| | 1 | = NIAID-UCSF 2024 Contract Statement of Work -- March 1 - September 30, 2024 = |
| | 2 | |
| | 3 | |
| | 4 | 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. |
| | 5 | |
| | 6 | == Part 1 == |
| | 7 | 1. General ChimeraX improvements to support NIAID-specific requirements to assist NIAID personnel to transition away from the unsupported legacy Chimera program, e.g.: |
| | 8 | a. Investigate and improve ChimeraX usability for very wide displays and touch screens |
| | 9 | i.Specific focus on the BioViz lab wall display |
| | 10 | b. Worms depiction |
| | 11 | c. More GUIs (notably, copy/combine, 2D labels) |
| | 12 | c. Support for showing the thermal ellipsoids |
| | 13 | 1. Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development |
| | 14 | a. Continuing support for NIH3D as needed |
| | 15 | i. Updating workflows |
| | 16 | i. Quick submits for AlphaFold database entries |
| | 17 | i. Improve GLTF output to include structure hierarchy |
| | 18 | a. Investigate adding support for ChimeraX sessions in NIH3D |
| | 19 | i. Both uploading and downloading |
| | 20 | i. Need to check on any possible security issues |
| | 21 | 1. Extend virtual reality support |
| | 22 | a. Implement use of pass-through video with the Quest 2/3/Pro for multi-person sessions in ChimeraX VR |
| | 23 | a. Improve molecular viewer for standalone headsets such as Quest 2/3. |
| | 24 | a. 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. |
| | 25 | 1. Explore pedagogical benefits of ChimeraX in VR vs. flat screen |
| | 26 | a. 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 |
| | 27 | 1. Medical Images |
| | 28 | a. Improve presets for medical images |
| | 29 | b. Move medical imaging functionality to toolshed |
| | 30 | a. Explore re-skinning the UI when switching to medical imaging |
| | 31 | a. Support for automated segmentation |
| | 32 | i. Investigate adding Total segmentator |
| | 33 | 1. Outreach |
| | 34 | a. Instructional material and tools documentation. |
| | 35 | i. Detailed instructions for all features shall be provided in a user manual. |
| | 36 | i. Written user guides and tutorials shall be available as HTML pages. |
| | 37 | i. Improve documentation for multi-person VR |
| | 38 | b. Attendance at meetings or workshops as required by NIAID |
| | 39 | 1. Administration Submit monthly written reports of accomplishments |
| | 40 | |
| | 41 | == Part 2 == |
| | 42 | 1. General ChimeraX improvements to support NIAID-specific requirements to assist NIAID personnel to transition away from the unsupported legacy Chimera program, e.g.: |
| | 43 | a. Energy minimization |
| | 44 | a. Support for MD analysis |
| | 45 | a. Improve the altloc explorer |
| | 46 | a. Rewrite ViewDockX |
| | 47 | a. Read VRML/X3D |
| | 48 | 1. Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development |
| | 49 | a. Continuing support for NIH3D as needed |
| | 50 | i. Adding support for total segmentator |
| | 51 | a. Investigate adding support for ChimeraX sessions in NIH3D |
| | 52 | i. Both uploading and downloading |
| | 53 | i. Need to check on any possible security issues |
| | 54 | 1. Extend virtual reality support |
| | 55 | a. Improve user experience in ChimeraX VR, e.g. |
| | 56 | i. Implement a VR ergonomic toolbar and Model panel user interface. |
| | 57 | i. Add support for a voice interface in VR mode |
| | 58 | 1. Explore pedagogical benefits of ChimeraX in VR vs. flat screen |
| | 59 | a. Collaborate with the University of Indiana (Andi), UCSF, and NIAID to conduct a task analysis comparing VR vs. flat screen for understanding biological macromolecules |
| | 60 | 1. Medical Images |
| | 61 | a. Implement new rendering and lighting modes for medical imagings |
| | 62 | a. 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. |
| | 63 | a. Improve VR experience for medical images |
| | 64 | i. Easier manipulation of windowing and leveling, especially for complex curves |
| | 65 | i. Particularly support for fine-grained changes |
| | 66 | i. Improve segmentation tool by adding commands to support multi-person VR |
| | 67 | i. Investigate adding support for 2D views in VR |
| | 68 | a. General usability improvements for using ChimeraX with medical images driven by TCIA data |
| | 69 | a. Support for automated segmentation |
| | 70 | i. Add support for ML-based tumor segmentation tool |
| | 71 | 1. Outreach Instructional material and tools documentation. |
| | 72 | a. Detailed instructions for all features shall be provided in a user manual. |
| | 73 | a. Written user guides and tutorials shall be available as HTML pages. |
| | 74 | a. Create videos demonstrating new capabilities. |
| | 75 | a. Present webinar and workshop tutorials to train users on existing and new capabilities. |
| | 76 | a. Create video tutorials for how to use multi-person VR. |
| | 77 | a. Do outreach using VR in particular (live presentations) |
| | 78 | a. Improve documentation for multi-person VR |
| | 79 | a. Attendance at meetings or workshops as required by NIAID |
| | 80 | 1. Administration |
| | 81 | a. Submit monthly written reports of accomplishments |
| | 82 | |
| | 83 | == Meeting Minutes == |
| | 84 | |
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
