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.