Difference between revisions of "Hinxton 2015.08- Meeting minutes"

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= August 2015 =
 
= August 2015 =
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 +
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==August 14, 2015 ==
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In attendance: KH, TD, PD, GW, BB, MP
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 +
=== Database migration ===
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 +
* Security discussion
 +
** Script will authenticate to the application using self-signed SSL certificates
 +
** What level of granularity for the certificates? Per center? Per user? Per update type (e.g. a separate cert for each build step)
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* Transaction log
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** Web app now allow unrolling of recent transactions
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** Functionality added to detect when unrolling of a T impacts on Ts made subsequently (e.g. T1 makes object, T2 refers to object, user attempts to undo T1).
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* Environment
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** GW had trouble previously getting Datomic running on EBI machine on nfd-mounted storage.
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** The free storage engine with Datomic assumes/requires low-latency (ideally directly attached) storage
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** GW to try again on acedb.ebi.ac.uk using /nfs/acedb/vol1 (purportedly low-latency storage)
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* 2-way XEFS with different attached # models at either end
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** e.g. Gene -> Variation (#Evidence), Variation -> Gene (#Molecular_change)
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** New db puts #model annotation of the edges of the graph, so does not currently support this.
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** Discussed possible workarounds
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* Loading Ace into Datomic
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** Some testing done by GW, works well
 +
 +
=== Build 250 ===
 +
 +
* Status
 +
** BLAST - all 9 species run, dumped and loaded
 +
** Compara - finished and loaded
 +
** RNASeq - in progress
 +
* General problems/fire-fighting
 +
** Transcript builder (mysteriously did not complete for two genomes)
 +
** InterProScan (found a bug in the Ensembl code, fixed and provided patch)
 +
** BLAST dumping (exceeded MySQL max connections. Needed to tweak server conf)
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 +
=== ParaSite ===
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* Redesign of homepage
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** Beta version demonstrated. Will circulate some other possible layouts
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* New blog for ParaSite
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** wbparasite.wordpress.com
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=== Data integration / curation ===
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* Brugia
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** Produced initial annotation of new assembly.
 +
**MP presented to Brugia analysis group in conference call
 +
* C. elegans
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** DB_remark clean up -> Brief_identification, pseudogenes (will go in as a note in ENA submissions)
 +
** Classification pseudogenes. Will need a new unitary pseudogene tag in ?Pseudogene model
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** Consolidation of UniProt product names into the database
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** SVM paper => gene curation
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** Proteomics data from Lamond lab
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== August 6, 2015 ==
 
== August 6, 2015 ==

Revision as of 12:12, 14 August 2015

August 2015

August 14, 2015

In attendance: KH, TD, PD, GW, BB, MP

Database migration

  • Security discussion
    • Script will authenticate to the application using self-signed SSL certificates
    • What level of granularity for the certificates? Per center? Per user? Per update type (e.g. a separate cert for each build step)
  • Transaction log
    • Web app now allow unrolling of recent transactions
    • Functionality added to detect when unrolling of a T impacts on Ts made subsequently (e.g. T1 makes object, T2 refers to object, user attempts to undo T1).
  • Environment
    • GW had trouble previously getting Datomic running on EBI machine on nfd-mounted storage.
    • The free storage engine with Datomic assumes/requires low-latency (ideally directly attached) storage
    • GW to try again on acedb.ebi.ac.uk using /nfs/acedb/vol1 (purportedly low-latency storage)
  • 2-way XEFS with different attached # models at either end
    • e.g. Gene -> Variation (#Evidence), Variation -> Gene (#Molecular_change)
    • New db puts #model annotation of the edges of the graph, so does not currently support this.
    • Discussed possible workarounds
  • Loading Ace into Datomic
    • Some testing done by GW, works well

Build 250

  • Status
    • BLAST - all 9 species run, dumped and loaded
    • Compara - finished and loaded
    • RNASeq - in progress
  • General problems/fire-fighting
    • Transcript builder (mysteriously did not complete for two genomes)
    • InterProScan (found a bug in the Ensembl code, fixed and provided patch)
    • BLAST dumping (exceeded MySQL max connections. Needed to tweak server conf)

ParaSite

  • Redesign of homepage
    • Beta version demonstrated. Will circulate some other possible layouts
  • New blog for ParaSite
    • wbparasite.wordpress.com

Data integration / curation

  • Brugia
    • Produced initial annotation of new assembly.
    • MP presented to Brugia analysis group in conference call
  • C. elegans
    • DB_remark clean up -> Brief_identification, pseudogenes (will go in as a note in ENA submissions)
    • Classification pseudogenes. Will need a new unitary pseudogene tag in ?Pseudogene model
    • Consolidation of UniProt product names into the database
    • SVM paper => gene curation
    • Proteomics data from Lamond lab


August 6, 2015

In attendance: KH, PD, MP, TD, BB

Build 250

  • In progress. MP doing all 9 core species (no precedent for this).
  • First build from github code base (no problems so far)
  • How long will BLAST for all 9 species take (all BLASTX and BLASTP will need to be re-done, since all of the worm proteomes have changed)
  • Problems
    • RNAis with bad DNA_text. Cleaned and reported to Caltech
    • NCBI taxonomy database at EBI changed location, config needed a patch

Data integration / curation

  • B. malayi
    • WS248 Brugia submission now live at ENA
    • Gene prediction on new assembly
      • Looking at RATT transfers from old assembly
      • Using HAL mapping to project genes also works quite well.
      • AUGUSTUS to fill in the gaps
    • Handover will be Monday 10th August (during Brugia conference call)
  • C. remanei
    • Bad data. Submitter does not have time right now to clean. Will be deferred from this build
  • General
    • Hawaain strain - will go in as T3. BLASTable.
    • Cleaning up T2. Getting rid of in-frame STOPs for P. pacific us
    • Cleaning up Brief_identifcation for protein-coding and pseudogenes.

Database migration

  • New interface for uploading ace files.
  • Discussed potential strategies for schema updates

ParaSite

  • New release out
  • BLAST
    • Fixed glitches in new service
    • Discussed potential minor improvements to font page
  • Analytics
  • Redesign of the home page. Make it more WormBase compliant.
    • Search box confusion