Difference between revisions of "WBConfCall 2020.02.06-Agenda and Minutes"
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= Agenda = | = Agenda = | ||
− | == | + | == Advisory Board Meeting == |
− | + | any dates/etc.? | |
+ | == RNASeq Meta-Data for AGR == | ||
+ | what are the plans? | ||
+ | * The EWG (high-throughput) has been discussing what kind of meta-data information to include for AGR 3.0. We will probably finalize the information table next Monday. Here is the meta-data table that we are looking at: | ||
+ | https://docs.google.com/spreadsheets/d/1H7bzMJVj6KevZHDGp61tCCdRo8ubHHzEKWaYu_7gn-w/edit#gid=0 | ||
+ | == Help Desk == | ||
+ | * Alaska memory bug? | ||
+ | Is there a link from WormBase to Alaska, and an announcement about its function? | ||
+ | |||
+ | == WormBase resources for non-coding RNA == | ||
+ | |||
+ | * Is it possible that Hinxton gives Caltech a tutorial on what kind of curation and resources that WormBase has for non-coding RNA? It will be very helpful for us to answer help-desk questions and future on-site tutorials. A zoom meeting will be good. | ||
------------- | ------------- | ||
Line 12: | Line 23: | ||
= Minutes = | = Minutes = | ||
− | == | + | == CalTech F2F meeting == |
− | * | + | * Need PS for this, but not on the call |
+ | |||
+ | SAB: | ||
+ | *Can teleconference for the grant and NIH | ||
+ | |||
+ | F2F: | ||
+ | * What do people want? Project meeting? | ||
+ | * AceDB datomic? - what do we want to do. | ||
+ | * Would be good to get together, could have a documentation session | ||
+ | * Punt this to the next call | ||
+ | * Have document of things to discuss as a group. | ||
+ | * What don't we want to discuss? | ||
+ | * Same room: Technical direction for the alliance Also curation priorities. Rebalancing what to prioritise, to produce a revised plan. | ||
+ | |||
+ | July 2018 OICR last one | ||
+ | |||
+ | Aim for F2F by June 2020 - California or alternative. | ||
+ | |||
+ | Doodle for meeting dates - April / May | ||
+ | |||
+ | Doc for agenda/topics | ||
+ | |||
+ | == RNASeq meta data == | ||
+ | * Mentioned in the DQM | ||
+ | * currently curated at both HX and CalTech | ||
+ | ** Need to have a working procedure. | ||
+ | ** Been through the whole table...almost have finalised schema - would be good to have the schema in the database | ||
+ | ** Deadline for V3 was last friday, but poss can add data in. | ||
+ | ** Wen will comunicate with Hinxton. | ||
+ | |||
+ | == Alaska == | ||
+ | * Project to J & Raymond working with Post Doc and UG student | ||
+ | * Post Doc moved on not sure of student support | ||
+ | * Not in state where WB can take it on? | ||
+ | * WB only getting bugs as Joseph put help@wormbase.org as contact | ||
+ | * Premature to release and link to WB. | ||
+ | |||
+ | == RNA resources == | ||
+ | Wen - added, not confident about answering HD issues. | ||
+ | Chris will be giving a talk so background would be good. | ||
+ | |||
+ | HelpDesk questions should be answering by HX | ||
+ | * Onsite meetings - Would be good to have knowledge provided to CalTech | ||
+ | * Some summarisation in the grant application. | ||
+ | * HX could create a tutorial with help from others about data mining etc. | ||
+ | * Persue feedback to drill down | ||
+ | * linking data types to references | ||
+ | * Follow with a blog | ||
+ | |||
+ | == Open Floor == | ||
+ | === Molecules === | ||
+ | * WormBase approached by Frank Schroeder + Others about having Molecules that don't have chemical structures | ||
+ | but do have Chem formula and retention times and MS peaks | ||
+ | |||
+ | * Karen working with this | ||
+ | * Molecule model update to store this. | ||
+ | * PD will help with model | ||
+ | * Retention times will need in-relation-to markers so all 4 groups will work from common protocols | ||
+ | * Questions people will want to know is what is there in the rel retention range that has these peaks | ||
+ | * People aren't going to synthesize and work out all 20k compounds | ||
+ | * Storage 1st then mining and analysis tools. | ||
+ | * Groups are competing so would be good for WB to bring data together | ||
+ | |||
+ | == Widget feedback == | ||
+ | * Adam - Several widgets are being developed to replace existing function | ||
+ | * Homology | ||
+ | * more widgets | ||
+ | |||
+ | To make comments on open tickets on the github for these. |
Latest revision as of 18:39, 6 February 2020
Contents
Agenda
Advisory Board Meeting
any dates/etc.?
RNASeq Meta-Data for AGR
what are the plans?
- The EWG (high-throughput) has been discussing what kind of meta-data information to include for AGR 3.0. We will probably finalize the information table next Monday. Here is the meta-data table that we are looking at:
https://docs.google.com/spreadsheets/d/1H7bzMJVj6KevZHDGp61tCCdRo8ubHHzEKWaYu_7gn-w/edit#gid=0
Help Desk
- Alaska memory bug?
Is there a link from WormBase to Alaska, and an announcement about its function?
WormBase resources for non-coding RNA
- Is it possible that Hinxton gives Caltech a tutorial on what kind of curation and resources that WormBase has for non-coding RNA? It will be very helpful for us to answer help-desk questions and future on-site tutorials. A zoom meeting will be good.
Minutes
CalTech F2F meeting
- Need PS for this, but not on the call
SAB:
- Can teleconference for the grant and NIH
F2F:
- What do people want? Project meeting?
- AceDB datomic? - what do we want to do.
- Would be good to get together, could have a documentation session
- Punt this to the next call
- Have document of things to discuss as a group.
- What don't we want to discuss?
- Same room: Technical direction for the alliance Also curation priorities. Rebalancing what to prioritise, to produce a revised plan.
July 2018 OICR last one
Aim for F2F by June 2020 - California or alternative.
Doodle for meeting dates - April / May
Doc for agenda/topics
RNASeq meta data
- Mentioned in the DQM
- currently curated at both HX and CalTech
- Need to have a working procedure.
- Been through the whole table...almost have finalised schema - would be good to have the schema in the database
- Deadline for V3 was last friday, but poss can add data in.
- Wen will comunicate with Hinxton.
Alaska
- Project to J & Raymond working with Post Doc and UG student
- Post Doc moved on not sure of student support
- Not in state where WB can take it on?
- WB only getting bugs as Joseph put help@wormbase.org as contact
- Premature to release and link to WB.
RNA resources
Wen - added, not confident about answering HD issues. Chris will be giving a talk so background would be good.
HelpDesk questions should be answering by HX
- Onsite meetings - Would be good to have knowledge provided to CalTech
- Some summarisation in the grant application.
- HX could create a tutorial with help from others about data mining etc.
- Persue feedback to drill down
- linking data types to references
- Follow with a blog
Open Floor
Molecules
- WormBase approached by Frank Schroeder + Others about having Molecules that don't have chemical structures
but do have Chem formula and retention times and MS peaks
- Karen working with this
- Molecule model update to store this.
- PD will help with model
- Retention times will need in-relation-to markers so all 4 groups will work from common protocols
- Questions people will want to know is what is there in the rel retention range that has these peaks
- People aren't going to synthesize and work out all 20k compounds
- Storage 1st then mining and analysis tools.
- Groups are competing so would be good for WB to bring data together
Widget feedback
- Adam - Several widgets are being developed to replace existing function
- Homology
- more widgets
To make comments on open tickets on the github for these.