wiki:MSC2019Deliverables

Version 13 (modified by pett, 6 years ago) ( diff )

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SOW Deliverables

End of contract: February 29, 2020

  1. Virtual Reality user interface development (Tom 348 hours, Elaine 87 hours, Eric 696 hours, Conrad 87 hours)
    1. Provide task specific user interfaces (i.e. GUI panels and/or appropriate icons) for the following areas:
      1. medical imaging
      2. cryoEM modeling -- rotamers, structure building and verification, minimization
    2. Measure and display distance between two specified points in space in VR, both molecular models and medical images.
    3. Investigate and optionally prototype control of VR sessions by speech recognition, using a controlled vocabulary and grammar. This will support better accessibility for disabled users, e.g., users with limb differences who would have trouble with some aspects of the VR hand controllers.
  2. Extend medical imaging data visualization and analysis (Tom 348 hours, Elaine 87 hours)
    1. Improve native .dcm support, e.g., compatibility for segmented dicom files.
    2. Provide presets for different tissue types in CT scans.
  3. Support for multiuser sessions in a virtual reality environment (Tom 87 hours, Eric 174 hours, Conrad 435 hours)
    1. The application will allow multiple ChimeraX users to enter a shared session to interact with a 3D representation of the data in virtual reality
    2. An ideal solution will allow users from both ends (remote, or in the same physical room) to start meetings on demand and to connect without opening firewalls.
  4. Outreach
    1. Workshops, Training and presentations (Tom 164 hours, Elaine 87 hours)
      1. If available, the subcontractor shall attend a meeting at NIAID’s Rocky Mountain Labs location in Hamilton, Montana. This is tentatively scheduled for August 5-9, 2019, as part of a NIAID/OCICB site visit to showcase virtual reality technology for scientific data visualization to support NIAID research.
      2. The subcontractor may propose one or more additional conference events relevant to the work, at which they will showcase the application in an oral presentation and/or hands-on conference exhibit or training. Justification shall be provided for how this will benefit NIAID.
      3. A virtual help desk for users
    2. Instructional Material and tools documentation (Elaine 609 hours)
      1. Detailed instructions for all features shall be provided in a user manual.
      2. Written user guides and tutorials shall be available as an HTML page and/or a downloadable PDF.
  5. Project planning, administration, and reporting (Tom 87 hours, Scooter 174 hours)
    1. A project schedule, implementation plan, and documentation plan will be provided.
    2. Reports will be provided for all subtasks described under each task.

Progress October 31, 2019

  1. Virtual Reality user interface development (Tom 348 hours, Elaine 87 hours, Eric 696 hours, Conrad 87 hours)
    1. Provide task specific user interfaces (i.e. GUI panels and/or appropriate icons) for the following areas:
      1. medical imaging
      2. cryoEM modeling -- rotamers, structure building and verification, minimization
        • ISOLDE integration with VR - initial test for feasibility
        • 'swapaa' command implemented.​documentation Largely a port of Chimera code, with the principal differences being:
          1. New code to handle the fact that Chimera treats alternate locations as separate atoms whereas ChimeraX treats them as a single atom.
          2. Refactored rotamer library handling so that the libraries are provided by separate bundles and therefore new rotamer libraries could be supplied by third parties via the Toolshed.
        • Rotamers tool largely implemented.​documentation It is also mostly a port of Chimera code, but required porting major Chimera infrastructure, e.g.:
          1. "Smart" table where the rows are directly based on ChimeraX data items (in this case rotamers) and the table knows how to show columns based on data item information and makes callbacks that provide the data items as arguments.
          2. Configurable and embeddable H-bonds GUI so that the Rotamers tool can add an H-bonds column to the rotamers table. As a "side effect" an H-bonds tool was implemented.​documentation
          3. Similar to the previous point, a configurable and embeddable clashes/contacts GUI needs to be ported/implemented. This will be the last major piece of the Rotamers tool. When completed, both embeddable GUIs will also be incorporated into the ViewDockX tool.
      • User interface improvements: menus and popup windows in VR, every tool is its own movable and closable panel, custom Oculus controller button depiction, Oculus thumbstick modes for zoom, rotate, others…
    2. Measure and display distance between two specified points in space in VR, both molecular models and medical images.
    3. Investigate and optionally prototype control of VR sessions by speech recognition, using a controlled vocabulary and grammar. This will support better accessibility for disabled users, e.g., users with limb differences who would have trouble with some aspects of the VR hand controllers.
  2. Extend medical imaging data visualization and analysis (Tom 348 hours, Elaine 87 hours)
    1. Improve native .dcm support, e.g., compatibility for segmented dicom files.
      • Improved DICOM read speed to be many times faster.
    2. Provide presets for different tissue types in CT scans.
  3. Support for multiuser sessions in a virtual reality environment (Tom 87 hours, Eric 174 hours, Conrad 435 hours)
    1. The application will allow multiple ChimeraX users to enter a shared session to interact with a 3D representation of the data in virtual reality (scene sharing)
    2. An ideal solution will allow users from both ends (remote, or in the same physical room) to start meetings on demand and to connect without opening firewalls.
  4. Outreach
    1. Workshops, Training and presentations (Tom 164 hours, Elaine 87 hours)
      1. If available, the subcontractor shall attend a meeting at NIAID’s Rocky Mountain Labs location in Hamilton, Montana. This is tentatively scheduled for August 5-9, 2019, as part of a NIAID/OCICB site visit to showcase virtual reality technology for scientific data visualization to support NIAID research.
        • Tom G attended workshop, presented ChimeraX cryoEM training, many VR demos, several new ChimeraX VR features requested by Rocky Mt people implemented (menu support, Oculus thumbstick controls)
      2. The subcontractor may propose one or more additional conference events relevant to the work, at which they will showcase the application in an oral presentation and/or hands-on conference exhibit or training. Justification shall be provided for how this will benefit NIAID.
      3. A virtual help desk for users
    2. Instructional Material and tools documentation (Elaine 609 hours)
      1. Detailed instructions for all features shall be provided in a user manual.
        • ​ChimeraX User Guide at the RBVI website note to Scooter because viewdockx was used as the test for the future documentation reorganization, the links to ViewDockX tool and viewdockx command help are broken in this website copy. The downloaded User Guide shown from ChimeraX help menu does not have this issue.
      2. Written user guides and tutorials shall be available as an HTML page and/or a downloadable PDF.
  5. Project planning, administration, and reporting (Tom 87 hours, Scooter 174 hours)
    1. A project schedule, implementation plan, and documentation plan will be provided.
    2. Reports will be provided for all subtasks described under each task.
  6. Other related developments
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