Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Users will need to rely heavily on query templates and lists | *Users will need to rely heavily on query templates and lists | ||
*Once a user has a basic understanding of certain Intermine procedures, many other queries are possible | *Once a user has a basic understanding of certain Intermine procedures, many other queries are possible | ||
| + | *We are generating many GitHub issues now; JD will have to triage | ||
| + | *How do we best indicate priority of issues? IWM milestone? | ||
| + | *JD may be willing to take in new tags for existing data types, but is unlikely to accept any new data types | ||
Revision as of 18:53, 24 May 2013
2013 Meetings
May 2, 2013
Intermine
- Google Doc for collecting questions, comments and data here
- Example queries/questions
- How to get GO terms for a list of genes?
- Check FlyMine as a positive control (for functionality and templates)
International Worm Meeting
- Souvenirs: espresso cups!
- Posters
- We will generate templates for posters and send around
- We can't/won't get the extra space we hoped to get, as of right now
- Will have to put posters in their designated locations, unless something changes
Computers
- Do we need new computers? Could order by June
- Spica getting old
- Elbrus? Tenaya?
- New server?
- Postgres backup? Currently on external hard drives. Amazon backup? Network hard drives?
- On tazendra, users can store files on /home2
- Mac users have local backup (Time Machine); critical content should be backed up elsewhere also, perhaps
May 9, 2013
Handling Dead Genes
- Dumping process changes outlined here
- Will get sorted out before the WS239 upload
- Chris will begin with Juancarlos
IWM Preparations
- Workshops
- Posters
- Need a template
- Text and figures can be assembled in meantime
- Souvernirs
- Espresso cups
- Need a logo: worm shape with "WormBase" above/below it
WormBase Outreach YouTube Channel
- Mac users can upload directly from Quicktime
- Can capture tutorials in response to user requests as well as for upcoming IWM Workshops
- YouTube account name: outreach@wormbase.org
Next citace upload
- By 10am on Friday June 21st, 2013
AMIGO2
- Slowly progressing at core development side
- Raymond & Juancarlos working on incorporation of AMIGO2 into WormBase
- Eventually we will embed AMIGO2 features into WormBase pages
May 16, 2013
New server
- Raymond ordered a new server computer
- Should be able to support services currently run on older hardware (e.g. Spica)
- Will (physically) live in the server room
- 2 cpus, 64 GB RAM
- Name? WormBase? WormBase 1?
WormMine Tutorial
- Next Wednesday, May 22, 2013 12pm
- Additional tutorial Friday at 2pm
WormMine
- Problem: many genes are in intermine only as UniProt IDs from the GO Gene Association File (GAF)
- We either want to:
- 1. Remove these (UniProt-based) gene entries entirely OR
- 2. Keep the gene entries, change the UniProt IDs to WBGene IDs, and pull in the "Assigned By" field from the GO GAF to appropriately attribute UniProt as the source for relevant GO Annotations
- GO pipeline still in flux, so we will have to wait until that is settled before we establish a long term pipeline for this
- GO Policy: Every MOD is responsible for their respective organism's GAF
- We rely on Protein-to-GO annotation/mapping followed by Protein-to-Gene mapping
March 24, 2013
IWM
- Giveaways - designed, planning the order now
- Workshops
- Posters
- Each of our posters gets a designated place during one of three sessions
- Room for two posters at the WormBase booth
Release Schedule
- Timeline proposal by Karen
- Upload can happen as early as models are frozen
- Need time to test data with models
- Need to allow time for errors/mistakes
- 3 days between models freeze and upload?
- Freeze models on Thursday morning (Pacific time), test for ~3 working days, upload data by Tuesday morning (Pacific time)
Historical genes
- Interaction and Gene_regulation OA dumpers working OK
- Can follow documentation on Interaction Wiki page
WormMine
- JD has been giving tutorials
- Not intuitive, learning curve
- Infinite nested loops from cross-references
- Users will need to rely heavily on query templates and lists
- Once a user has a basic understanding of certain Intermine procedures, many other queries are possible
- We are generating many GitHub issues now; JD will have to triage
- How do we best indicate priority of issues? IWM milestone?
- JD may be willing to take in new tags for existing data types, but is unlikely to accept any new data types
