= 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 
  - [https://github.com/nf-core/proteinfold 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 =