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| | [[WormBase-Caltech_Weekly_Calls_January_2013|January]] | | [[WormBase-Caltech_Weekly_Calls_January_2013|January]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_February_2013|February]] |
| − | = February 7, 2013 =
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| − | Person Cytoscape
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| − | *Person-person network viewing on website
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| − | *Use person lineages
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| − | *Will discuss with web team
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| − | WormBook History
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| − | *Paul editing a person history section, starting with John White
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| − | *Can use history info to link people
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| − | Binary vs. Non-binary interaction display
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| − | *Cytoscape and interaction table are only displaying interactions as binary interactions, regardless of number of interactors
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| − | *We need to assess how many interactions we have that have more than 2 interactors
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| − | *Once we have assessed that, we should discuss with web team about how to display these cases
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| − | | |
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| − | Curation Statistics
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| − | *Wen can generate numbers for Citace AND the complete build (rather than Hinxton)?
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| − | *Will let Hinxton build the queries
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| − | *End-of-build summary for curators (with more database technical numbers) separate from the Release Notes for public (with more biologically interesting numbers)
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| − | *Will separate Wiki page into two sections to reflect this
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| − | *Public info will continue to be displayed in Release Notes
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| − | *Internal info - where should that be displayed?
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| − | Postgres info table (on [[OA_forms,_tables,_scripts,_etc|Wiki page]])
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| − | *Curators will continue to add info to Wiki on scripts, dependencies, ontologies, etc. for each Ontology Annotator
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| − | | |
| − | | |
| − | Intermine
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| − | *JD gave short demo yesterday
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| − | *Will give another tutorial next week (Thursday, Feb 14, 2013 - 8:30am PST)
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| − | *Curators can/should test
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| − | | |
| − | | |
| − | Nick Brown visit
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| − | *PI of FlyBase Cambridge
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| − | *Will be here tomorrow around 11am
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| − | | |
| − | = February 21, 2013 =
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| − | | |
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| − | WS237 Upload March 1, 2013
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| − | *Citace upload on February 28
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| − | | |
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| − | WS236 will go live on April 5, 2013
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| − | *One week later than previously planned (March 29th)
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| − | | |
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| − | New genome assemblies and gene names across species
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| − | *How do we handle independent, conflicting genome assemblies and gene models?
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| − | *Can we collect all gene models, for example, without any bias and display any info we have?
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| − | *How might we display conflicting models, etc.?
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| − | *Should we prioritize easier-to-handle, "more important" genomes?
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| − | *Can we establish automated (minimal manual effort) pipeline to handle these issues?
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| − | | |
| − | | |
| − | Expression graphs
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| − | *Wen and Daniela have been generating expression graphs
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| − | *Yanai probes need to be mapped
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| − | *Multiple probes mapped to the same gene will be averaged
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| − | *SPELL construction has changed; all data sets exist as separate flat files
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| − | | |
| − | | |
| − | Expression table
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| − | *Table of expression data to display all details of an expression pattern object
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| − | *Place in separate widgets on the gene page
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| − | *Perhaps, separate large-scale from small-scale studies
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| − | | |
| − | | |
| − | Phenotype Ontology
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| − | *How stable/complete is the current phenotype ontology?
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| − | *Good, but we may consider a reconstruction/re-ordering of existing terms
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| − | *Group phenotypes by e.g. anatomy term, life stage, etc.?
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| − | *Link anatomy terms, life stages to relevant phenotypes (at .ACE level or website level)
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| − | *Perhaps use cross-products of various ontologies to get the same effect?
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| − | *May want to consider using .OWL format as opposed to .OBO
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| − | *Need a sustainable, long-term approach to maintaining the ontologies
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| − | *AMIGO 2 only consumes .OWL format, not .OBO
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| − | *Should we consider switching to Protege, as a local ontology browser/editor (as opposed to OBO-Edit)?
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| − | | |
| − | | |
| − | LEGO Call
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| − | *How to use annotation extensions for LEGO model?
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| − | *Consistent use?
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| − | | |
| − | Intermine
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| − | *Target for first release, minimal functionality for sequence-based queries
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| − | *JD working on importing sequence-based data
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| − | *How much can we get into Intermine by the first freeze/release (in April)?
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| − | *How should we prioritize?
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| − | *Can we build a "worm-version" of FlyMine (existing classes, e.g.)?
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| − | **Probably not a good approach for first release in April, but maybe useful for long-term
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| − | *Production server (unstable) vs live/testing server (more stable)
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| − | *Major testing will start in April
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| − | | |
| − | | |
| − | Staging tests
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| − | *WS236 Staging site now available
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| − | *Everyone should test rigorously
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| − | | |
| − | | |
| − | [http://www.celegans.org/2013/ 2013 International Worm Meeting]
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| − | *WormBase workshop
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| − | *What do we need to consider/prepare for, for the meeting?
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| − | *Someone should be in touch with organizers?
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| − | *Who are the organizers?
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| − | **Monica Colaiacovo and Ralf J. Sommer
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| − | *WormBase souvenirs?
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| − | | |
| − | | |
| − | Dead genes
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| − | *Going to add "Historical_gene" tag to relevant class models (e.g. ?Interaction, ?Expr_pattern, ?Transgene, etc.)
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| − | *Will modify OA dumping scripts with Juancarlos to automate recognition of dead genes and replace them (if merged)
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| − | *Dumper will add remark about existence of dead gene in original object
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| − | *Will consider adding original gene reference through #Evidence hash under "Published_as" tag, as Other_name (gene synonym), as possibly as a separate free-text tag in the models that captures the verbatim reference to the original gene
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| − | *Will not try to re-annotate old objects WRT the gene synonyms/verbatim references, but can consider doing this going forward only
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| − | | |
| − | | |
| − | Transgenes
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| − | *CGC transgenes have been completed/unified with existing WBTransgene objects
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| − | *Updating new CGC strains will become a monthly task
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| − | | |
| − | | |
| − | GO task
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| − | *Can we link two or more genes based on ,e.g., process for enrichment analysis?
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| − | *What should we be getting out of enrichment analyses that we aren't currently?
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| − | *Link all genes as part of "FGF signaling", "DAF-2 signaling", "PAR genes", etc.
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| − | *Gene sets based on pathway, process, etc.
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| − | *Intermine should be able to filter by these means (eventually)
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| − | | |
| − | | |
| − | | |
| − | = February 28, 2013 =
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| − | | |
| − | WS237 Upload
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| − | *Upload happening today
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| − | *May be some delay due to script issues (being fixed)
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| − | *Transgene and Life Stage are all set
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| − | | |
| − | | |
| − | BioCurator meeting coming up
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| − | *Karen, Kimberly, Michael, and Daniela going
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| − | *Topics: entity recognition, curation pipelines
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| − | | |
| − | | |
| − | Kimberly attended [http://www.nescent.org/ NESCENT] summit
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| − | *Meeting: Resource Coordination for NESCENT group, Text mining for annotations
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| − | *Kimberly spoke about Textpresso
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| − | *Setting up Textpresso for butterfly?
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| − | *Amer Soc Plant Bio attended, wanted to know more about Genetics/G3 markup pipeline
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| − | | |
| − | | |
| − | [http://wiki.galaxyproject.org/Events/Caltech2013 Galaxy workshop] next Tuesday, March 5, 2013
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| − | *Biologists workshop 11am - 2pm, in Braun 151
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| − | *Lunch provided
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| − | *Register [https://docs.google.com/forms/d/1BaJHJT0HmnGe9E_hY21t62rWdb2MyocO1bo-bYMY1a8/viewform here]
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| − | *Web-based platform for sequence analysis
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| − | *Protein trees, alignments, RNA-seq data
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| − | *Run remotely or locally as a server
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| − | | |
| − | | |
| − | Bioinformatics Club
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| − | *Could start a LinkedIn group (Caltech BioInformatics "huddle" group?)
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| − | *Main goal: find out who's on campus and what they do
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| − | *What are most people interested in?
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| − | *Create forum and wiki page?
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| − | *Mitch Guttman coming this summer, maybe give intro talk?
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| − | *Georgi Marinov in Wold lab
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| − | | |
| − | | |
| − | Xiaodong visited two labs in Bejing
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| − | *Gave WormBase tutorials
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| − | *Lab is still using legacy site
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| − | *Said they had trouble finding things on new site
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| − | *Xiaodong showed SPELL and modENCODE data
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| − | *WormMart demo and some queries
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| − | *~30 C. elegans labs in China, and growing?
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| − | *Xiaodong encouraged them to send questions to WormBase Help
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| − | *Someone (WB person) should go to the Asia WormBase meeting (every 2 years)
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| − | | |
| − | | |
| − | Intermine/Wormmine workshop at 2013 IWM
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| − | *Organizers:
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| − | **Monica Colaiacovo (mcolaiacovo AT genetics DOT med DOT harvard DOT edu)
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| − | **Ralf J. Sommer (ralf DOT sommer AT tuebingen DOT mpg DOT de)
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| − | *WormMine session in WormBase workshop
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| − | *Who (at WB) will organize workshop? Michael Paulini
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| − | | |
| − | | |
| − | WormBase website questionaire:
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| − | *What do people find on the legacy that they can't find on the new site?
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| − | **SNPs, validated vs. predicted
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| − | *Have posters and/or live demos at poster sessions? Walk around with tablets?
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| − | *We can make YouTube videos:
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| − | **5 minutes or less
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| − | **Could triage topics in a topics tree on Wiki page
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| − | **Curators could check-off certain queries as they make them
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| − | | |
| − | | |
| − | WikiPathways
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| − | *Building templates with genes and an "Arrow" key, with different connection types
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| − | *They're building now (should be done soon)
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