Thursday Aug 20th, 2015: Difference between revisions
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* bring in OSU Conferences cordinators to help manage logistics | * 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 | |||
- Chris' update/demo of new AmiGO curation pathway. | - Chris' update/demo of new AmiGO curation pathway. | ||
"11am next wed" | "11am next wed" | ||
- Next all hands: sept 24th (likely to change) | - Next all hands: sept 24th (likely to change) | ||
- Justin Elser | - Justin Elser | ||
Revision as of 19:00, 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
- Chris' update/demo of new AmiGO curation pathway. "11am next wed" - Next all hands: sept 24th (likely to change)
- 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.
- 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:
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.