Thursday Aug 20th, 2015: Difference between revisions

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Fixed annotation loading issue (well, a workaround)
Fixed annotation loading issue (well, a workaround)
*Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development.
*Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development.
- Justin Elser
  - all files (minus SVN) are over on github
  - AmiGO2.0
    - Far FAR faster
    - won't load any annotations
      - found a workaround with an old version of OWLtools
        "not ideal"
      - GO doesn't have this issue
    - Can ChrisS help?
      - can't help until the beginning of Sept.
      - if JE can't figure it out by sept, ChrisS can help
    - Post issues to Github's issues tracker on the Planteome-amigo2 repository
    - JE will have it up and down frequently, so be wary when you're 'testing' it.
    - iPlant won't get looked at until it is working on the live version
  - iPlant
    - where are we going to put the association files?
    - the association files are too big for Github
    - they are cluttered within the SVN
      - keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.
    - irods: iPlant's 'big iron' is a possibility
    - In the long run, it makes more sense to keep annotation/association files on iPlant
      - mirror the latest version from version control(SVN) over on iPlant for 'bulk download' options for end users.


== D. Update from AISO/BisQue group- Justin Preece==
== D. Update from AISO/BisQue group- Justin Preece==

Revision as of 19:05, 20 August 2015

Agenda

Topic: Planteome Project All Hands Meeting Time: Aug 20, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada) Join from PC, Mac, iOS or Android: https://zoom.us/j/431144926

  • Who: LC, PJ, AM, JE, JP, MAL, GG, JD, CM, EZ
  • Regrets: BS, EA, DWS
  • Link to recording- Video: TBA
  • Link to recording- Audio: TBA

Minutes

A. General Comments and Updates:

Introductions:

  • Any new faces- Updates on new hires:
    • Georgios moving to Birmingham, has not hired a postdoc, will readvertise, joint position with John
    • Austin Meier:

Pankaj Announcements

Ontology Development Workshop

  • Goal is to hold it this fall - possibly Nov-Dec, in Corvallis
  • goal: not just ontology training (OWL/Protege)
  • stay for a couple days (1 week total) for actual hands on
  • get people actually comfortable in the system.
  • bring in OSU Conferences cordinators to help manage logistics

NSF PI meeting Sept 9th to 11th, Washington DC

  • Need 2 pager report
  • Poster for presenting- needs photos of all participants
  • End of Year One coming up- will need to prepare annual report soon

Other items:

  • Chris' could demo update of new AmiGO curation pathway for the data viz meeting next 11am next wed?
  • GG and JD show their data structure- When?
  • Next all hands: planned for Sept 24th- LC will send out a doodle poll



- Justin Preese

 - Main goal:  getting a web module for people to segment images, and link those segments to ontology terms/metadata
   - There are desktop programs/algorithms that work, they are moving them to the web as 'modules'
     - TL;DR-Newer/better/shinier graph cuts
   - putting a module on iPlant BisQue that allows you to segment an image, and annotate it with ontologies.
     - Doing a test environment locally, will expand to testing groups that are larger
   - working with two students from CompSci 
     - 1. C++ and Matlab under the hood
     - 2. Matlab and python on the surface for UI

B. Update from Ontologies Working Group:

- LoL update:

 - moved from SVN to Github
   - all 4 of ours
   - some Crop ontology (maize wheat, rice, casava)
   - everyone needs github IDs for access to our project
     "john and george still need"

- Maria Angelique

 - Crop ontologies
   - uploading the 12 ontologies
   - mapping between crop ontologies, and ref. ontologies
 - RTB dev meeting
   - 3 days
   - discussing NGS
   - RTB with BTI will split the work
 - converting spreadsheets to ontology, but they lack complex mapping
   - Priority is mapping
   - using an automated tool
   - working with chris to develop a workflow
     - MAL has tried tools, chris has tools, need to find out what tool works best.
     - prospective mapping is better than reterospective mapping
   - Pankaj:  ideal goal is to have a tool available for the workflow
     - goal is to map back to reference ontology
       - power comes from the xproducts

C. Update from IT group- Data Store, AmiGO2- Justin Elser

Migration to github

  • Seems to be mostly complete. Let me know if there are any more files to transfer with history.

AmiGO 2

Fixed annotation loading issue (well, a workaround)

  • Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development.

- Justin Elser

 - all files (minus SVN) are over on github
 - AmiGO2.0
   - Far FAR faster
   - won't load any annotations
     - found a workaround with an old version of OWLtools
       "not ideal"
     - GO doesn't have this issue
   - Can ChrisS help?
     - can't help until the beginning of Sept.
     - if JE can't figure it out by sept, ChrisS can help
   - Post issues to Github's issues tracker on the Planteome-amigo2 repository
   - JE will have it up and down frequently, so be wary when you're 'testing' it.
   - iPlant won't get looked at until it is working on the live version
 - iPlant
   - where are we going to put the association files?
   - the association files are too big for Github
   - they are cluttered within the SVN
     - keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.
   - irods: iPlant's 'big iron' is a possibility
   - In the long run, it makes more sense to keep annotation/association files on iPlant
     - mirror the latest version from version control(SVN) over on iPlant for 'bulk download' options for end users.

D. Update from AISO/BisQue group- Justin Preece

E. Other Comments:

Next meeting Thursday Sept 24th, 2015