NIAID-UCSF 2024 Contract Statement of Work -- March 1 - September 30, 2024

This SOW is split into two parts. Part 1 is intended to be accomplished in the first 6 months of the contract. If specific items are completed, items from part 2 will be brought forward. Should NIAID extend the contract to 1 year, those items in part 2 not completed during the first 6 months will be worked on.

Part 1

1. General ChimeraX improvements to support NIAID-specific requirements to assist NIAID personnel to transition away from the unsupported legacy Chimera program, e.g.:
   1. Investigate and improve ChimeraX usability for very wide displays and touch screens i.Specific focus on the BioViz lab wall display
   2. Worms depiction
   3. More GUIs (notably, copy/combine, 2D labels)
   4. Support for showing the thermal ellipsoids
2. Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development
   1. Continuing support for NIH3D as needed
      1. Updating workflows
      2. Quick submits for AlphaFold database entries
      3. Improve GLTF output to include structure hierarchy
   2. Investigate adding support for ChimeraX sessions in NIH3D
      1. Both uploading and downloading
      2. Need to check on any possible security issues
3. Extend virtual reality support
   1. Implement use of pass-through video with the Quest 2/3/Pro for multi-person sessions in ChimeraX VR
   2. Improve molecular viewer for standalone headsets such as Quest 2/3.
   3. Add “disable/enable buttons” commands to support better support for handing off the controls to another user to prevent the scene from getting inadvertently changed.
4. Explore pedagogical benefits of ChimeraX in VR vs. flat screen
   1. Provide support to the University of Indiana (Andi), UCSF, and NIAID to conduct a task analysis comparing VR vs. flat screen for understanding biological macromolecules as needed
5. Medical Images
   1. Improve presets for medical images
   2. Move medical imaging functionality to toolshed
   3. Explore re-skinning the UI when switching to medical imaging
   4. Support for automated segmentation
      1. Investigate adding Total segmentator
6. Outreach
   1. Instructional material and tools documentation.
      1. Detailed instructions for all features shall be provided in a user manual.
      2. Written user guides and tutorials shall be available as HTML pages.
      3. Improve documentation for multi-person VR
   2. Attendance at meetings or workshops as required by NIAID
7. Administration Submit monthly written reports of accomplishments

Part 2

1. General ChimeraX improvements to support NIAID-specific requirements to assist NIAID personnel to transition away from the unsupported legacy Chimera program, e.g.:
   1. Energy minimization
   2. Support for MD analysis
   3. Improve the altloc explorer
   4. Rewrite ViewDockX
   5. Read VRML/X3D
2. Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development
   1. Continuing support for NIH3D as needed
      1. Adding support for total segmentator
   2. Investigate adding support for ChimeraX sessions in NIH3D
      1. Both uploading and downloading
      2. Need to check on any possible security issues
3. Extend virtual reality support
   1. Improve user experience in ChimeraX VR, e.g.
      1. Implement a VR ergonomic toolbar and Model panel user interface.
      2. Add support for a voice interface in VR mode
4. Explore pedagogical benefits of ChimeraX in VR vs. flat screen
   1. Collaborate with the University of Indiana (Andi), UCSF, and NIAID to conduct a task analysis comparing VR vs. flat screen for understanding biological macromolecules
5. Medical Images
   1. Implement new rendering and lighting modes for medical imagings
   2. Continue improvements to the DICOM reader by including more data types such as segmentations, and making it more robust by testing against the NCI TCIA repository.
   3. Improve VR experience for medical images
      1. Easier manipulation of windowing and leveling, especially for complex curves
      2. Particularly support for fine-grained changes
      3. Improve segmentation tool by adding commands to support multi-person VR
      4. Investigate adding support for 2D views in VR
   4. General usability improvements for using ChimeraX with medical images driven by TCIA data
   5. Support for automated segmentation
      1. Add support for ML-based tumor segmentation tool
6. Outreach Instructional material and tools documentation.
   1. Detailed instructions for all features shall be provided in a user manual.
   2. Written user guides and tutorials shall be available as HTML pages.
   3. Create videos demonstrating new capabilities.
   4. Present webinar and workshop tutorials to train users on existing and new capabilities.
   5. Create video tutorials for how to use multi-person VR.
   6. Do outreach using VR in particular (live presentations)
   7. Improve documentation for multi-person VR
   8. Attendance at meetings or workshops as required by NIAID
7. Administration
   1. Submit monthly written reports of accomplishments

Meeting Minutes

4/11/24

3/28/24

Scooter, Eric, Zach, Elaine; Andi Bueckle

notes