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Changes between Version 9 and Version 10 of MSC2019Deliverables
- Timestamp:
- Oct 24, 2019, 4:32:05 PM (6 years ago)
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MSC2019Deliverables
v9 v10 30 30 i. medical imaging 31 31 i. cryoEM modeling -- rotamers, structure building and verification, minimization 32 - ISOLDE integration with VR32 - [[span(style=color: #00AA00, ISOLDE integration with VR - initial test for feasibility )]] 33 33 - [[span(style=color: #00AA00, 'swapaa' command implemented.[http://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html documentation] Largely a port of Chimera code, with the principal differences being: )]] 34 34 1. [[span(style=color: #00AA00, New code to handle the fact that Chimera treats alternate locations as separate atoms whereas ChimeraX treats them as a single atom )]] 35 35 1. [[span(style=color: #00AA00, 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 )]] 36 - User interface improvements: better menus and UI appearance36 - [[span(style=color: #00AA00, 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... )]] 37 37 b. Measure and display distance between two specified points in space in VR, both molecular models and medical images. 38 38 - [http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tapemeasure Tape measure VR and mouse mode added. For maps only currently.] … … 40 40 2. Extend medical imaging data visualization and analysis (Tom 348 hours, Elaine 87 hours) 41 41 a. Improve native .dcm support, e.g., compatibility for segmented dicom files. 42 - [[span(style=color: #00AA00, Improved DICOM read speed to be many times faster. )]] 42 43 a. Provide presets for different tissue types in CT scans. 43 44 3. Support for multiuser sessions in a virtual reality environment (Tom 87 hours, Eric 174 hours, Conrad 435 hours) … … 47 48 A. Workshops, Training and presentations (Tom 164 hours, Elaine 87 hours) 48 49 a. 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. 50 - - [[span(style=color: #00AA00, 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) )]] 49 51 b. 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. 50 c. A virtual help desk for users [http://www.rbvi.ucsf.edu/pipermail/chimerax-users/index.html chimerax-users archive] 52 c. A virtual help desk for users 53 - [http://www.rbvi.ucsf.edu/pipermail/chimerax-users/index.html chimerax-users archive] 51 54 B. Instructional Material and tools documentation (Elaine 609 hours) 52 a. Detailed instructions for all features shall be provided in a user manual. 53 [http://rbvi.ucsf.edu/chimerax/docs/user/index.html 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. 55 a. Detailed instructions for all features shall be provided in a user manual. 56 - [[span(style=color: #00AA00, [http://rbvi.ucsf.edu/chimerax/docs/user/index.html 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. )]] 54 57 a. Written user guides and tutorials shall be available as an HTML page and/or a downloadable PDF. 55 [http://www.rbvi.ucsf.edu/chimerax/tutorials.html ChimeraX tutorials index ] 56 ...includes [https://www.rbvi.ucsf.edu/chimerax/data/rml-sep2019/synuclein.html Alpha-synuclein fibrils ChimeraX tutorial for Rocky Mountain Laboratories workshop. September 2019.] and 57 [https://www.rbvi.ucsf.edu/chimerax/data/rml-sep2019/proteasomes.html EM tomography ChimeraX tutorial looking at proteasomes around aggregated fibrils in neurons for Rocky Mountain Laboratories workshop. September 2019.] 58 - [[span(style=color: #00AA00, [http://www.rbvi.ucsf.edu/chimerax/tutorials.html ChimeraX tutorials index ] ...includes [https://www.rbvi.ucsf.edu/chimerax/data/rml-sep2019/synuclein.html Alpha-synuclein fibrils ChimeraX tutorial for Rocky Mountain Laboratories workshop. September 2019.] and [https://www.rbvi.ucsf.edu/chimerax/data/rml-sep2019/proteasomes.html EM tomography ChimeraX tutorial looking at proteasomes around aggregated fibrils in neurons for Rocky Mountain Laboratories workshop. September 2019.] )]] 58 59 5. Project planning, administration, and reporting (Tom 87 hours, Scooter 174 hours) 59 60 a. A project schedule, implementation plan, and documentation plan will be provided. … … 61 62 6. Other related developments 62 63 - Exploratorium demonstration 63 [https://www.exploratorium.edu/visit/calendar/after-dark-october-24-2019 Exploratorium After Dark Party, October 24, 6-10 pm. ChimeraX VR will be used to show programmed cells form 3D structures. Data from Wendell Lim's lab; the cells are genetically engineered to self-organize by signaling and adhesion.]64 [https://www.exploratorium.edu/visit/calendar/after-dark-october-24-2019 Exploratorium After Dark Party, October 24, 6-10 pm. ChimeraX VR will be used to show programmed cells form 3D structures. Data from Wendell Lim's lab; the cells are genetically engineered to self-organize by signaling and adhesion.] 64 65 - Makers Lab demonstration 65 [https://calendars.library.ucsf.edu/event/5961014 ChimeraX used for a virtual reality look at molecules, cells, and tissues in the UCSF Library Makers Lab, Parnassus Campus, noon-1pm November 15.2019.]66 [https://calendars.library.ucsf.edu/event/5961014 ChimeraX used for a virtual reality look at molecules, cells, and tissues in the UCSF Library Makers Lab, Parnassus Campus, noon-1pm November 15.2019.] 66 67 - UCSF news article highlighting ChimeraX VR and drug resistance 67 [https://pharmacy.ucsf.edu/news/2019/10/vr-drug-discovery-makes-precision-therapy-reality VR Drug Discovery Makes Precision Therapy a Reality] and 68 [https://youtu.be/S4lDzUEUFL0 video from article on YouTube] 68 [https://pharmacy.ucsf.edu/news/2019/10/vr-drug-discovery-makes-precision-therapy-reality VR Drug Discovery Makes Precision Therapy a Reality] and [https://youtu.be/S4lDzUEUFL0 video from article on YouTube]
