Attendees

• Lars, Nadya, Zach, Eric, Elaine, TomG, Scooter

On-site Genentech Hall N436A

Agenda

• Lars Jensen presenting on proteomics work
• ChimeraX 1.5 roadmap 5 minute quick look
• Review Action Items listed below

Discussion Notes

• Lars Jensen on proteomics data sources, visualization and VR
  • Lars is from NOvo Nordisk Foundation Center for Protein Research.
  • Talk: Visualizing omics data on protein networks in 2D and 3D
  • Explained 10 ways to see that genes are functionally related
  • Talked about text mining including deep learning
  • Collecting all data sources is hard and boring
  • Can assign confidence scores to protein-protein functional interactions
  • Can transfer interaction knowledge to orthologs
  • Talked about Cytoscape String app for making meaning full omics graph depictions.
  • Testing if virtual reality feasible for large network visualization
  • Quest 2 standalone headset is cheap, 10 million sold, can reach large audience
  • Browser WebXR apps simple to deliver
  • VR apps for single cell expression data and also general network viz exist, but they need a Windows PC.
  • Lars used U-CIE coloring app and A-frame web vr on quest 2 and got smooth viewing of 14000 point data set.
  • Lars also tried 3400 node, 16000 edge Cytoscape exported network wrapped on a hemisphere in VR -- also fine performance.
  • Have not yet tried any data interaction in VR.

• ChimeraX roadmap
  • Did not have time in today's meeting to look at this.

Action Items

• Clean up VirtualHosts on our web servers -- Greg/Scooter
• Document new vpn setup on Linux -- Scooter
• Audit followup -- Scooter