Changes between Version 11 and Version 12 of GrantAims2


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Timestamp:
Jan 23, 2023, 5:15:47 PM (3 years ago)
Author:
Tom Goddard
Comment:

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  • GrantAims2

    v11 v12  
    33January 23, 2023
    44
    5 ==  R01 2022-2026 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling ==
     5==  R01 September 2022-2026 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling ==
     6
     7Resubmission [https://docs.google.com/document/d/1AUesVj2Pfv2-v2fT90ykiClz0OZsMdKT45g0mmqQ37w plan].
     8Original [https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2021.pdf plan] and
     9[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2021_aims.pdf aims]
    610
    711* Aim 1: Interactive visualization and analysis platform (ChimeraX)
    … …  
    3640    - Cloud-based building of ChimeraX and plugins.
    3741
     42== NIAID contract, March 2022 - 2023 ==
    3843
    39 ==  R01 2018-2022 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling ==
     44[https://docs.google.com/document/d/1GIfQusdCn6sLbI5RoRvphjGax_9QGer0m7kA1m_O8jM Statement of work]
     45
     46
     47- General ChimeraX improvements to support NIAID.
     48  - Specific improvements to assist NIAID personnel to transition away from the unsupported legacy Chimera program.
     49- Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development.
     50- Virtual reality for molecular structure, cryoEM and medical imaging.
     51- CryoEM modeling utilizing machine learning structure prediction.
     52- DICOM
     53- Outreach
     54- Administration
     55
     56==  Phenix R24 May 2021-2026 - Phenix interaction with ChimeraX ==
     57
     58[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/Phenix_R24_2021.pdf Plan]
     59
     60* Implement ChimeraX/Phenix communication APIs.
     61* Implement fragment extension ChimeraX user interface.
     62* Implement ligand placement ChimeraX user interface.
     63* Implement restraint specification ChimeraX user interface.
     64* Implement validation ChimeraX user interface.
     65
     66== CZI Essential Open Source Software August 2021-2023 - Molecular Visualization: Transitioning Chimera to ChimeraX ==
     67
     68[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/CZI_EOSS_2021.pdf Plan]
     69
     70* Export Chimera sessions to ChimeraX.
     71* Port multiple sequence alignment and homology modeling web services.
     72* Update the Qt window toolkit from version 5 to 6.
     73* Replace OpenGL graphics with Vulkan.
     74* Distribute a native ChimeraX for Mac ARM CPUs.
     75* Develop a !PyPi library to distribute non-UI components of ChimeraX.
     76
     77= Completed =
     78
     79
     80==  R01 July 2018-2022 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling ==
    4081
    4182[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]
    … …  
    5697
    5798
    58 == NIAID contract, Feb 2021 - Feb 2022 ==
     99== NIAID contract, March 2021 - 2022 ==
    59100
    60101[https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/NIAID_2021.pdf Plan]
    … …  
    68109* Outreach - Instructional material and tools documentation (Elaine 20%)
    69110* Administration (Scooter 10%)
    70 
    71 ==  Phenix R24 2021-2026 - Phenix interaction with ChimeraX ==
    72 
    73 [https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/Phenix_R24_2021.pdf Plan]
    74 
    75 * Implement ChimeraX/Phenix communication APIs.
    76 * Implement fragment extension ChimeraX user interface.
    77 * Implement ligand placement ChimeraX user interface.
    78 * Implement restraint specification ChimeraX user interface.
    79 * Implement validation ChimeraX user interface.
    80 
    81 == CZI Essential Open Source Software 2021-2023 - Molecular Visualization: Transitioning Chimera to ChimeraX ==
    82 
    83 [https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/CZI_EOSS_2021.pdf Plan]
    84 
    85 * Export Chimera sessions to ChimeraX.
    86 * Port multiple sequence alignment and homology modeling web services.
    87 * Update the Qt window toolkit from version 5 to 6.
    88 * Replace OpenGL graphics with Vulkan.
    89 * Distribute a native ChimeraX for Mac ARM CPUs.
    90 * Develop a !PyPi library to distribute non-UI components of ChimeraX.
    91 
    92 == R01 2022-2026 - proposed renewal ==
    93 
    94 [https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2021.pdf Plan] and
    95 [https://www.rbvi.ucsf.edu/chimerax/data/grant-plans-oct2021/R01_2021_aims.pdf aims]
    96 
    97 * Aim 1: Interactive visualization and analysis platform (ChimeraX)
    98   - 1A: Analysis capabilities
    99   - 1B: Dissemination of results
    100 * Aim 2: Visualizing electron microscopy of molecular assemblies, cells and tissues
    101   - 2A: Developments for electron microscopy of molecular assemblies
    102   - 2B: Developments for electron tomography of cells and tissues
    103 * Aim 3: Community development platform for new algorithms and methods
    104   - 3A: New capabilities for plugin development
    105   - 3B: Expanding the distribution of plugins
    106 
    107 
    108