extensions

• Report from last meeting:

  • 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

• Overview and update of the Legume Federation (By Ethy)

  • Effort to get legume databases to communicate and share data, services and software.

  • Attendees:  SoyBase, PeanutBase, LegumeInfo, Medicago Genome (JCVI), iPlant.

  • Other groups: Noble Foundation (Alfalfa), and hope that other groups will join in.

  • Development efforts will be focus on Tripal development (e.g. phylotree out of NCGR, blast with U Sask Lacey S).  

  • Want to redo CMAP in JavaScript and D3.

  • Want to integrate InterMine.

  • Araport has some Drupal/Tripal modules that may be of interest to others.

  • QTL meta-data.  And some ontologies

  • Tripal is an integral part of the effort

  • Kick-off meeting a few weeks ago.  Will have a web page soon.

  • May have weekly phone calls.

  • Things of importance:  

    • Tripal REST services for inter-site communication and

    • cross-site querying.

    • 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.

    • 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).

• Chado / Tripal Stress Testing

  • Issue arose from the USDA organized Databases group’s July meeting.

  • Many have criticized Chado for not being able to support large data and use this as a reason not to use it.

  • Foreseeable problem for i5K (but all of us as well)

  • When is there too much data for Chado as it is currently designed.

  • Form committee to:

    • Identify use cases for testing.

    • Generate fake data for each use case.

    • Identify computational resources that can handle the testing.

    • Publish results to help others plan for future

    • Use results to guide future direction of Tripal/Chado.

  • 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 ).

• Status of Tripal Web Services

  • Chado-centric access has prototype.  Available for browsing on the Tripal 2.x  demo site: http://demo.tripal.info/2.x/web_services

  • Designed centered on controlled vocabularies.  

  • Slowed by difficulties hiring.

  • Testing design and on two test cases:

    • genomics

    • germplasm (breeding)

  • Will have a meeting in August (perhaps second half of august) to submit design to the community and test cases for feedback.

  • Trying to have an implementation available by October/November.

  • iPlant AGAVE API uses Hypermedia Transport Language (HAL)

  • Furthermore, Drupal 8 uses HAL: https://drupalize.me/blog/201401/introduction-restful-web-services-drupal-8

• Search-all functionality, Especially across multiple sites

• Action item:

  • sitewide indexing for searching.  Should come up with a recommended method and put formal documentation online on tripal.org.

  • Setup a separate meeting to discuss a site-wide searching method.

  • Setup a separate meeting for stress testing of Chado.

• ASPB, Legume Meetings in Niagra Canada.  Will anyone attend?

  • http://www.uoguelph.ca/hosted/bic2015/

  • https://www.eventbrite.com/e/north-american-pulse-association-2015-biennial-meeting-tickets-16159927779

• Non Chado Data?

• • Andrew Farmer:  a bit of prototyping trying to associate URLs to BAM files via biomaterial table.  Metadata for experiment for RNA-seq data would be stored there.  Focusing on importing data from NCBI BioSample/BioProject.

  • Stephen Ficklin: a file module.

  • Nathan Weeks:  Brilliant Gallery for showing image data.  Also using customized version of FileBrowser Drupal module, for browser based access to Excel spreadsheets with metadata.

  • Chris Childers: documents (tutorials/guides/etc.) including flat files, PDF documents and other documents.

  • Gerard Lazo:  Drupal wrapper around GrainGenes.  Looking to migrate.

• RNA-Seq Module (Meg Staton)

  • Adding RNASeq expression data to chado is not intuitive. Here is a google doc describing some potential ways forward.

  • Andrew Farmer:  was importing XML from BioProject/BioSample and meta data fit nicely into existing Chado tables.  Did not represent experimental design.  Interested in pursuing work on RNA-seq.  

  • Should we request table changes or new module for RNA-Seq Data

  • Perhaps a link between biomaterial + library and biomaterial + stock.

  • SolGenomics Network is developing and RNA-Seq module. Perhaps not in Chado but is willing to talk Chado.

  • Where to put quantitative information.  Link features to samples and linking expression quantities.

  • Meg can make available to the code for others to see.

  • Andrew’s group can share the code with importing form NCBI BioSample/BioProject.

• Page redesign & gene pages.

  • Would folks be interested in i5K templates for gene pages?  They can share.

• Site-wide indexing

  • Meeting notes from 2015/7/24

  • Meeting notes from 2015/7/16

  • Summary:

    • Goal: provide a recommended method, perhaps a module, and set of documentation to help others setup site-wide indexing on their site.

    • Discussed different implementations for a site-wide searching method:  Drupal default search, Apache Solr, Elastic Search

    • Needs:

      • Only data made available to end-user should be indexed. Not necessarily everything in Chado

      • Search results should highlight matched words on page.

      • Would like to integrate with a “basket” system for later transformation of data.

    • Vijaya Tsavatapalli of USDA/NAL working on an Apache Solr module

    • Valentin Guignon (Bioversity International, CGIAR) working on an Elastic Search module.

  • Action Items

    • Vijaya will work on administrative section of her Apache Solr module to provide more customization.

    • Documentation for the module on tripal.info

    • More input from Valentin.

• Chado/Tripal Sustainability (Stress Testing)

  • Meeting notes from 2015/7/22

  • Summary:

    • Goal:  plan for, test and attempt to resolve issues related to poor performance:

      • Syncing takes too long

      • Setting URL alias takes too long

      • Loading GFF?

      • Missing indexes in Chado

      • Bulk loader can be slow for large data sets.

      • ND tables:  takes a large number of records for a single genotype/phenotypes.  

      • MViews bloat the database.

    • Ideas:

      • Stress test by creating dummy data to explore limits of Chado.

      • Improved interface for MViews:  better way to share, track FK constraints between them.

      • Improve accessibility of documentation for solutions to common problems.

      • Maybe something similar to testing (https://travis-ci.org/, https://jenkins-ci.org/).  Looks like a Drupal module also available for testing. https://github.com/sonnym/travis-ci-drupal-module-example

    • Action Items

      • Chris created a python script takes a GFF and set of FASTA files (assembly/CDS/cDNA/peptide) and generates a set of new data.

        • https://github.com/NAL-i5K/test_data_gen

      • Andrew is working on a test server at iPlant.

      • Lacey: it will likely be a month before I get some time to work on this :(

      • Stephen: will see if there’s another solution.  Can we get AWS credits for it.  

      • Stephen & Chun-huai to discuss creating data for data at Mainlab.

      • Some needed improvements

        • Stephen try to fit in improvements the Materialized Views + documentation in the coming months.

        • Restrict setting url alias to a limited set of items.  Crashing because of memory issues.

      • Stephen to work in patch into Tripal package so folks can at least apply the patch for syncing that Nathan created.

• Chado/Drupal Stress Testing

  • Chris Childers provided example script for generating sample genomic data: https://github.com/NAL-i5K/test_data_gen

    • Put scripts for generating test data together in a github account.

    • Is there a place on the database where we could store database dumps?  A repository to see how folks store data in Chado?

      • The Galaxy folks solve this by having individual instance admins give a 5-10 minute talk about “how we’ve set up our instance” at our monthly admin meetings.

  • Andrew Farmer exploring a test server for testing Chado/Tripal at iPlant?  Jeremy DeBarry here to discuss options.

    • Potentially useful: iPlant atmosphere.  Could set up an atmosphere instance and play with to see if it would work for our stress testing trials.

    • Can tie into iPlant data store.

    • Potentially a place for a Chado dump.

    • TODO: Stephen will explore iPlant atmosphere.

  • Can a new community database using Tripal use iPlant for hosting the site?

    • long term cost of ownership for maintenance of web servers is an issue.  iPlant could be used for a short term option…  

    • iPlant can help with data and metadata management.

      • Allocation for a user is 100GB by default, but allocation can be upgrade upon request.

      • users can add “tuples” to annotate data and can add “template” based metadata, with custom templates designed.

        • template based metadata will use ontologies.  

      • Will be bringing online bulk metadata association using CVS file.

      • iPlant Data commons will have minimal meta data standards to promote re-use and discoverability of the data.  

• CV module & ontology search

  • SO loading link is old, should be https://github.com/The-Sequence-Ontology/SO-Ontologies

    • TODO:  need to update the sequence ontology to the new location.

  • no PURL prefixes in db records

  • Relationship Ontology has changed such that it no longer loads.  Missing namespace, has fields not defined in OBO v1.2 format, includes terms for other ontologies.

    • TODO: stephen will follow up with RO about issues

  • ENVO ontology has terms with no names that break the Tripal loader; have not heard back from the group about the meaning and purpose of these, don’t know if it’s proper OBO.

    • TODO: Ethy will follow up with ENVO.

  • Ideas for a Tripal ontology search module.

  • Will it be ontology hierarchy aware?

    • Yes, that is the fundamental purpose.

  • Latest OBO specification is 1.4. This spec does allow terms without names whereas 1.2 did not. So the Tripal loader should be updated accordingly.

• Developer Best Practices & Tips

  • Tips for debugging Drupal and Tripal modules

    • Use devel module https://www.drupal.org/project/devel.  Use ‘dpm’ function call to expose variables.

    • Use drupal_debug() calls when dpm not useful.

    • Eclipse for PHP very useful for coding and maintaining coding standards.

    • Never tried, but can use Eclipse + Xdebug + Drupal.  Tutorial here: http://programmingbulls.com/debugging-drupal-php--xdebug-eclipse

  • Review techniques for customization (to keep customizations out of core Tripal code)

  • Handling (or avoiding) inter-module dependencies

    • TODO: talk on this one next month.

• Site-wide Indexing.

  • i5K group working on Apache Solr module that can be shared with others.  With customizable admin interface.

  • Will refactor to make more generalizable to share with others.

  • Valentin has an ElasticSearch module, but it’s not yet available for others to use.  

  • Valentin:  could it be possible to separate key/value pairs used for indexing and the actual underlying infrastructure consumes the key/value pairs regardless of the indexing method.

  • TODO: valentin will send an email with suggestions.

• Tripal v3.0 (Drupal Entities, Web Services, Semantic Web, Controlled Vocabulary centric)

  • Currently under design.  

  • Will support Drupal Entities

  • Centered on controlled vocabularies rather than Chado.

    • Controlled vocabularies are more intuitive than Chado-centric organization

    • Controlled vocabularies lends itself to bringing Tripal into the realm of the semantic web.  Thus allowing web services that afford data exchange between sites.

  • Will necessitate page redesign, where we will try to account for recent input on pages (e.g. gene pages).

  • Benefits

    • Continues to use Chado as the primary database back-end storage.

    • But, supports integration of non-Chado data stores (e.g. noSQL options)

    • Presentation of data is more intuitive… not Chado-centric.

    • Simplified admin interface…. not organized according to Chado tables.

    • Drupal entities are manageable using the Drupal web interface, therefore the need for template customizations is greatly reduced.

    • Web services and page displays contain the same information.

    • We have greater control over “syncing” and setting of URLs so we can better control performance.

    • Potentially smaller code-base for Tripal, hopefully supporting faster times for releases.

  • Migration Plans

    • This represents a major change in how data is presented. We will do everything in our power to make transition from Tripal v2.0 to v3.0 as seamless as possible.

    • We will provide a “beta” test period for folks to help us resolve issues related to conversion.

  • Goal to have an alpha release by end of the year.

  • TODO: stephen to share design spec for that

• Tripal Codefest at PAG (Meg)

  • How much interest?  Stephen, Lacey, Meg, Valentin, Ralph Mosely.  Some folks interested but too busy.

  • Need a room at PAG conference.

  • TODO: doodle poll Meg.

• Migration of Tripal code to GitHub (but continued syncing with Drupal git).

  • TODO: migration of Tripal to Github.

• Extension module paper.

  • TODO: item to discuss next month.

• Major Tripal Fixes/Updates

  • Ontology Loader:  

    • Support new Relationship Ontology (RO).

    • Support new link for Sequence Ontology (SO).

    • Latest OBO spec is 1.4, which permits terms that lack names (found in the ENVO ontology).

    • Would be nice to have prefix URLs too, to be used to build PURLs. BioPortal?   How to deal with RO as some terms have different namespaces.

    • TODO: have loader fixed by November Monthly

  • Chado v1.3 Support

    • Need Testing -- Valentin (custom views check)

  • Chado installation has a substitution that has converted the word ‘public’ as ‘chado’... take a look at this.

  • CVterm synoyms has some sort of related issues (Andrew F. will send more information).

• GitHub Tripal community page

• Chado/Drupal Stress Testing

  • Chris Childer (i5K) -- create and shared loading script.

  • Andrew Farmer (NCGR) -- working with iPlant. Atmosphere system (analgous to Amazon web services for creating a VM spun up on demand).  Created an instance with a vanilla install of Drupal.

    • Been thinking of frameworks for regression testing (Jenkins).  

    • Atmosphere can be linked up to the iPlant data store.  

    • Chris: may need to request a VM with more resources for testing.

    • Nathan: TravisCI?

    • Stephen:  

      • TODO: will try to look into Jenkins/Travis CI

      • TODO: look into atmosphere on iPlant.

      • TODO: coordinate by email the stress testing a plan for genomic testing (will communicate on gmod-tripal-devel mailing list.

    • Agree on where the base installation stops and what setup we need for test operations.  (i.e. which Tripal modules are needed, based on which tests we want to do).

      • Base Install:

        • Drupal installed

        • Tripal modules:  tripal_core, tripal_organism, tripal_analysis, tripal_cv, tripal_db, tripal_feature, tripal_stock (ND module??).

        • Chado Installed v1.2

        • CV’s loaded: sequence, (need to perhaps settle on an community ontology for what we’re storing).  What other ontologies do we need?

          • TODO:  determine which ontologies are needed.

    • Use Cases:  Phase #1: start on genomic data for stress testing (using sequence ontology, GO).

• Site-Wide Indexing

  • Valentin recommendations: http://sourceforge.net/p/gmod/mailman/message/34426451/

  • Suggests creating a new module that separates the keyword identification from the search engine module.  This way we can all use the same admin interface but use our search engine of choice on the back-end.

  • Look at integrating this suggestion with Entities for Tripal v3.

    • Still need the ability to pre-process and convert data for indexing.

  • Codefest Idea:  come up with a more unified approach (perhaps code merging?) for site-wide indexing.

• PAG (Lacey Sanderson & Meg Staton Co-chairs; Stephen assisting).

  • Oral Presentation Abstracts (Due next Friday Oct 16th). please email to mestato@gmail.com

  • Poster Presentation Abstracts (Due October 30th)

  • Codefest (Jan 8th Friday.  9-5pm).  

• Revisit downloading via views_data_export (currently being tested for LIS)

  • TODO:  might be recommended on Tripal documentation. If so need to take off.

  • TODO:  design for Tripal v3.0… explore export options for entity with ability to filter which properties are included.

  • Perhaps ask Lacey? (past comments… didn’t clean up itself).

• Tripal feature: GFF Downloader.   

  • TODO:  look at the status of this and report where it left off.

• Developer Best Practices & Tips

  • Handling (or avoiding) inter-module dependencies

  • Tips for debugging Drupal and Tripal modules

    • Use devel module https://www.drupal.org/project/devel.  Use ‘dpm’ function call to expose variables.

    • Use drupal_debug() calls when dpm not useful.

    • Eclipse for PHP very useful for coding and maintaining coding standards.

    • Never tried, but can use Eclipse + Xdebug + Drupal.  Tutorial here: http://programmingbulls.com/debugging-drupal-php--xdebug-eclipse

  • Review techniques for customization (to keep customizations out of core Tripal code)

  • Handling (or avoiding) inter-module dependencies

    • Suggestion:  to create a custom in-house only module for customizations specific for your site.

• Last Month’s Notes

• TODO items from October:

  • Ontology loader needs fixing. It does not properly load the new Relationship Ontology.  Work has started on this… still working on it..

  • Stress Testing Plan:  test atmosphere on IPlant, look into Jenkins/Travis CI. No movement has been made on this issue.

  • Remove recommendations for Views Data Export on Tripal documentation. Verified no longer recommended on the documentation.

  • Status of GFF Downloader:  Initial code exists for it.  But it needs further development and testing.

  • Add to Tripal v3.0 design the topic of data export and filtering.   Export of Entities (e.g. genes) and attached fields (properties, dbxref, locations, etc) has not yet progressed to design exporting and filtering.  But it will be kept on the TODO list.

• Expect the following:

  • Trying for a Tripal v3 alpha release before PAG.  Will not support all Chado tables but will give folks opportunity to explore initial functionality with entities and web services.

    • Any experience with cross-origin request (e.g. how will work with future Tripal web services)?  How to setup Drupal server to allow these requests to be made.

    • https://www.drupal.org/project/cors

  • Integration of Chado v1.3 into Tripal 2.x.  We will try to have this ready before Jan 1st 2016.

  • Fix for OBO import problem. Possibly an OWL parser for ontologies as well.

  • Tripal PAG workshop.  Jan 10th at 4pm PST.

• Tripal PAG codefest.  Friday Jan 8th.

  • Tentative agenda, please edit!!!: https://docs.google.com/document/d/1jarLU2EwzQ2Gl9LiHVTfDW9ju-MmP-LPTJsDPeNqJHk/edit?usp=sharing

  • Will there be ability to login and remotely attend.

• Drupal 8 Release:  Nov 19th.

  • Porting Modules and themes: https://www.drupal.org/drupal-8.0.0-rc1#porting

  • Conversion of PHP tpl.php template to twig: https://www.drupal.org/node/2025313

  • Tripal v3.0 will be Drupal 7 compatible.   This will give the Drupal community time to catch up with porting dependent modules (and give us time as well).

• Status of extension modules

  • Blast Module (Ethy/Lacey).  Visualization of hits, can edit and resubmit a blast analysis job. Keeps track of previous results.  

    • Stephen will explore merging two blast modules after Ethy & Lacey’s module is released.

  • Bibtex importer for the publication module.  Not quite support of full Bibtex.  Currently a separate module.  Could potentially be imported into Tripal pub module.  Only has drush not yet a web interface.

  • Expression Module (Meg/Nate).  Will be available in beta from by PAG.  Using MAGE tables.  

    • In future work on setting up meeting for modifying MAGE module or create RNA-seq module for Chado… and also perhaps an interaction module.

  • Phylogeny module (Andrew):  working on ability to interact between synteny viewers and trees.  Synteny viewer uses AngularJS.  Andrew will give demo if someone is interested.

    • In January -- perhaps merge in genericized code into Tripal v2.x core.

    • Anyone interested in discussing how to genericize code feel free to contact Stephen, and we can talk specific for your project.

    • TODO:  a demo for Andrew’s synteny viewer (see news items on legumeinfo.org site for links).

      • An Example displaying segments of genomes with similar gene content to that surrounding the example “Fin” gene: http://legumeinfo.org/lis_context_viewer/index.html#/search/phavu.Phvul.001G189200?numNeighbors=8&numMatchedFamilies=6&numNonFamily=5&algorithm=smith&match=5&mismatch=-1&gap=-1&threshold=15&order=distance

  • Protein Domains (Andrew):  goes further than the existing InterPro Analysis module but goes a bit further.  Hits becomes pair-wise alignments between protein and domains and adds features to Chado.  Those features are linked to gene records.

  • Apache Solr site-wide indexing (Chris/Vijaya): still working on genercizing the module.  

  • Elastic Search (Valetin): Meg’s group is communication to hopefully merge efforts.

  • Breeding Management System:  converting previous breeders toolbox to Tripal and adding new functionality.  Breeders will be able to import their own data. Will have preliminary information by PAG.  

• Future Discussion:  How to code such that you can make your module shareable but at the same time tailored for your own needs.

• What is most needed?

Due to upcoming year-end deadlines the Tripal Developer's Meeting was cancelled.  Instead we had an open call for anyone wishing to discuss their own sites and talk to Tripal core developers.

Due to the upcoming Plant and Animal Genome Conference, the Tripal Developer's Meeting was cancelled.

• Apollo + Chado + Tripal:  workflow for publication of curated results.

  • preference for the workflows

  • data staging methods?

  • For i5K:

    • Possible of export to Chado directly to help alleviate QC rather than to a GFF3 file.

    • ID systems.  Want to convert gene IDs to local ID system.

    • Merging issues: merge curated gene models w/ existing data sets.

    • Apollo -> Chado.   DB authentication, require firewall port to DB server if on separate servers.

    • Apollo Services Tripal could pull from using a Apollo Tripal module.

    • Where to do QC checks on Apollo side or on import to Chado side.

  • Knowpulse (Lacey)… interested in integrating Apollo + Tripal.

  • Legume Info (Andrew)... interested in using tripal modules like phylotree/genome context viewes to help identify missing gene models between species and provide feedback into annotation system

  • Planaria…. etc… (Sofia), has WA now.

  • GenSAS uses Apollo.  Integration of GenSAS with GDR, CottonGen, etc.

• Ethy:  Adoption of Phylotree (example)

  • It would help to both increase the urgency to complete the module and to ensure Tripal compliance if a group would like to deploy it.

  • Anyone else interested in a phylotree module?

    • i5K is interested but not yet ready.  

    • Chado loader for Newick formatted data exists.

    • Interest in using this for taxonomy, but not yet pursued.

• Results of the Tripal PAG Codefest

  • Meeting Notes

  • Meeting Summary on Tripal.info

• Site-wide searching overview

  • Tripal 3 Tutorial

• Chado v1.3 integration

• Tripal v3

  • Overview from PAG talk.

  • Status

    • Currently expanding to support additional tables (Stephen)

    • Adding site-wide indexing (Lacey)

      • Tripal 3 Tutorial

    • Working on Panels display (Chun-huai)

    • Shooting for a beta release in summer of 2016

    • User’s Guide is in progress.

    • Introduction meeting?

    • We think we can make v2 sites fully backwards compatible with v3.

      • We will work to include conversion scripts from “nodes” to “entities”

    • Web services…. have a special meeting next month to talk solely on this.

    • Will include unit testing!

    • TODO:  setup a separate meeting for a Tripal v3 overview.

  • Requests

    • Data Export

  • Questions?

• Tripal v2

  • Status

    • A v2.1 release coming soon

• Galaxy Integration

  • Working on PHP library to interact with Galaxy API.

  • Alpha module coming Fall of 2016

• Round table

  • Any new modules?

  • Status of existing modules.

• Tripal.info site

  • Please add your modules

• Paper:

  • Extensions and site papers.

  • Give credit to folks for their work.

  • Motivate to finish up.

  • Too big?

  • Oxford Database virtual issue?

  • Dorrie’s group will release several modules, will do a paper on those.  Would like to submit as a separate paper.  Something published by the summer.

  • TODO:  Is there a way to link a project extension on the tripal.info site to a GitHub account.

  • TODO: how many publications do we need for a virtual issue.

  • LegumeInfo and PeanutBase were recently published but not ready for another publication.

This is our bi-monthly open agenda meeting.  There is no formal agenda in order to allow attendees to bring up topics of interest to them.

Items for discussion of time permits

• Google School of Code 2016:  add any project ideas

  • Open Genome Informatics Group accepted into program.

  • http://gmod.org/wiki/GSOC_Project_Ideas_2016.

  • Contact Robin Haw if you want to add a project and be a mentor: Robin.Haw@oicr.on.ca

• Tripal v3 Meeting with Web Services

  • Schedule a date in March.  TODO: send out a doodle poll.

  • Currently adding support for more linker tables (e.g. relationships, pubs, cvterms, dbxrefs, etc.)

  • Currently working on backwards compatibility with Tripal v2.x.

• Help with mailing list responses.

• Tripal GitHub organization:  consider moving your Tripal modules there.

• Nathan: Introducing Deepak who is working on Apollo to Chado transition.

• Question:  Tripal v2.1 when will it be available?

  • A few things still needed:  support of Chado v1.3

  • TODO:  send out notification for a timeline for Tv2.1 release.

• Feature requests for Tripal v2 or v3?

• Status of Modules that folks are working on

  • Tripal.info: please add your modules

  • QTL   (U. Iowa, WSU, U. Sask)

    • Original module was developed in Dorrie Main’s group.  Collaborating with Ethy.

    • Met to discuss data templates, vocabularies

    • Current plan is to release QTL support as part of Mainlab Module because development of collaborative module is slow going.

    • Plans are to create a collaborative QTL module for Tripal v3.

  • BLAST (U. Iowa, U. Sask)

    • Used at http://knowpulse.usask.ca/portal/blast, http://peanutbase.org/blast, http://legumeinfo.org/blast

    • New functionality added to support custom link-outs; documentation on the github wiki (https://github.com/laceysanderson/tripal_blast/wiki )

    • New version coming soon (essentially ready)

    • Working towards making available through web services, to see target databases and set blast parameters to run a job remotely via API. Results would be accessible via API.   Idea is to allow blasting across sites (need to show proper attribution).

    • Future plans, Stephen, plans to integrate current Blast Analysis module so in the end there’s only one blast module.

  • Mainlab_chado_search (WSU) - includes gene search, marker search, germplasm search and QTL search

    • QTL, stock, genes, marker,

  • Mainlab_tripal (WSU) - custom display in mainlab sites

    • Sites that use this module:  https://cottongen.org, https://coolseasonfoodlegume.org, http://rosaceae.org GDR (using Drupal 6 version).

    • Handles customized displaying: genes, mRNA, marker and stock pages.

    • Contains a set of Perl loaders for loading data, uses custom tables, and loads data into prop tables.  

    • Contains a variety of in-house vocabulary terms.

    • Creating administrative interface to control

    • Data template dictionary and data loaders for

    • If data is loaded using Perl loaders then the module can automatically display them,

  • RefTrans  (WSU)

    • Reference transcriptome

    • Assemblies ESTs, RNA-seq into reference transcriptomes.

  • Tripal Maps (WSU)

    • A replacement for CMAP.

    • Will use d3 Javascript library.

    • Plan is to have finished summer of 2016 with a possible release this summer.

    • Work going in in Legume Federation for a CMAP 2 that is independent of Tripal / Chado, to serve as a replacement for the old CMAP.

      • looking at a whole genome drawing system based on PaperJS.

  • Breeding Information Management System, BIMS (WSU)

    • Unknown release date, but currently under development

    • Can be used by public/private breeding projects.  

    • Has an application-style interface, but it directly tied to Tripal/Chado

    • Decision making tools.

    • Most likely a release next year.

  • Networks (WSU, Clemson)

    • https://www.drupal.org/sandbox/spficklin/1796198

  • Phylotree (NCGR, U. Iowa)

    • https://github.com/ncgr/tripal_phylogeny

    • http://legumeinfo.org/search/phylotree

    • Need to get another group interested to finish up the “generic” version.

      • Meg’s group is interested.

      • i5K would like to use it but not near ready to use it.

      • TODO:  have a meeting month to discuss Phylotree module.

      • Documentation for data loading requirements?

    • The goal was to integrate into default Tripal v2.x.

  • Pedigrees/d3 support (U Sask)

    • https://www.drupal.org/project/tripald3

    • No recent development

    • In active use on KnowPulse but pages using it are private

  • GO Analysis Module Issues (WSU)

    • https://www.drupal.org/project/tripal_analysis_go

  • (Gene) Ontology Browser (CIRAD)

    • Gaëtan Droc (CIRAD) started to implement a gene ontology browser.

    • http://stage.banana-genome.cirad.fr/

    • http://stage.banana-genome.cirad.fr/ontology_browser

    • Currently not implemented as a Tripal extension (rather a Drupal module) but will be.

  • KEGG module issues (WSU)

    • https://www.drupal.org/project/tripal_analysis_kegg

  • Chado Controller (Bioversity International)

    • https://www.drupal.org/sandbox/guignonv/2428743

    • Currently in testing phase on a new private instance of the sugarcane genome; some issues came up and are currently being solved. The administration interface requires documentation and a tutorial. Some queries are quite slow and need optimizations/tricks.

  • Multi-Chado (Bioversity International)

    • https://www.drupal.org/sandbox/guignonv/2429515

    • Currently in testing phase. Currently supports different postgreSQL user accounts on a same Chado instance. Implementing the support for Chado instances stored on a different schema or different database. Code has been wrote but needs testing. Currently setting up testing Chado instances. Needs documentation/use-case tutorials.

  • Ecommerce style shopping cart (NCGR) for collecting data. Currently gene oriented has some sequence download functionality.

    • Perhaps use “flag” module to emulate this functionality.

    • Support for this at some level in Tripal v3 web services.

  • File module (associating images too). (WSU)

    • https://www.drupal.org/sandbox/spficklin/2458713

    • Goal is to integrate with new storage backend of Tripal v3.

  • Daemon API/Drush Daemon API / Tripal Daemon (USask)

    • https://www.drupal.org/project/drushd

    • https://www.drupal.org/project/tripal_daemon

    • No recent development.

    • Request for concurrent processes which is in theory supported by Drush Daemon but not tested/implemented in the Tripal Daemon

      • interest but need to limit the number able to run concurrently

  • Expression Module (U Tenn)

    • Actively developing.   Currently using the MAGE module of Chado. But this may not be the ideal solution.

  • Elastic Search (U Tenn)

    • Actively developing.

    • Full site text searching, supports misspelling

    • Tripal v3 will support easier integration with Elastic Search.

    • By the way, a point of vue about how to interface with the Search API engine: https://www.drupal.org/node/2649256

  • Cross Management Module (Usask)

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

    • Meant to help breeding programs manage crosses. It provides forms for easier data input and a dashboard. All data is stored as chado stocks

    • Release sometime in the summer.

  • Raw Phenotypic data support (USask)

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

    • Supports import of XLSX phenotypic data

    • Has some general visualization and download of subsets of data

    • currently very UofS-specific -plans to make generic

    • won’t support pages per phenotype. Meant to handle the current wave of data coming at us. analyzed phenotypic data module to follow (will be for Tripal 3)

    • Generic release by fall

  • Chado export for Apollo (LBNL, University of Missouri)

    • Export Apollo annotations to a clean Chado database

    • Export Apollo annotations to an existing Chado database

    • Compatibility of exported Chado database with Tripal

    • Exporting to 'Chado' schema in the default database accessed by Tripal

Announcements / Requests

• Tripal Phylogeny module meeting in mid April.

  • http://doodle.com/poll/pugdmbhpb7cerb9h

  • Currently Wed, April 20 at 10am CST, 11am EST seems like the best time but we’ll leave the poll open a little longer.

  • Hopefully will include a demo

  • Look at the data structure and how flexible it would be to accommodate other types

  • Data Generate and input format for loading into chado

  • What features are people most interested in seeing in a generic module

  • Could be used as part of a gene annotation pipeline to determine where some annotations might be improved

  • Might be helpful to have screenshots distributed before the meeting

• Please consider adding your Tripal extension modules to our Tripal organization on GitHub

  • We will give you temporary admin access for the organization to move your project.

• Remember to add/update your module status on tripal.org

• Please help with response to the mailing list if you are able.

Report on Tripal Core Development

V2.1

• Chado v1.3 has been integrated.

• Release of Tripal v2.1 forthcoming once testing of Chado v1.3 is done.

V3

• Development is currently focused on backwards compatibility with Tripal v2.

• • Once upgraded, “nodes” from Tripal v2 sites will still work

  • Site admin can gradually switch over to use new “entities” on a per content-type basis

    • You choose to create entities for your nodes of a given type. The entities start off unpublished so admin can configure them to look as intended. When ready you just publish the entities and turn off the node content type. The URLs will be kept unless you’re using node/[nid]

    • Nodes and Entities can live side-by-side in harmony so you can switch some types (ie: features => genes, mRNAs, etc.) and leave others (ie: stock) until you’re ready

  • Templates for “nodes” will work, and we are working to try and make node templates work for entities (for those not ready to switch to tripal_panes).

• Web services is taking a bit longer to be ready for demonstration. We are expecting to have a demo meeting by mid-late April.

• Current release target date: July 1st.

Round table

Bimonthly Training

• Brought up by Lacey

• Propose to alternate between developer meetings and Tripal/Drupal training for Developers

• There would be a different topic each meeting

• Possible Topics:

  • Drupal coding standards.

  • Writing generic code for sharing.

  • Creating custom hooks.

  • How to use the d3 module.

• Seemed to be interest in these

• Like the idea of keeping our number of meetings the same but alternating between developer meetings and training-like meetings

• Some concern that due to the number of people they might not be very efficient but we’ll try them out and change the format as needed.

Views Download

• Several issues with views data export (slow, memory leaks, extremly complicated) but generic and export in several formats https://www.drupal.org/project/views_data_export

  • Main problem is currently speed which is caused by Views Data Export creating a temporary table emulating the View and then querying it repeatedly through the web interface to build the file chunk by chunk.

• Discussion about changing Views Data Export to meet our needs better.

  • If we do come up with something that extends the views data export module we should submit an issue: feature request

• Perhaps we could use live streaming instead of creating the table

• What about export through tripal jobs. This would break our tie to the web interface meaning we could simply execute the views query rather than create a temporary table.

• We Need a solution for this!

Apollo

• Who is currently using it: NAL, U of S, Meg & Nate

  • and other groups are interested in installing it in the future

• Drupal supports openAuth which works with Cyverse

  • Valentins group (CIRAD) has tested a single sign on (SSO) system including Drupal and other systems; The Breeding API Tripal extension is supposed to support OAuth (only password “protocol”)

• Concern that there are different flavours of OAuth

• Steven would prefer it as a non-core part of Tripal

• Perhaps Tripal/Drupal could use OAuth “out of the box”

• Some link: https://www.digitalocean.com/community/tutorials/an-introduction-to-oauth-2

Module Status

Valentin: Multi-Chado

• About to release the first release candidate in less than 2 weeks

• Working on an installation tutorial

  • Will be included in the module documentation

• Requires patches (for Tripal 2.0 core) at this time

Action Items

• Find a time/person (Valentin?) to demo the flag module for shopping cart functionality.

• Explore OAuth and how it could be combined with Tripal to make for easier coordination between GMOD software (ie: Apollo, maybe even Galaxy)

• Look at patches currently submitted and try to incorporate them into Tripal v2.1
• Bring up Bimonthly training calls on the mailing list for suggestion of topics, etc.