SOW Deliverables

End of contract: February 29, 2020

1. Virtual Reality user interface development (Tom 348 hours, Elaine 87 hours, Eric 696 hours, Conrad 87 hours)
   1. Provide task specific user interfaces (i.e. GUI panels and/or appropriate icons) for the following areas:
      1. medical imaging
      2. cryoEM modeling -- rotamers, structure building and verification, minimization
   2. Measure and display distance between two specified points in space in VR, both molecular models and medical images.
   3. Investigate and optionally prototype control of VR sessions by speech recognition, using a controlled vocabulary and grammar. This will support better accessibility for disabled users, e.g., users with limb differences who would have trouble with some aspects of the VR hand controllers.
2. Extend medical imaging data visualization and analysis (Tom 348 hours, Elaine 87 hours)
   1. Improve native .dcm support, e.g., compatibility for segmented dicom files.
   2. Provide presets for different tissue types in CT scans.
3. Support for multiuser sessions in a virtual reality environment (Tom 87 hours, Eric 174 hours, Conrad 435 hours)
   1. The application will allow multiple ChimeraX users to enter a shared session to interact with a 3D representation of the data in virtual reality
   2. An ideal solution will allow users from both ends (remote, or in the same physical room) to start meetings on demand and to connect without opening firewalls.
4. Outreach
   1. Workshops, Training and presentations (Tom 164 hours, Elaine 87 hours)
      1. If available, the subcontractor shall attend a meeting at NIAID’s Rocky Mountain Labs location in Hamilton, Montana. This is tentatively scheduled for August 5-9, 2019, as part of a NIAID/OCICB site visit to showcase virtual reality technology for scientific data visualization to support NIAID research.
      2. The subcontractor may propose one or more additional conference events relevant to the work, at which they will showcase the application in an oral presentation and/or hands-on conference exhibit or training. Justification shall be provided for how this will benefit NIAID.
      3. A virtual help desk for users
   2. Instructional Material and tools documentation (Elaine 609 hours)
      1. Detailed instructions for all features shall be provided in a user manual.
      2. Written user guides and tutorials shall be available as an HTML page and/or a downloadable PDF.
5. Project planning, administration, and reporting (Tom 87 hours, Scooter 174 hours)
   1. A project schedule, implementation plan, and documentation plan will be provided.
   2. Reports will be provided for all subtasks described under each task.

Progress October 31, 2019

1. Virtual Reality user interface development (Tom 348 hours, Elaine 87 hours, Eric 696 hours, Conrad 87 hours)
   1. Provide task specific user interfaces (i.e. GUI panels and/or appropriate icons) for the following areas:
      1. medical imaging
      2. cryoEM modeling -- rotamers, structure building and verification, minimization
         • ISOLDE integration with VR
      • User interface improvements: better menus and UI appearance
   2. Measure and display distance between two specified points in space in VR, both molecular models and medical images.
      • ​Tape measure VR and mouse mode added. For maps only currently.
   3. Investigate and optionally prototype control of VR sessions by speech recognition, using a controlled vocabulary and grammar. This will support better accessibility for disabled users, e.g., users with limb differences who would have trouble with some aspects of the VR hand controllers.
2. Extend medical imaging data visualization and analysis (Tom 348 hours, Elaine 87 hours)
   1. Improve native .dcm support, e.g., compatibility for segmented dicom files.
   2. Provide presets for different tissue types in CT scans.
3. Support for multiuser sessions in a virtual reality environment (Tom 87 hours, Eric 174 hours, Conrad 435 hours)
   1. The application will allow multiple ChimeraX users to enter a shared session to interact with a 3D representation of the data in virtual reality (scene sharing)
   2. An ideal solution will allow users from both ends (remote, or in the same physical room) to start meetings on demand and to connect without opening firewalls.
4. Outreach
   1. Workshops, Training and presentations (Tom 164 hours, Elaine 87 hours)
      1. If available, the subcontractor shall attend a meeting at NIAID’s Rocky Mountain Labs location in Hamilton, Montana. This is tentatively scheduled for August 5-9, 2019, as part of a NIAID/OCICB site visit to showcase virtual reality technology for scientific data visualization to support NIAID research.
      2. The subcontractor may propose one or more additional conference events relevant to the work, at which they will showcase the application in an oral presentation and/or hands-on conference exhibit or training. Justification shall be provided for how this will benefit NIAID.
      3. A virtual help desk for users
   2. Instructional Material and tools documentation (Elaine 609 hours)
      1. Detailed instructions for all features shall be provided in a user manual.

​ChimeraX User Guide at the RBVI website note to Scooter because viewdockx was used as the test for the future documentation reorganization, the links to ViewDockX tool and command help are broken in this website copy. The downloaded User Guide shown from ChimeraX help menu does not have this issue.

1. Written user guides and tutorials shall be available as an HTML page and/or a downloadable PDF.

​ChimeraX tutorials index ...includes Alpha-synuclein fibrils ChimeraX tutorial for Rocky Mountain Laboratories workshop. September 2019. and EM tomography ChimeraX tutorial looking at proteasomes around aggregated fibrils in neurons for Rocky Mountain Laboratories workshop. September 2019.

5. Project planning, administration, and reporting (Tom 87 hours, Scooter 174 hours)
   1. A project schedule, implementation plan, and documentation plan will be provided.
   2. Reports will be provided for all subtasks described under each task.
6. Other related developments
   • Exploratorium demonstration

​Exploratorium After Dark Party, October 24, 6-10 pm. ChimeraX VR will be used to show programmed cells form 3D structures. Data from Wendell Lim's lab; the cells are genetically engineered to self-organize by signaling and adhesion.

• Makers Lab demonstration

​ChimeraX used for a virtual reality look at molecules, cells, and tissues in the UCSF Library Makers Lab, Parnassus Campus, noon-1pm November 15.2019.

• UCSF news article highlighting ChimeraX VR and drug resistance

​VR Drug Discovery Makes Precision Therapy a Reality and ​video from article on YouTube