Tripal Developer's Meeting 2016-03-01

Meeting Date

Tue, 03/01/2016 - 12:00

Attendees

Stephen Ficklin (WSU)

Lacey-anne Sanderson (UofS)

Monica Poelchau, Vijaya Tsavatapalli, Chris Childers (NAL)

Nathan Dunn (LBL)

Valentin Guignon (Bioversity International, CGIAR)

Andrew Farmer (NCGR)

Dorrie Main, Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble (WSU - Mainlab)

Meg Staton, Ming Chen, Nate Henry (University of Tennessee)

Sends Regards

Ethy Cannon (Iowa State)

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

Meeting Type

Users