NIAID SOW Proposed deliverables (based on 2 FTE), January 2020

Original ​Google doc version. Earlier SOW draft.

1. Extensions to ChimeraX to support the NIH 3D pipeline
   1. Support the conversion of existing NIH 3D Print Exchange Chimera scripts to ChimeraX, advising on ChimeraX syntax for capabilities where available and noting missing features in ChimeraX where comparable features don’t exist
      1. Investigate using Smart Display
      2. Discuss Python vs. ChimeraX command line
   2. Implement essential missing features discovered above, including:
      1. PubChem fetch
      2. Additional import formats, including mol and sdf
      3. PDB biounit fetch #3515
   3. Sequence conservation coloring in ChimeraX
   4. Fetch sequence annotations (UniProt, domains, disease-associated mutations) (Eric)
      1. Automatic labels
   5. Enhancements to X3D export format (Greg)
      1. Look at GLTF export improvements (support for both per vertex coloring and texture coloring)
   6. Read and visualize segmentation models (see deliverable 2) (Tom)

2. Significantly enhance ChimeraX’s segmentation capabilities for 3d electron microscopy, light microscopy, and medical imaging
   1. Interactive SimpleITK use in ChimeraX (Tom)
   2. Allow loading, visualizing, creating, measuring and saving segmentations. (Tom)
   3. Support new EMDB-SFF segmentation file format from the EM Databank (Tom). #3639 in progress
   4. NOTE: some example data sets would be useful - AI Detected Lesions in lungs. Phil will get some data to TomG. Could also look at some data sets from SimpleITK. Bryan Hansen and Beth Fisher could also get some data sets

3. Medical imaging
   1. Metadata browser for DICOM files (Tom)
   2. Support radiologist collaborator needs by adapting ChimeraX to better suit standard workflows and to provide critical missing features identified by our collaborators (Tom)
      1. Need to get a collaborator
      2. Les Folio / Ron Summers
      3. New NIAID section focused on lung imaging
      4. Roberto Rodriguez Rubio, MD at UCSF director of ​Skull Base lab, interested in VR. Emphasis on dissections, no medical imaging.

4. Improve multi-person VR beyond work accomplished in 2019 SOW
   1. Localizable connection server solution - deliver a rendezvous server that can easily be deployed by institutions or enterprises. (Conrad/Greg)
      1. Fix cxconference TLS security #3629
      2. Get TLS certificate for plato cxconference server (Greg)
      3. Make cxconference work with VR #2892, #2893, #3498, #3512
      4. Greg to help containerize cxconference
5. Human Biomolecular Atlas Program (HuBMAP) multiscale visualization
   1. Engage with the HuBMAP group to evaluate the potential for ChimeraX extensions to support exploration and analysis of HuBMAP data, particularly as those extensions align with NIAID areas of interest. This will include determining the programmatic interfaces to access the HuBMAP data and initial efforts to scope the task of supporting the various HuBMAP data formats.
      1. Discuss needs with Meghan McCarthy and Darrell Hurt
6. Outreach
   1. Workshops, Training and presentations
   2. 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 an HTML page
7. Administration
   1. A project schedule, implementation plan, and documentation plan will be provided
   2. Monthly status reports detailing progress on each subtask will be delivered

Additional Requests from Users

1. Adding Coulombic coloring (Eric) #3596 (Elaine: this is one of the essential missing features mentioned in 1b above)
   1. 90% cases covered
2. Colada import/export
3. Add support for SDF V3000 (Eric)

NIAID SOW Additional Proposed Deliverables (based on 2.5 FTE)

1. Medical Imaging -- in addition to the above proposed deliverables (#3 above), suggest that UCSF Staff engage with a small set of radiologists who can act as close collaborators to improve and drive our efforts. This would include supporting:
   1. Measuring changes in time progression, alignment, sizes, color differences
   2. Implement “cinematic lighting” for improved perception of details.
2. Improve multi-person VR beyond work accomplished in SOW #2
   1. Support the ability of any participant to bring in new models
   2. Support integrated audio chat