= ChimeraX Grant Funding Specific Aims =

January 23, 2023

==  R01 September 2022-2026 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling ==

Resubmission [https://docs.google.com/document/d/1AUesVj2Pfv2-v2fT90ykiClz0OZsMdKT45g0mmqQ37w plan].
Original [https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2021.pdf plan] and
[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2021_aims.pdf aims]

* Aim 1: Develop visualization and analysis tools for atomic structures and associated data, including assemblies, ensembles, maps and sequences.
  - 1A: Analysis capabilities (.45 FTE)
    - Prepare structures for docking/modeling.
    - Sequence-structure analysis.
    - Dimensionality reduction.
  - 1B: Dissemination of results (.45 FTE)
    - Animations.
    - New glycan depictions.
    - Improved interoperability with wwPDB repositories.
* Aim 2: Develop visualization and analysis tools for electron microscopy of molecular assemblies and cells.
  - 2A: Developments for electron microscopy of molecular assemblies (.35 FTE)
    - Machine learning structure predictions.
    - Visualization of molecular conformational heterogeneity using machine learning.
    - Interactive molecular dynamics for fitting atomic models in maps. 
    - Faster map contouring and masking.
    - Additional building and validation tools.
  - 2B: Developments for electron tomography of cells (.53 FTE)
    - Improved volumetric visualization using lighting.
    - Visualizing, quantifying, and creating segmentations.
    - Analysis tools for subtomogram averaging.
    - Virtual reality visualization of tomograms.
* Aim 3: Provide a diverse software foundation enabling labs around the world to develop and distribute new molecular and cellular structure analysis software.
  - 3A: New capabilities for plugin development (.35 FTE)
    - A standard platform for machine-learning algorithms.
    - Simple programming to access web services.
    - Providing complex calculations with good user experience (long-running calculations).
    - Programming examples.
  - 3B: Expanding the distribution of plugins (.17 FTE)
    - Utilizing the PyPi and Anaconda Python package managers.
    - Cloud-based building of ChimeraX and plugins. 

== NIAID contract, March 2022 - 2023 ==

[https://docs.google.com/document/d/1GIfQusdCn6sLbI5RoRvphjGax_9QGer0m7kA1m_O8jM Statement of work], meeting [https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/NIAID2022 minutes]


- General ChimeraX improvements to support NIAID.
  - Specific improvements to assist NIAID personnel to transition away from the unsupported legacy Chimera program.
- Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development.
- Virtual reality for molecular structure, cryoEM and medical imaging.
- CryoEM modeling utilizing machine learning structure prediction.
- DICOM
- Outreach
- Administration

==  Phenix R24 May 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 August 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.

= Completed =


==  R01 July 2018-2022 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling ==

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

* 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
* 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
* 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, March 2021 - 2022 ==

[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%)
* 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%)