wiki:NIAID2024

Version 5 (modified by Elaine Meng, 19 months ago) ( diff )

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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, Phil, Kristen, Darrell, Meghan, Bhinnata

Some discussion of Andi's scary (almost-real-looking) avatar since he is Zooming using the Vision Pro. The varying amounts of transparency and the unrealistic mouth movements are the giveaway.

Phil: Kristen had an interesting idea to output files for Mesoscape. Scooter: I talked to some people at VIZBI... planning a collaboration for publishing data to Schol-AR; the developer (Tyler) happens to also be a radiologist and may be helpful in evaluating our medical image stuff. Discussed maybe having a ChimeraX REST interface to publish to Schol-AR. Kristen and Phil: we may be interested in adding a connection to Schol-AR from NIH3D.

Scooter: Eric has a present for you, especially Darrell. (Zoom technical difficulties, disconnected, reconnected.) Eric demonstrates worms, everybody is enthusiastic. Darrell: would be fun to try 3D printing. Might need struts. Kristen: is this in other programs? Elaine: yes, Pymol, Chimera, etc. Phil: re NIH3D I also wanted to discuss the quick-submit workflows for alphafold... we need to decide which are the standard outputs: pLDDT and PAE domain coloring, ribbons and surfaces, maybe hide low-pLDDT parts? Transparency? Elaine: pLDDT coloring shows low confidence as red, or it could be gray in combination with PAE domain coloring. In ChimeraX you can specify all residues with bfactor (pLDDT is in the bfactor field) greater than some value.

Scooter: this all ties into what metadata we want to have in the GLTF output. Groups of residues predefined, e.g. "high pLDDT" or by chain ID or domain, etc. Phil: Darrell, maybe you can help us decide on the standard set of outputs. Darrell: should be useful and include ones that are harder for some people to generate on their own, which used to be the case for ESP coloring. We'll have to put our heads together and decide on an edited set. Kristen: maybe we could offer checkbox choices of which outputs the user wants.

Phil: ChimeraX gltf outputs look washed out when embedded into Microsoft documents (Powerpoint and Word). Due to their oversaturated lighting model, which is unlikely to be addressed by Microsoft, so we have to try to work around it. I can generate ChimeraX gltf files that look better after embedding in such documents by using different settings in ChimeraX (I have my own preset for this, which uses "color modify" to lighten the colors) but that may require yet another set of output options. Kristen: I hacked Powerpoint to get around it but it's not trivial. See this in the forum for the Microsoft lighting: ​https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-inside-powerpoint/d0c0c316-8019-4c25-b0f6-86500e512f91

Meghan posted another link in the chat ​https://answers.microsoft.com/en-us/msoffice/forum/all/powerpoint-uses-gltf-but-doesnt-support/002d1f4e-061d-4ab6-a692-ed217945724a

Meghan: are there ways to fix the gltf after it's output? Blender, but having to download Blender is another barrier. Kristen: maybe NIH3D could have a "optimize gltf for Microsoft documents" service that runs our own Blender. Phil, Darrell: it may be a useful utility. Darrell: does gltf outputs from ChimeraX include lights? Kristen: I just checked, and no, these gltf files do not include lights or camera. Darrell: we might also look at providing U3D which can be embedded in PDFs. Greg: it hasn't been used much. Darrell: probably because it is rather difficult to generate.

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