| 579 | | == 3/3/2022 == |
| 580 | | |
| 581 | | Phil, Philip, Darrell, Meghan; Scooter, Elaine, Eric, TomG, Zach, Greg |
| 582 | | |
| 583 | | Discussion of on-site work; HHS has a mandate of twice per pay period which for them amounts to one day a week. |
| 584 | | |
| 585 | | Main subject is SOW. Scooter will take notes on our copy. Darrell didn't get a chance to look before this meeting and encourages Meghan, Phil, et al. to chime in with any opinions they may have. |
| 586 | | |
| 587 | | Phil would like GUIs for copy/combine, renumbering, change chain ID, etc.; he says these actions were much easier in Chimera for this reason. However, ChimeraX commands are easier and more mnemonic than Chimera commands. |
| 588 | | |
| 589 | | When there is an NIH 3D website, Philip would like Eric, Tom G, Zach, et al. to give it a try. |
| 590 | | |
| 591 | | Discussion of data transfer when adding models in multiperson VR sessions. |
| 592 | | |
| 593 | | Darrell: MSC is new vendor! MSC has been acquired by Guidehouse but procedures ane people should be basically same. Especially if fixed-price contact, may need to clarify in SOW that some of these items will be initial basic implementations, not necessarily the most complete and perfect realizations of the product. |
| 594 | | |
| 595 | | Phil: maybe improved visualization of DICOM is too vague a statement. |
| 596 | | |
| 597 | | TomG: we will add more details, e.g. medical imaging toolbar shown in VR, ability to adjust transfer function/thresholds/coloring. Also would like to add capabilities for interactive segmentation in VR. |
| 598 | | |
| 599 | | Phil: take a look at features in Medical Holodeck, some of them are nice. 7-day trial, can be run standalone on Quest2. Meghan: but it's not free, so not as accessible to collaborators (e.g. in Africa) as ChimeraX. |
| 600 | | |
| 601 | | TomG: we can't run standalone on Quest2. |
| 602 | | |
| 603 | | Darrell: Re outreach, would like to have something like the Rocky Mountain workshop we had before. Can we add something like a specific number of workshops requiring travel? Scooter: how about "as required"? Darrell: that may be OK. |
| 604 | | |
| 605 | | Darrell: what about segmentation for cryoEM? TG: that's also of interest (not just for DICOM). ChimeraX already has marker tools like those in Chimera. |
| 606 | | |
| 607 | | Darrell: should prioritize 16-bit image data (e.g. DICOM). Elaine: we couldn't read Meghan's knee scan either. TG: ...because it was lossless jpeg. |
| 608 | | |
| 609 | | Phil: any plans for a native Apple Silicon version? Scooter: Zach is working on that too. TG: should be ~50% faster. |
| 610 | | |
| 611 | | == 3/17/2022 == |
| 612 | | |
| 613 | | Phil, Philip; Elaine, Eric, TomG, Zach, Greg |
| 614 | | |
| 615 | | Eric: is it OK to put NIH3D presets bundle on toolshed? Yes. |
| 616 | | |
| 617 | | Phil describes the problem with changing model coordinates to center on 0,0,0. Requires finding center and then subtracting it off with 3 "move" commands using the "models" and "coordinateSystem" options. Would be nice for to have a single-step option to reset coordinates of a structure to put the center at 0,0,0. Useful for NIH3D pipeline in general. TomG: could also be an option of export scene. Phil: also useful in another context, before solvating an atomic structure. |
| 618 | | |
| 619 | | Phil: the NIAID folks are good with what's in our new SOW. |
| 620 | | |
| 621 | | Phil: sometime next week is world TB day, and our website is going to have a new TB & VR section. Featured data is lung CT scans with information about drug-resistant TB. Phil shows his screen with 5uhb in ChimeraX: TB transcription initiation complex with inhibitor drug, resistance mutations occur in binding pocket. Will tell that story using ChimeraX export to GLB (this was the reason to want center at origin). Uses IP3 Connect web VR. TomG: I would like to preview the site! Phil will send the URL and some hints on how to use it. Can be viewed without VR, but there is a button for using VR if you have the equipment. |
| 622 | | |
| 623 | | Elaine and Phil commiserate on difficulties with learning Horos. Elaine has been trying to use 3D Slicer and Horos to view time series but neither works (or she just can't figure out how to make them work). Phil doesn't use these for 4D data, suggests asking Kristen since she uses 3D Slicer a lot. |
| 624 | | |
| 625 | | TomG: Phil, any advice for in-person VR demos in the time of COVID? Phil: we just wipe down the parts in face contact with isopropyl alcohol wipes. This was pre-delta, though. We made a show of carefully wiping the equipment. We also have a box that does UV sterilization but it may not get the light into the nooks and crannies. |
| 626 | | |
| 627 | | == 3/31/2022 == |
| 628 | | |
| 629 | | Phil, Philip; Elaine, Eric, TomG, Zach, Greg |
| 630 | | |
| 631 | | Status of SOW? Still being negotiated. Phil: what is highest priority? TomG: We're told it won't start until May 1, so we haven't thought mcuh about it yet. The SOW includes machine learning & !AlphaFold stuff. Phil: everybody's interested in using that now. TomG: shows !AlphaFold "predicted aligned error" (PAE) plot just added to ChimeraX. Google Colab version doesn't use templates, so PAE domain identification is based on residue covariance. PAE plot and interaction with structure in ChimeraX is similar to that available at the !AlphaFold Database, except the ChimeraX one is better if you highlight an off-diagonal box on the plot (shows 2 colors on structure). |
| 632 | | |
| 633 | | Discussion of importance/predominance of disordered regions in proteins. Phil: simulations don't model these well. |
| 634 | | |
| 635 | | Phil used to work at Tripos. Elaine: my first modeling work was with SYBYL (from Tripos) on the Evans & Sutherland! Phil: booting up the E & S took forever. |
| 636 | | |
| 637 | | TomG: I added a tug command to fix up linkers after building a large, complicated protein structure. |
| 638 | | |
| 639 | | Elaine: figured out how to show time series in 3D Slicer. At least some of the problem was due to the version of 3D Slicer - time series example files for one version don't work in the other (without additional steps needed to define a set of maps as a time series). |
| 640 | | |
| 641 | | TomG: looked at the NIAID TB-VR experience website, sent feedback to Phil. Phil: here's the URL, public now: https://tbportals.niaid.nih.gov/tb-in-vr TomG: "save" GLTF has a "center" option. Maybe we should make the default "center 0,0,0" ... downside is when the user wants to preserve the relative locations of multiple structures. |
| 642 | | |
| 643 | | == 4/14/2022 == |
| 644 | | |
| 645 | | Phil, Philip; Elaine, Eric, TomG, Zach, Greg |
| 646 | | |
| 647 | | Today Darrell authorized "MSC" (or logical equivalent) to act on UCSF’s final proposal against the SOW! |
| 648 | | |
| 649 | | Phil: I hear that the new NIH3D workflow will be deployed soon. Kristin will be project coordinator, maybe she will attend some of our meetings in the future. |
| 650 | | |
| 651 | | Phil: Eric, please add the GLTF (glb) saving option "center 0,0,0" to the workflow. TomG: don't bother, I'll make that the default. |
| 652 | | |
| 653 | | Eric: I still can't upload the bundle to the toolshed, because... Greg: dependency field issue with comma in string. Will be solved by upgrading to newer mariadb, should be done within a week. |
| 654 | | |
| 655 | | Eric is working on joining models, starting with peptide bond. |
| 656 | | |
| 657 | | Phil: gave a talk to the structural biology group, showed alphafold PAE plots -- people were very interested and liked the ability to switch between domain and confidence (pLDDT) colorings. Elaine: there's a Youtube video of TomG's recent SBGrid workshop on that topic. |
| 658 | | |
| 659 | | TomG: maybe we can also color by conservation calculated from the giant sequence alignment alphafold uses to covariance. |
| 660 | | |
| 661 | | Phil: people had several suggestions: |
| 662 | | (1) to predict every chain in an existing PDB. TomG: you can do that now, just open that structure first and use "alphafold match" ... however, what you get may have a different albeit similar sequence (top BLAT hit) |
| 663 | | (2) another request was to draw chain boundaries on the PAE plot for the multichain case. |
| 664 | | (3) for selected residue, color others by their PAE with the selected residue. Could also color-code pseudobonds, or only draw pseudobonds for certain range of PAE values. |
| 665 | | (4) report X,Y cursor location when over the plot (e.g. residue numbers, chain IDs) TomG: what about on the structure? select the 2 residues? draw a pseudobond between them? |
| 666 | | (5) allow zooming in to regions within the plot |
| 667 | | |
| 668 | | Phil: does predicting in ChimeraX work with a user's Colab Pro or Pro+ plan? TomG: yes, since you sign in to Google it knows you have an account. |
| 669 | | |
| 670 | | TomG: do you have any experience with Vive focus 3? Phil: we may be getting one soon, as well as HP Reverb and Pico (sp?), which has eye tracking... the hot new headsets. Will let you know. TomG: I like the Vive pro 2, higher resolution, eye tracking. |
| 671 | | |
| 672 | | == 5/12/2022 == |
| 673 | | |
| 674 | | Phil, Philip, Meghan; Elaine, Eric, Zach, Greg, Scooter |
| 675 | | |
| 676 | | Scooter: we are planning a group off-site get-together, maybe October, maybe sailing. |
| 677 | | |
| 678 | | Scooter: contract agreement is done! Tom G is the unofficial lead on this NIAID funding, but he's on vacation now, so we don't have much to say yet. Zach will be working on the DICOM stuff. Status of NIH 3D? |
| 679 | | |
| 680 | | Phil: last I recall, still waiting on progress with the workflow server to handle new submission process and use of presets. Eric & Greg worked out the toolshed issue, and the bundle is available there. Philip got called to another project and another developer (Mihal?) is taking over the NIH 3D workflow programming. Kristin is now the development coordinator for NIH3D. |
| 681 | | |
| 682 | | Scooter: maybe that person can present at our next meeting? Meghan & Phil agree. Meghan will ask Mihal about doing this. |
| 683 | | |
| 684 | | Scooter: progress on !AlphaFold but we would also like to look into !RosettaFold calculations too. Phil: !RosettaFold is harder to use. It was also reasonable to start with !AlphaFold since EBI is providing a database of already-calculated models. Scooter: there was some talk of RCSB starting a !RosettaFold database. |
| 685 | | |
| 686 | | Scooter: Elaine's been presenting DICOM and DICOM viewers, and we have a couple of possible people to work with for real data & applications, Jason Rubenstein at Medical College of Wisconsin, and previously there was somebody else in South America. Of course we still want to hear any requests or suggestions your group has for DICOM in VR, which would be top priority for this contract. |
| 687 | | |
| 688 | | Meghan: we've had a lot going on, not to mention the pandemic disruptions, so we need to revisit VR medical applications along with our collaborators in Uganda. We're meeting with them in a couple of weeks. We're also working with other groups in VR medical applications (NHS in UK for health training) and come up with our next strategy and get back to you later. I'm glad this is back on the radar! We will also be getting more hardware. |
| 689 | | |
| 690 | | Scooter: we have a good wifi setup for untethered Quest headset now. Required wrangling with UC IT to allow setting up our own wifi6 router (?) only for this limited purpose. Campus wireless was unusable for this purpose. |
| 691 | | |
| 692 | | Phil: in ChimeraX, a big advantage is that we can go inside models in VR. Medical Holodeck doesn't really allow this, framerate goes way down. |
| 693 | | Meghan: Medical Holodeck is just too heavyweight for convenient use in many situations. |
| 694 | | |
| 695 | | Phil: we like that the mapping of buttons to the cones shown in VR. However, the mapping is not good for some of the controllers where the buttons are in different places. So we would like Tom G to take a look at making different mappings that better match the different controllers. Elaine: I'll make a ticket and maybe Phil can add comments about which ones are mismatched. |
| 696 | | |
| 697 | | Phil, Meghan: Another recent problem with old (Chimera) pipeline may be related to EMDB metadata. Eric: new (ChimeraX) pipeline gets recommended contour level; don't know what the old pipeline does. Phil: I think the problem is not in Chimera but in some other step. |
| 698 | | |
| 699 | | Scooter: 1.4 release is coming soon, release candidate is available. |
| 700 | | |
| 701 | | == 5/26/2022 == |
| 702 | | |
| 703 | | Phil, Philip, Darrell (Meghan sick today); Zach, Eric, Elaine, Greg, TomG, Scooter |
| 704 | | |
| 705 | | Presentation by new NIH3D workflow developer, Michal? Not scheduled yet, maybe next time. Phil: will see if he's available to join this meeting. |
| 706 | | |
| 707 | | Phil: have done a little testing on the latest bundle from the toolshed, will send (minor) comments via e-mail. Main issue this week was NIH3D pipeline breaking due to changes in metadata, but has been dealt with. |
| 708 | | Darrell: was not related to Chimera, was caused by a change in the XML from EMDB. |
| 709 | | |
| 710 | | Darrell: how can we get an approximate contour level if we fail to get one from EMDB? Eric: there is already some iterative process to setting a contour level that makes a coherent blob. Darrell: sounds good. |
| 711 | | |
| 712 | | Darrell: we would like TomG to come to Wash DC and also Rocky Mtn Labs. Scooter: we budgeted for those two trips. Phil: maybe for the Biovis lab opening events. Darrell: time frame is uncertain, originally planned for fall but there are many other important meetings at about the same time, so it may be delayed. Darrell: will be going to Nigeria for an NIH meeting (the last "H3" meeting; had demoed VR there in 2018). VR demo has been requested for a meeting in Mali, at rather short notice. Phil: there was a VR-collab demo between Mali and Uganda not long ago. |
| 713 | | |
| 714 | | Darrell: what systems are good to show in VR? Phil: TB drug resistance. Is this a demo? Darrell: maybe a video but not by this Sunday when they wanted. |
| 715 | | |
| 716 | | Phil: I've been trying the release candidate from 5/20, haven't found problems. |
| 717 | | |
| 718 | | Darrell: do you have an M1 version? Zach: In progress. Elaine: I've been using the existing download (via emulation) on an M1 machine without problems, works well. Phil: everything seems twice as fast, even with the emulation, on my M1 machine. |
| 719 | | |
| 720 | | TomG: CPU speed on M1 is great. I made a benchmark page https://www.rbvi.ucsf.edu/chimerax/data/czi-nov2021/apple_m1.html |
| 721 | | |
| 722 | | Philip: what are the Rocky Mountain cluster. Darrell: GPUs are the one before A100, something starting with a different letter. Scooter: We are using A40 and A100 on our cluster. |
| 723 | | |
| 724 | | Scooter: would like to discuss DICOM at a later meeting. Elaine: are we hearing from Michal next time? Phil: I'll check with him and get back to you. |
| 725 | | |
| 726 | | Darrell: Brad and Ziv may be able to provide datasets. Scooter: maybe we can also get them to join the discussion. Elaine: to say how they analyze the data. Darrell: focus on visualization component, not to replace these other packages like Slicer3D. Phil: maybe some analyses would be great to combine with VR. Darrell: maybe should get Dave (he's responsible for the Visible Human stuff) to present as well. How about we get them to view DICOM in ChimeraX and give comments? Scooter: that would be good, too. TomG: we need a VR-specific perspective, though. Scooter: maybe NIH folks can set up a DICOM-VR session. Phil: maybe Dave + TomG in VR meeting. TomG: sounds OK, but I still think that we need to get more feedback from Jason Rubinstein (or other people that really work with both medical imaging and VR). Remote meetings have limitations, however; talking face-to-face in the same room is really the best if possible, say during my visits. Darrell: then maybe Jeff Solomon, perhaps NIAID's most DICOM-oriented scientist. Dave certainly knows DICOM, too. Maybe we could fly Jason Rubinstein in from Wisconsin. TomG: can we afford to fly Zach in too? Scooter: currently contract has 2 trips for one person. Darrell: maybe we can find additional funding. |
| 727 | | |
| 728 | | == 6/9/2022 == |
| 729 | | |
| 730 | | Phil, Philip, Michal Stolarczyk and David Liou from 3D pipeline team, Meghan (last half); Zach, Eric, Elaine, Greg, TomG, Scooter |
| 731 | | |
| 732 | | Self-introductions from both teams. |
| 733 | | |
| 734 | | Michal is currently the primary developer working on NIH3D, working for last month on infrastructure. ChimeraX script has been running without issues, so he hasn't been working on that part. ~10-min slide presentation. |
| 735 | | |
| 736 | | Running Ubuntu 20.4 0 within EC2 instance within VPC within AWS. Involves Prefect and GraphQL. |
| 737 | | |
| 738 | | Recent updates: |
| 739 | | - workflow deployment: standardized flow names, external Postgres database |
| 740 | | - workflow handling: https://niaid.github.io/nih_3D_workflows, JSON-based configuration |
| 741 | | |
| 742 | | Planned enhancements: |
| 743 | | - switch to ECS for running flows (to handle more at the same time) |
| 744 | | - increase reproducibility of results by including code versioning |
| 745 | | - use newer version of NIH3D presets provided by Eric |
| 746 | | |
| 747 | | Phil: Eric please explain unified script and presets |
| 748 | | |
| 749 | | Eric: originally all the types of view/displays that could be requested by the user were in a giant script with lots of commands, and we decided to refactor that as a set of presets where each preset generates one type of view. Now a smaller script calls the individual presets as needed. This set of presets is available as a bundle on the ChimeraX toolshed. Would have to re-install if ChimeraX is not persistent between runs. |
| 750 | | |
| 751 | | Michal: ChimeraX is persistent on the same machine, but different machines are used. When we use ECS it will deploy a docker image that could have the bundle already installed. |
| 752 | | |
| 753 | | Eric: how long to deal with my pull request? Michal: about a couple of weeks. |
| 754 | | |
| 755 | | Eric: ChimeraX now has "renumber" command, on the way towards having a GUI to do it. |
| 756 | | |
| 757 | | Some discussion of reproducibility, ChimeraX preferences and fetch caching. |
| 758 | | |
| 759 | | Phil: are ChimeraX-calculated values saved somehow? Eric: currently, the script sends them to standard-out with a standardized prefix to facilitate grepping the lines. Could be changed if needed. |
| 760 | | |
| 761 | | TomG: new "alphafold contacts" command to draw pseudobonds as explained in https://www.rbvi.ucsf.edu/chimerax/data/alphafold-contacts-jun2022/afcontacts.html |
| 762 | | |
| 763 | | Phil: what about similar pseudobonds for contacts? Elaine: can be done with "contacts" command but we don't have anything to color them continuously by length yet. Scooter: might be interesting to show histogram by length with "crosslinks histogram". Elaine: clicking a histogram bar interacts with corresponding pseudobonds. |
| 764 | | |
| 765 | | Zach: has reached out to Jason Rubinstein, he will take a look at his data using our latest DICOM/VR and get back to us |
| 766 | | |
| 767 | | Meghan: we still need to give feedback on where the buttons are on different VR hand-controllers, for better mapping to the cone display in the headset. TomG: we currently use two different layouts, one for Vive and one for Oculus Rift. So more could be added. |
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