Difference between revisions of "WormBase-Caltech Weekly Calls"
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*GO Policy: Every MOD is responsible for their respective organism's GAF | *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 | *We rely on Protein-to-GO annotation/mapping followed by Protein-to-Gene mapping | ||
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| + | = March 24, 2013 = | ||
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| + | Topics | ||
| + | *IWM | ||
| + | **Workshops | ||
| + | **Posters | ||
| + | *Historical genes | ||
| + | *WormMine | ||
Revision as of 18:04, 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
Topics
- IWM
- Workshops
- Posters
- Historical genes
- WormMine
