Changes between Initial Version and Version 1 of NeteSOW

Timestamp:

Aug 20, 2020, 1:33:23 PM (5 years ago)

Author:

Tom Goddard

Comment:

--

NeteSOW

@@ +1 @@
+= NIAID SOW Proposed deliverables (based on 2 FTE) =
+
+1. Extensions to ChimeraX to support the NIH 3D pipeline
+   a. Support the conversion of existing NIH 3D Print Exchange Chimera scripts to ChimeraX, advising on ChimeraX syntax for capabilities where available and noting missing features in ChimeraX where comparable features don’t exist
+   a. ~~Implement essential missing features discovered above, including:
+      i. ~~!PubChem fetch
+      i. ~~Additional import formats, including mol and sdf
+      i. ~~PDB biounit fetch[a]
+   a. ~~Sequence conservation coloring in ChimeraX
+   a. Fetch sequence annotations (!UniProt, domains, disease-associated mutations) (Eric)
+   a. Enhancements to X3D export format (Greg)
+   a. Read and visualize segmentation models (see deliverable 2) (Tom)
+2. Significantly enhance ChimeraX’s segmentation capabilities for 3d electron microscopy, light microscopy, and medical imaging
+   a. Interactive SimpleITK use in ChimeraX (Tom)
+   a. Allow loading, visualizing, creating, measuring and saving segmentations. (Tom)
+   a. Support new EMDB-SFF segmentation file format from the EM Databank (Tom)
+      i. In progress
+3. Medical imaging
+   a. Metadata browser for DICOM files (Tom)
+   a. Support radiologist collaborator needs by adapting ChimeraX to better suit standard workflows and to provide critical missing features identified by our collaborators (Tom)
+      i. Need to get a collaborator
+4. Improve multi-person VR beyond work accomplished in 2019 SOW
+   a. Localizable connection server solution - deliver a rendezvous server that can easily be deployed by institutions or enterprises. (Conrad/Greg)
+      i. Greg to help containerize cxconference
+5. Human Biomolecular Atlas Program (HuBMAP) multiscale visualization
+   a. Engage with the HuBMAP group to evaluate the potential for ChimeraX extensions to support exploration and analysis of HuBMAP data, particularly as those extensions align with NIAID areas of interest.  This will include determining the programmatic interfaces to access the HuBMAP data and initial efforts to scope the task of supporting the various HuBMAP data formats.
+6. Outreach
+   a. Workshops, Training and presentations
+   a. Instructional material and tools documentation. 
+      i. Detailed instructions for all features shall be provided in a user manual
+      i. Written user guides and tutorials shall be available as an HTML page
+7. Administration
+   a. A project schedule, implementation plan, and documentation plan will be provided
+   a. Monthly status reports detailing progress on each subtask will be delivered
+
+
+Additional Requests from Users
+1. Adding Coulombic coloring (Eric)
+   a. 90% cases covered
+
+
+== NIAID SOW Additional Proposed Deliverables (based on 2.5 FTE) ==
+1. Medical Imaging -- in addition to the above proposed deliverables (#3 above), suggest that UCSF Staff engage with a small set of radiologists who can act as close collaborators to improve and drive our efforts.  This would include supporting:
+   1. Measuring changes in time progression, alignment, sizes, color differences
+   2. Implement “cinematic lighting” for improved perception of details.
+2. Improve multi-person VR beyond work accomplished in SOW #2
+   1. Support the ability of any participant to bring in new models
+   2. Support integrated audio chat
+
+
+NIAID SOW draft Dec, 2019
+Group meeting Dec 19, 2019
+
+
+R01 ChimeraX proposal
+~2 FTE
+
+
+1. NIH 3D pipeline using ChimeraX (Eric) ~.8
+   * NIH 3D Print Exchange pipeline using Chimera will be migrated to new NIH 3D pipeline for both printing and VR.  New pipeline will use ChimeraX. Current scripts are those named Chimera*py in their github site.
+   * Current Chimera pipeline uses these features not in ChimeraX (from Elaine); unclear if any are “must haves”:
+      * PubChem fetch
+      * VRML export - Meghan’s 2016 email said of X3D and VRML “we only need X3D”
+      * Import of fchk, gro, mol, sdf files
+      * PDB biounit fetch
+      * Combine structures, maybe not needed if only for molecular surfaces
+      * Coulombic coloring, requires charge assignment
+   * Export of other formats (possibly Collada, GLTF (ascii), FBX, OBJ with texture colors), X3D enhancements.
+   * Sequence conservation coloring
+   * Fetch sequence annotations (UniProt, domains, disease-associated mutations)
+   * Read and visualize segmentation models.
+2. Human Biomolecular Atlas Program (HuBMAP) multiscale visualization (Tom) ~.1
+   * Models from medical imaging, 3d light microscopy, 3d electron microscopy
+   * Connection with Nils Gehlenborg at Harvard, HIVE
+   * Tom G sent email to Phil Cruz to ask for more details about BCBB’s role in HuBMAP
+   * Oct 2019 Nature overview of HuBMAP overview article:
+      * “focus of HuBMAP [is] on spatial molecular mapping”
+      * “We anticipate that the first round of data will be released in the summer of 2020”
+      * “HuBMAP, in collaboration with other NIH programs, plans to hold a joint meeting with the Human Cell Atlas initiative to identify and work on areas of harmonization and collaboration during the spring of 2020.”
+      * “To ensure that browsers and visualization tools from HuBMAP are valuable, the consortium will work closely with anatomists, pathologists, and visualization and user experience experts, including those with expertise in virtual or augmented reality.”
+      * “Ultimately, we hope to catalyse novel views on the organization of tissues, regarding not only which types of cells are neighbouring one another, but also the gene and protein expression patterns that define these cells, their phenotypes, and functional interactions. In addition to encouraging the establishment of intra- and extra-consortium collaborations that align with HuBMAP’s overall mission, we envision an easily accessible, publicly available user interface through which data can be used to visualize molecular landscapes at the single-cell level, pathways and networks for molecules of interest, and spatial and temporal changes across a given cell type of interest. Researchers will also be able to browse, search, download, and analyse the data in standard formats with rich metadata that, over time, will enable users to query and analyse datasets across similar programs.”
+3. Segmentation capabilities for medical imaging, 3d light microscopy, 3d electron microscopy (Tom) ~.25
+   * Interactive SimpleITK use in ChimeraX
+   * Allow loading, visualizing, creating, measuring and saving segmentations.
+   * Support new EMDB-SFF segmentation file format from the EM Databank
+4. Medical imaging (Tom) ~.25 - ~.5
+   * Metadata browser for DICOM files
+   * Support radiologist collaborator needs
+   * Measuring changes in time progression, alignment, volume measurement, difference coloring
+   * Enhanced lighting for improved perception of details.
+5. Virtual reality (Conrad) ~.25 - ~.50
+   * Improve multi-person VR beyond work accomplished in SOW #2
+      * Any participant can bring in new model
+      * Audio chat, third-party or built-in solution
+      * Localizable connection server solution
+   * Recording VR sessions (for VR playback? Or conventional video playback?)
+6. Drug docking (Conrad)
+   * VR UI
+   * Turn on and off surface display
+   * Show hydrogen bonds - for induced-fit docking results? (already have this and clashes for single-receptor multi-ligand situation)
+   * Local minimization (use OpenMM), needs ligand parameterization, DockPrep/Antechamber
+7. Documentation and training materials for above new capabilities. (Elaine) ~.4
+   * NIH 3D pipeline
+      * Provide ongoing advice on ChimeraX commands due to syntax and parameter differences (lighting, cartoon style, etc.)
+   * Segmentation capabilities
+   * Medical imaging
+   * Virtual reality
+8. Administration ~.1
+
+
+
+
+
+
+NIAID SOW Ideas – Dec 2019
+Initial discussion on next SOW goals, Dec 5, 2019 group meeting.  Followed up Dec 12, 2019 with video conference with Phil Cruz, Meghan McCarthy and Darrell Hurt.
+
+
+* MSC/NIAID suggestions
+   * Migration of NIH print-exchange to NIH 3D (use ChimeraX)
+   * Updates to ChimeraX to support pipeline (Elaine’s missing pieces)
+   * See below (scripts are all on github)
+   * Extended to VR/AR as well as 3D printing
+      * Need to be able to handle differences
+   * Allow uploads of ChimeraX session files?
+   * GLTF text form support
+   * Learning about python interface to ChimeraX[c]
+   * Additional file types (Collada, etc.)
+* previous SOW Google doc with crossouts
+* previous SOW discussion on ChimeraX wiki
+* feature list in DICOM viewer notes (some are done or partially done, some are linked to tickets)
+* many possibilities relating to segmentation
+   * see especially the ChimeraX wiki link above
+   * investigate use of machine learning to identify and annotate features
+   * They are extending the itk toolkit to microscopy images
+   * Focus has been on medical imaging
+* TomG: try to steer more toward data types with which we are more familiar, e.g. light microscopy and EM
+   * Particularly as an overlap with simple itk uses for segmentation[d]
+* better support for multi-person VR sessions, hard to make reliable
+   * firewall issues
+   * VPN
+   * AWS - rendezvous service? Conrad will investigate.
+   * if our own service, we don't want everybody on it
+   * investigate audio services (possibly integrated)
+   * enable any participant to load new data without deleting others' data
+   * material for multi-person VR sessions for remote training
+* advancing VR/ViewDockX capabilities
+   * Dock Prep
+      * Antechamber?
+   * anything else?
+   * A lot of general interest.  Great VR use case.
+   * Turn on and off surface display
+   * Hydrogen bonding
+   * Local minimization (use OpenMM)
+      * How do we get force field for ligands?
+   * Kudos for the tape measure tool
+* 3D printing: enable porting workflow from Chimera to ChimeraX
+   * any tie into segmentation?
+   * are they still interested in pursuing this?[e]
+* Tom F: avoid overlap with NIGMS grant
+* Sequence analysis/MAV?
+   * coloring by conservation (conserved regions may be better vaccine targets, e.g. universal flu vaccine as in the PBS VR segment from June 2019)
+   * fetch annotations or info (UniProt, domains, disease-associated mutations, ...)
+* hierarchy & smart level of detail in large and complex data and segmentations
+   * segmentation browser[f]
+   * Support transition easily between different levels of detail
+   * Google-earth style for the models
+   * Look at potential synergy with HubMap[g]
+* DICOM enhancements
+   * DICOM browser showing data hierarchy, metadata[h]
+      * Show 5 most important things, but support showing more metadata at the user request
+   * better/more presets for different tissue types in DICOM data
+   * provide “smart” initial coloring (bones, organs, tissue types)[i]
+   * provide photorealistic lighting to visualize 3D images and volumes
+* Wendell Lim's engineered cells - infectious disease tie-in? Opportunity to get NIAID more interested in light (optical) microscopy. Max Krummel.
+* recording VR sessions (augmented reality, etc.)
+* HTML documentation for any of these new features, of course
+* Educational uses of ChimeraX and VR (e.g. undergraduate education -- multi-user especially)[j]
+   * Would an animation tool fit here?
+* Other types of measurement (coupled with segmentation)
+   * Volume measurement
+   * Comparison capabilities (e.g. progression over time)
+* Other sources of collaborators for medical imaging VR
+   * Dmitri, other VA collaborators, Viv in addition to Beth
+Other crossouts from previous SOW:
+* select and/or highlight voxels in volumetric data representations. Save the selection, and apply visualization commands to just the selection.
+* provide “smart” initial coloring (bones, organs, tissue types)
+* provide photorealistic lighting to visualize 3D images and volumes
+* additional material may be presented in video format, e.g., “How-to” screen capture videos, mixed reality video capture showing person and data for tutorials and for explaining research results to the public