Attendees

Scooter, Greg, Eric, Elaine, TomF (zoom), Selina (zoom), 2 guests (Jim, Alex, from VisB)

March 21, 2024

Agenda

• Jim presenting Jalview (multiple sequence alignment editor)
• VizBi Recap

Discussion Notes

• Jalview Presentation
  • Group behind it sits at the center of biological research in Europe ("biology's CERN")
  • Original release 1997 as standalone/Java applet
    • 2.0 in 2005, desktop/applet
    • 2.11 in 2019, desktop/web based JalviewJS
    • 2020, combined codebase
    • Experimental projects split off from JalviewJS codebase
    • 2022, added support for ChimeraX, PyMol, 3D Beacons
    • 2024, planning Slivka Services, HMMR search, embeddable JalviewJS
  • Jalview demo
    • showed multiple sequence alignment and structure search using 3D Beacons
    • many visualizations: PAE matrix, PAE clustering, structure visualization, among others
    • discussion of EPAS1_RAT with predicted helix that's hard to call significant or not
  • ​nf-core/proteinfold runs 4 different predictions at once
  • Future plans: Rebuild and Reassess
    • Figure out what people need from molecular alignment & analysis
    • Key FAIR -- Interoperable and Reproducible
    • Investigate scalability for large MSAs: Foldseek/DIAMOND2
• VizBi
  • Of particular interest to RBVI:
    • David Koes talk on 3DMol
    • Schol-AR, a tool that creates QR codes that let phone users pull up models in AR (.obj, interested in .gltf)
      • We could have a ChimeraX tool that publishes models to Scholar and get their QR codes back
    • Jane Richardson talk
    • Alex McDowell

Action Items