ChimeraX Grant Funding Specific Aims

October 21, 2021

R01 2018-2022 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling (NIH Reporter)

Plan, aims, ​NIH Reporter

• Specific Aim 1: Interactive visualization and analysis platform (ChimeraX)
  • 1A: Support very large homogeneous and heterogeneous data sets
  • 1B: Integrate visualization of non-spatial 2D data with 3D graphics
  • 1C: Implement novel analysis and modeling tools
  • 1D: Export ChimeraX data for web-based visualization
• Specific Aim 2: Atomic resolution modeling from cryo-electron microscopy datasets
  • 2A: Develop analyses of map quality for model building
  • 2B: Create interactive model building and measurement tools
  • 2C: Devise new model validation tools
• Specific Aim 3: Community development platform for new algorithms and methods
  • 3A: Create and document APIs for ChimeraX libraries
  • 3B: Design and implement web-based ChimeraX bundle repository
  • 3C: Develop bundle contribution method for community developers

NIAID contract, Feb 2021 - Feb 2022 - NIH 3D pipeline, Multi-person VR, HuBMAP, Segmentation, DICOM, Outreach.

Plan

• General ChimeraX improvements to support NIAID (Eric: 20%)
• Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development. (Eric: 15%)
• Improve multi-person VR (Tom: 35%)
  • Create video tutorials in how to use multi-person VR
  • Hold VR office hours to train researchers to use VR capabilities
  • Allow participants to add models from local files during a VR session
  • Set up VR meeting servers for Africa, Europe, Asia
• Human Biomolecular Atlas Program (HuBMAP) multiscale visualization (Eric: 30%)
  • Develop ChimeraX tool to browse and select HuBMAP datasets for loading
• Enhance ChimeraX’s segmentation capabilities
  • Investigate increased use of simple ITK to support segmentation (Tom: 15%)
  • Investigate utilizing web services to support more complex machine learning-based segmentation algorithms (Tom: 15%)
  • Investigate reading and displaying segmentation format(s) available from imaging databases (tissue microscopy, cancer imaging data, etc.) (Tom: 10%)
• DICOM (Tom: 25%, Eric: 5%)
  • Improve ability to visualize and analyze medical images in VR with ChimeraX
  • Develop browser-style interface to show DICOM dataset contents and associated metadata such as sample characteristics
• Outreach
  • Instructional material and tools documentation. (20%)
    • Detailed instructions for all features shall be provided in a user manual
    • Written user guides and tutorials shall be available as an HTML page
• Administration (10%)
  • Submit monthly written reports of accomplishments

Phenix R24 2021-2026 - Phenix interaction with ChimeraX

Plan

• Implement ChimeraX/Phenix communication APIs.
• Implement fragment extension ChimeraX user interface.
• Implement ligand placement ChimeraX user interface.
• Implement restraint specification ChimeraX user interface.
• Implement validation ChimeraX user interface.

CZI Essential Open Source Software 2021-2023 - Molecular Visualization: Transitioning Chimera to ChimeraX

Plan

• Export Chimera sessions to ChimeraX.
• Port multiple sequence alignment and homology modeling web services.
• Update the Qt window toolkit from version 5 to 6.
• Replace OpenGL graphics with Vulkan.
• Distribute a native ChimeraX for Mac ARM CPUs.
• Develop a PyPi library to distribute non-UI components of ChimeraX.

R01 2022-2026 - proposed renewal

Plan