WormBase-Caltech Weekly Calls August 2021

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August 5, 2021

Proxy issue resolved

  • Not clear what the problem was, but Sibyl transferred to new machine and now it works
  • Could be a firewall issue somewhere but it isn't clear

Textpresso-Dev transfer

  • Michael ordered hard drive
  • Working on transfer
  • Do we need more backup? Have partial backup on AWS; will make complete

August 12, 2021

CeNGEN graph on gene pages

  • We would like to show an expression level graph on each gene page. CeNGEN prefers something similar to what we have for FPKM expression.
  • Sibyl drafted a prototype that is 2D so that it solves the issue of fitting into one page width while making highly expressing cells prominent.

August 19, 2021

Caltech hosted CGIs

  • Caltech IMSS is blocking some WB IP addresses likely from nefarious actors on AWS, thereby breaking WB links to Caltech-hosted CGIs
  • Although WB uses dedicated AWS IPs, those some how still got on a black list.
  • The ultimate solution is to move all services answering WB queries to AWS, so there is no extr-AWS network traffic.
  • Could non-SObA CGIs move to different servers (AWS?)?
  • SObA is resource intensive when new releases are being built but otherwise memory requirements can be tuned (affecting caching) for serving queries. We can use a local machine for building a release and then transfer the built database to a live machine in the cloud. This approach also alleviates some sysadmin load for Caltech.

August 26, 2021

New Wormicloud features

  • Clustering similar words in word clouds
  • Counter with the number of objects already curated by WB for papers returned by searches

Changes to Transgene OA autocomplete