ChimeraX Grant Funding Specific Aims

October 21, 2021

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

Plan and aims and ​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%)
• Human Biomolecular Atlas Program (HuBMAP) multiscale visualization (Eric: 30%)
• Enhance ChimeraX’s segmentation capabilities (Tom 40%)
• DICOM (Tom: 25%, Eric: 5%) Outreach - Instructional material and tools documentation. (Elaine 20%)
• Administration (Scooter 10%)

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