Difference between revisions of "WBConfCall 2016.03.17-Agenda and Minutes"
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* Datomic (Adam) | * Datomic (Adam) | ||
* Visualizing human variations on worm genome (Siby) | * Visualizing human variations on worm genome (Siby) | ||
− | * JBrowse (Scott) | + | * JBrowse & GBrowse (Scott) Looking at up grading to recent release of JBrowse, includes [http://dev.wormbase.org:10004/?data=data%2Fc_elegans_simple&loc=I%3A9859465..9880430&tracks=PHA-4%20(Pol%20II%20ChIP)%3A%20Combined%2CCurated%20Genes%20(protein%20coding)%2CCurated_Genes&highlight= "fancier" glyphs and subtracks that don't quite work] :-/ (the subtracks only load after you pan from the original starting position) |
+ | ** Scott will write a tutorial for uploading and sharing data | ||
+ | ** Will also inquire about JBrowse supporting UCSC track hub | ||
== OMIM linking to WormBase == | == OMIM linking to WormBase == | ||
Line 15: | Line 17: | ||
=Minutes= | =Minutes= | ||
+ | == Progress update by web team members == | ||
+ | * (Todd can't make today's call due to a conflict with RRID call) | ||
+ | === Datomic (Adam) === | ||
+ | * Transitioning Datomic build process to EBI team | ||
+ | * Setting up website to partially backed by Datomic | ||
+ | * Will have a version of the website running partially on Datomic available for testing | ||
+ | * Q: what does DynamoDB do? | ||
+ | ** A: it runs the production Datomic database on Amazon cloud. It’s intended for high performance and low maintenance. | ||
+ | |||
+ | === Visualizing human variations on worm genome (Siby)=== | ||
+ | * creating a schematic drawing for human and worm gene comparison and map variations onto it | ||
+ | * getting alignment and annotation (exon and domain) from ParaSite API | ||
+ | * will have a prototype ready for testing in a week | ||
+ | * will check out Ensembl REST API for mapping and searching by variation RRSID | ||
+ | |||
+ | === JBrowse & GBrowse (Scott)=== | ||
+ | * Looking at up grading to recent release of JBrowse, includes [http://dev.wormbase.org:10004/?data=data%2Fc_elegans_simple&loc=I%3A9859465..9880430&tracks=PHA-4%20(Pol%20II%20ChIP)%3A%20Combined%2CCurated%20Genes%20(protein%20coding)%2CCurated_Genes&highlight= "fancier" glyphs and subtracks that don't quite work] :-/ (the subtracks only load after you pan from the original starting position) | ||
+ | ** Scott will write a tutorial for uploading and sharing data | ||
+ | ** Will also inquire about JBrowse supporting UCSC track hub | ||
+ | |||
+ | === OMIM linking to WormBase === | ||
+ | From Ranjana: Kevin and Paul D, I see that you both are working on this (#4656 on GitHub), for WS253? Would you please get in touch with OMIM to let them know? | ||
+ | * EBI will run code that replaces the outdated file with symlinks to files built in the latest release | ||
+ | * Ranjana and Paul will communicate with OMIM about the options for updating the links | ||
+ | |||
+ | ==Unresolved Help Desk Issues== | ||
+ | * Many thanks to you all for helping me answering questions submitted to help desk! | ||
+ | * gene_interactions FTP file not made during website staging process [https://github.com/WormBase/website/issues/4655 4655] | ||
+ | ** Todd and Sibyl will work on | ||
+ | * Account email & password reset request [https://github.com/WormBase/website/issues/4659 4659] | ||
+ | ** Todd and Sibyl will come up with protocol for: password and user email reset for WormBase account and migrating existing account to 3rd party login | ||
+ | * transpozable element sequence | ||
+ | ** Q: How to get the full sequence (not just the mRNA region) | ||
+ | ***A: not available as a precomputed file. User has to parse the GFF and sequence file to get it. |
Latest revision as of 17:29, 17 March 2016
Agenda
Progress update by web team members
- (Todd can't make today's call due to a conflict with RRID call)
- Datomic (Adam)
- Visualizing human variations on worm genome (Siby)
- JBrowse & GBrowse (Scott) Looking at up grading to recent release of JBrowse, includes "fancier" glyphs and subtracks that don't quite work :-/ (the subtracks only load after you pan from the original starting position)
- Scott will write a tutorial for uploading and sharing data
- Will also inquire about JBrowse supporting UCSC track hub
OMIM linking to WormBase
From Ranjana: Kevin and Paul D, I see that you both are working on this (#4656 on GitHub), for WS253? Would you please get in touch with OMIM to let them know?
Unresolved Help Desk Issues
- Many thanks to you all for helping me answering questions submitted to help desk!
- gene_interactions FTP file not made during website staging process 4655
- Account email & password reset request 4659
Minutes
Progress update by web team members
- (Todd can't make today's call due to a conflict with RRID call)
Datomic (Adam)
- Transitioning Datomic build process to EBI team
- Setting up website to partially backed by Datomic
- Will have a version of the website running partially on Datomic available for testing
- Q: what does DynamoDB do?
- A: it runs the production Datomic database on Amazon cloud. It’s intended for high performance and low maintenance.
Visualizing human variations on worm genome (Siby)
- creating a schematic drawing for human and worm gene comparison and map variations onto it
- getting alignment and annotation (exon and domain) from ParaSite API
- will have a prototype ready for testing in a week
- will check out Ensembl REST API for mapping and searching by variation RRSID
JBrowse & GBrowse (Scott)
- Looking at up grading to recent release of JBrowse, includes "fancier" glyphs and subtracks that don't quite work :-/ (the subtracks only load after you pan from the original starting position)
- Scott will write a tutorial for uploading and sharing data
- Will also inquire about JBrowse supporting UCSC track hub
OMIM linking to WormBase
From Ranjana: Kevin and Paul D, I see that you both are working on this (#4656 on GitHub), for WS253? Would you please get in touch with OMIM to let them know?
- EBI will run code that replaces the outdated file with symlinks to files built in the latest release
- Ranjana and Paul will communicate with OMIM about the options for updating the links
Unresolved Help Desk Issues
- Many thanks to you all for helping me answering questions submitted to help desk!
- gene_interactions FTP file not made during website staging process 4655
- Todd and Sibyl will work on
- Account email & password reset request 4659
- Todd and Sibyl will come up with protocol for: password and user email reset for WormBase account and migrating existing account to 3rd party login
- transpozable element sequence
- Q: How to get the full sequence (not just the mRNA region)
- A: not available as a precomputed file. User has to parse the GFF and sequence file to get it.
- Q: How to get the full sequence (not just the mRNA region)