add additional fields.

2. Anyone going to PB meeting in Honolulu this summer?

3. Watch for a PAG Hackathon/User's Meeting Survey

4. Revisit cv loading: propose that cvterm_relationships should be removed if not present in a subsequent version of the obo file. (Ethy)

   1. circular "is_a" relationships, "has_part" relationships.

   2. Suggestion path: OBO loader will remove relationships before updating.  Band-aid fix is to ignore the 'has_part' on GO.

   3. TODO: add a link here for has_part problem.

5. Questions/Thoughts on Tripal v3?

   1. Need how to migrate nodes to entities.

   2. Which PHP is required?  

      1. Can we use PHP 5.3 with Tripal v3?

         1. CentOS 6.5 (PHP 5.3.3 / Postgres 8.4)

      2. TODO: look into this for Tripal v2.1 release.

   3. Adding properties to existing entities very easy with Tripal v3.

   4. Integration of Contact module with Drupal User module.

6. Galaxy: Meg Staton's group working on Galaxy workflows.  Talk to Meg if you have a workflow of interest you want to collaborate on.

7. Baskets for Tripal v3 for storing data and integrating with Galaxy coming in the future.

8. Round table

   1. Any new modules?

      1. Meg's group working on updating GO modules.

      2. Ethy's group working on an ontology browser??

   2. Any help needed for site setup, module creation, Tripal v3 migration?

9. March Training

   1. How to write customize and write new fields for Tripal v3

   2. Proposed Date: 3/24 at 8am PST

   3. Send out a Doodle Poll for time on that day.

• Tripal 2.1 was released on April 1

  • Includes major bug fixes, support for Chado v1.3 and a number of community contributions!

  • Upgrade from Tripal v2.0 to v2.1:  http://tripal.info/tutorials/v2.x/upgrade_2.0_to_2.1

  • Upgrade from Tripal v1.1 to v2.1:  http://tripal.info/tutorials/v2.x/upgrade_6.11_to_2.1

• Tripal Issue Queue has moved to GitHub

  • All pre-existing issues have been moved over and checked to be sure they still exist

  • Please add any problems you encounter with either Tripal 2 or 3 and label/tag them appropriately

  • This issue queue is friendly to help requests as well as the typical bugs or feature requests :-)

• We have added a “Powered by Tripal” block in Tripal 2.1

  • Please consider adding this block to the footer section of your site

  • There are also a number of “Powered by Tripal” images if you would rather include it in an About page or some other appropriate place :-)

  • http://tripal.info/logos

• A Big Thank you to everyone who has contributed bug fixes and features! For anyone else who wants to contribute to core Tripal development, we welcome pull requests and would Love to hear from you :-)

• Training meeting on Friday April 14th at 8am Pacific Daylight Time.   

  • Expect 3 hours.

  • Training will be on using the bulk loader to load custom file formats.

  • We will try to provide a Docker container that you can use to follow along with the training.  

  • Watch for an email early in the week.

Reminders

• You can add your modules into the Tripal GitHub organization.  This allows all of our Tripal extension modules to be in one place but you still maintain control of your repository.  

  • If you want to move your extension module let us know so we can coordinate it.

  • Or consider just creating new repositories right there in the Tripal organization.

• Remember to update the status of your modules on the Tripal.info site.  

  • All modules that were 2.0 compatible have been automatically marked as 2.1 compatible as well.  

• 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.

Agenda:

• Views in Tripal 3.x

  • Do you currently have views containing chado content not shown on your node pages?

  • Do you use the Tripal Views integration configuration to change field/filter/sort handlers and/or add relationships?

• Module Releases/Updates

  • Please update your repository to use GitHub “topics”. This allows your modules to be more easily found even if they are not under the Tripal Organization.

    • You can add “Topic:tripal” in the search box to bring up all Tripal modules tagged on Github:

    • https://github.com/search?utf8=%E2%9C%93&q=topic%3Atripal&type=Repositories

  • With the release of Tripal 2.1 there was also a new release of many Tripal Analysis Extension modules

    • These changes are mostly user contributions --Thanks!

    • Includes Tripal Analysis: Interpro, KEGG, Blast, GO

  • ND Genotypes (Lacey)

    • https://github.com/UofS-Pulse-Binfo/nd_genotypes

    • First beta version just released.

    • Has already had extensive use in a production setting.

  • VCF Filter (Lacey)

    • https://github.com/UofS-Pulse-Binfo/vcf_filter

    • Provides a simple interface to users to filter VCF files and export them in a variety of formats using VCFtools.

    • Users only have access to a set of admin supplied VCF files to keep down server load from unrelated users.

    • Think of it as a more helpful way to distribute bulk genotype sets.

    • Release will be available early next week (just adding 2 more format options).

  • CViT Embed (Lacey)

    • Embeds CViTjs diagrams (LegumeFederation) in Tripal sites to provide whole genome diagrams.

    • https://github.com/UofS-Pulse-Binfo/cvitembed

    • Beta version just released.

  • CV Browser (VG)
    
    A CV browser like the GO Browser ( http://banana-genome-hub.southgreen.fr/ontology_browser )  has been developped and will be released soon (already fully functionnal). Git: https://github.com/SouthGreenPlatform/tripal_cvb This browser allows to browse any (hierarchical) CV (or sub-CV from a root CV term) and associate actions to terms like, for instance, displaying the number of features tagged by a gene ontology term, or displaying a detailed page (next to the browser) regarding a CV term. This module will be moved to drupal.org (my sandbox) soon and will be announced on the Tripal mailing list once a tutorial has been done. (VG)

  • Updates on other modules?