= ChimeraX Grant Funding Specific Aims =

October 21, 2021

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

[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2017.pdf Plan], [https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2017_aims.pdf aims], [https://reporter.nih.gov/project-details/9578921 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. ==

 [https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/NIAID_2021.pdf 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 ==

[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/Phenix_R24_2021.pdf 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 ==

[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/CZI_EOSS_2021.pdf 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 ==

[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2021.pdf Plan]