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| | [[WormBase-Caltech_Weekly_Calls_January_2011|January]] | | [[WormBase-Caltech_Weekly_Calls_January_2011|January]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_February_2011|February]] |
| − | == February 2, 2012 ==
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| − | EPIC data into WormBase
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| − | *Daniela spoke to John Murray
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| − | *Need to modify model and display for data
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| − | *3D movies as ?Movie objects
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| − | Endrov
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| − | *Tom Burglin and student Johan Henriksson developed Endrov.net (http://www.endrov.net)
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| − | *May be able to incorporate Endrov visualizations of Blender model and cell lineage into WormBase website?
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| − | *Need to talk to Todd and Web team
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| − | Elsevier legal issues
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| − | *Science-direct website links to-and-from WormBase website
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| − | *Daniela still working with contacts at MGI (Mouse Genomics Institute/Jackson Labs) & Elsevier
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| − | *MGI already has established links with Elsevier
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| − | New ?Interaction model
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| − | *Update old objects and speak to web team about new model before officially incorporating new ?Interaction model
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| − | == February 9, 2012 ==
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| − | Interaction model
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| − | *Added some XREFs (in Interactor tag) and Chromatin_IP to Detection method
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| − | *Co-Immunoprecipitation would be captured under Detection method "Affinity Capture Western"
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| − | *Worked out changes needed for old *.ACE files to fit new model; will give to Juancarlos to script
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| − | Transgene
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| − | *Daniela, Juancarlos, and Karen imported Extrachromosomal array transgenes into the Transgene OA
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| − | *Extrachromosomal array transgenes for which authors have not provided a name will be named Expr####_Ex
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| − | *Maybe we will name according to paper e.g. "WBPaper########_Ex####"
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| − | *Daniela and Karen will discuss cost-benefit of objectifying Ex transgenes
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| − | *Rather than determine transgene sequence (or partial sequence), curators will (as they have been for Expr_pattern) add free-text describing the sequence
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| − | **This includes: primer sets, restriction digest sites, etc.
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| − | **Continue to place this info in the Reporter_gene tag
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| − | **Maybe add an additional free-text field (Sequence_info tag?)
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| − | Displaying curator names on new website
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| − | *Should we display curators' names on their curated objects?
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| − | *Currently only on concise description; why not do all objects?
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| − | *Keep curator name info only internal?
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| − | *Prevent curator names from being dumped for build/release?
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| − | *Should include 'Date-last-updated' Evidence dump
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| − | *Curator confirmed note could be placed in Tree View for all data types
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| − | Incremental Updates
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| − | *Should we perform incremental updates?
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| − | *Update as frequently as possible?
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| − | *Web display (of updates) served from Postgres/Tazendra?
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| − | *Serve RESTful widget from Caltech?
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| − | *Caltech in agreement about pushing forward with incremental updates
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| − | | |
| − | == February 16, 2012 ==
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| − | Gene product annotation for variation
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| − | *Variation affects gene product: absent, disfunctional, isoform-specific effects
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| − | *How is this best captured?
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| − | *Report as a phenotype? "RNA expression variant", "protein expression variant", etc...
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| − | *Capture as a gene_regulation event? Soon will be interaction object...
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| − | *Sequence ontology?
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| − | *Captured in ?Variation?
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| − | *Ask Hinxton/Mary Ann Tuli
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| − | Interaction model
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| − | *Old objects updated OK and read into ACEDB without problems
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| − | *Need to discuss updates with Web team
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| − | *Will send all updated *.ACE files with old Gene_regulaion, Interaction, and YH objects
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| − | *Add two zeros to the Interaction IDs in postgres OA tables once all current interaction objects uploaded to the Interaction OA
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| − | | |
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| − | Transgene naming
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| − | *New extrachromosomal arrays will get "WBPaper###_Ex###" type of ID
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| − | | |
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| − | SPELL Issues
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| − | *Problems coming up as data size increasing
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| − | *SPELL server at Amazon running at lowest paid instance ($1000/yr)
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| − | *4GB memory needed (more than 132-bit machine can provide) for loading data
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| − | *64-bit machine will cost $4000 per year
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| − | *Run SPELL on canopus? Yes but, have to take care of sys-admin issues
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| − | *$500/quarter for IMSS machine maintenance
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| − | *Talk to Matt Hibbs? Maybe need to optimize the process at that step
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| − | | |
| − | | |
| − | BioCreative/BioCurator meetings
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| − | *Kimberly working with DictyBase
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| − | *Kimberly will give 2 talks (CCC and molecular function automated curation)
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| − | *WormBase workflow; Kimberly will discuss with individual curators in March
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| − | *Arun submitted abstract
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| − | | |
| − | | |
| − | GO Consotrium meeting in a week and a half
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| − | *Paul, Michael (Muller) and Kimberly going
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| − | | |
| − | | |
| − | Human diseases will be objectified
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| − | == February 23, 2012 ==
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| − | | |
| − | | |
| − | BioCurator Meeting
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| − | *Karen, Arun, Kimberly, Michael and Yuling are going
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| − | *QCFast poster accepted for presentation
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| − | | |
| − | | |
| − | GO Consortium meeting this weekend
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| − | *Things to bring up at meeting?
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| − | *Responses to questionnaires
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| − | | |
| − | Purchase OA Domain name?
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| − | *Move to a more formal link aside from mangolassi
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| − | *wormbase domain name?
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| − | *Cost? ~$11/year
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| − | *"Ontology Annotator" may not be best name
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| − | *"Curatool" and "Biocuratool" available; the "curinator"? Curate at your "curinal"? ;)
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| − | *Currently only a static site
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| − | *GO Consortium may want to use the tool
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| − | | |
| − | | |
| − | GO Upload
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| − | *Going back and forth on deciding frequency of upload
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| − | *Currently back to two-month uploads
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| − | *We can certainly change frequency
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| − | *Two-month cycle for upload (in sync with WormBase) is too long of a cycle for GO curation
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| − | *Change GO curation upload to once per month (twice per month?)
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| − | *Things will change when curating through a GO curation interface
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| − | | |
| − | | |
| − | SPELL server on Amazon
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| − | *1)Existing paid service doesn't seem to be stable
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| − | **Looking at log file did not reveal anything
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| − | **No reply from Matt Hibbs
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| − | *2)Amazon installation cannot be updated to WS229 because the dataset demands more memory
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| − | **Raymond tried to install a 64-bit machine (free); wouldn't work
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| − | *We're stuck without more technical support (wrt Amazon service)
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| − | *Host ourselves (on canopus?) until OICR will take over? (When OICR is ~done with Beta site)
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| − | *Host through IMSS?
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| − | *WormMart is the only function of caprica; maybe setup SPELL on caprica for time being (next couple of months)
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| − | *Will Gary Williams et al add more RNA-Seq data?
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| − | *Athena (8GB memory?)
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| − | *Instead of virtual machines, have one machine that does everything
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| − | *SPELL usage? Not very much, but several (consistent users (300-900 queries per month)
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| − | *Farm out to Matt Hibbs? Matt not serving data
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| − | *Who is in charge of SPELL at SGD? How does SGD feel about SPELL? Ask Mike Cherry
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| − | *Problem with hosting at OICR if SPELL needs tinkering...
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| − | *Can Wen access and manipulate if at OICR? Not easy
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| − | *SPELL has LOTS of data (millions of lines)
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| − | *Will try to run locally for short term; meanwhile look for more resilient plan
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| − | *Kimberly can ask Cara Delinsky (sp?) about SPELL
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| − | | |
| − | | |
| − | RNAi parsing script
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| − | *Wen would like to work on
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| − | *Updated more than a year ago
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| − | *Should be able to parse interaction data directly into OA
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| − | *Would like to handle new variations and transgenes
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| − | *Script should look in Postgres tables
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| − | *Still need to deal with DNA sequence text mapping to genome/genes
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| − | *Elbrus a very old machine; very slow
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| − | *Install ace-server on tazendra?
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| − | *Ideal: OA takes/handles bulk of data; just run a script on the side to handle mapping DNA sequence to the genome
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| − | *We will build the RNAi OA
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| − | | |
| − | | |
| − | Transgene naming strategy
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| − | | |
| − | *We will stick to the Expr1234_Ex naming as naming after WBPaper was giving problems (i.e. dealing with 430 objects with no Paper attached and other minor issues).
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| − | *For a complete record of the process check wiki: http://wiki.wormbase.org/index.php/Expression_Pattern#Exporting_Reporter_Gene_description_from_Expr_pattern_OA_to_Transgene_OA
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