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From: Steve A. <ste...@gm...> - 2021-10-09 11:42:11
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Hi Frank, Thanks for arranging this. I’ll try to register for COMBINE, but could you send me the zoom link anyhow, just in case? I’m currently traveling, so things are a bit more complicated than usual. Thanks! -Steve On Fri, Oct 8, 2021 at 10:06 AM Frank T. Bergmann < fra...@bi...> wrote: > Dear all, > > To break the silence in this list, I have signed us up for a time slot at > COMBINE 2021. We can meet: > Wednesday, October 13 * 16:00 - 17:00 (CEST) > > In the session, I would be hoping that we could just like last year: > > * exchange some examples between software tools, > * find if there are any last issues to be addressed, > * and prepare to move the package for acceptance. > > If you have registered for COMBINE, you can access the zoom link shortly > before the event here: > > https://combine2021.sched.com/event/nYHV/sbml-level-3-package-for-spatial-processes-next-steps > > (should you have been unable to register for COMBINE you could still do > so, but I can also send you the zoom link directly). > > Hope to talk to you next week, > Thanks > Frank > > > _______________________________________________ > sbml-spatial mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-spatial > |
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From: Frank T. B. <fra...@bi...> - 2021-10-08 14:06:25
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Dear all,
To break the silence in this list, I have signed us up for a time slot at COMBINE 2021. We can meet:
Wednesday, October 13 * 16:00 - 17:00 (CEST)
In the session, I would be hoping that we could just like last year:
* exchange some examples between software tools,
* find if there are any last issues to be addressed,
* and prepare to move the package for acceptance.
If you have registered for COMBINE, you can access the zoom link shortly before the event here:
https://combine2021.sched.com/event/nYHV/sbml-level-3-package-for-spatial-processes-next-steps
(should you have been unable to register for COMBINE you could still do so, but I can also send you the zoom link directly).
Hope to talk to you next week,
Thanks
Frank
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From: Frank T. B. <fra...@bi...> - 2021-03-24 16:26:54
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Dear all, This is to let you know, that the online validator has now been updated, to carry out the validation as spatial models. I recommend that you do compress the SBML file prior to uploading, in case it gets too big: http://sbml.org/validator Please let me know in case you encounter any issues Cheers Frank |
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From: Lucian S. <luc...@gm...> - 2021-03-23 00:32:21
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OK, let's try Wednesday: https://doodle.com/poll/hpmwhmmyrv7st5nw?utm_source=poll&utm_medium=link This is being added to the HARMONY schedule; it'll be just before the PETab breakout. See you then! -Lucian On Thu, Mar 18, 2021 at 4:31 PM Lucian Smith <luc...@gm...> wrote: > Hey, everyone! We should meet at HARMONY and see if we can trade some > spatial models and finalize this specification. I believe a > morning-my-time would work, but feel free to suggest a different time. > Here's a doodle poll to see what might work best for us: > > https://doodle.com/poll/hpmwhmmyrv7st5nw?utm_source=poll&utm_medium=link > > -Lucian > >> |
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From: Lucian S. <luc...@gm...> - 2021-03-18 23:32:13
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Hey, everyone! We should meet at HARMONY and see if we can trade some spatial models and finalize this specification. I believe a morning-my-time would work, but feel free to suggest a different time. Here's a doodle poll to see what might work best for us: https://doodle.com/poll/hpmwhmmyrv7st5nw?utm_source=poll&utm_medium=link -Lucian > |
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From: Michael H. <mh...@li...> - 2021-02-15 04:41:22
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Hello Medha, Thank you again for your participation in GSOC 2020 and your hard work on this project! I'm very sorry it's taken so long for me to do this, but I have finally added an item to the (upcoming new) SBML website about your project. You can see it in the preview web server at https://synonym.caltech.edu/about/contributors/ (in the section on "summer of code"). Please let me know if it looks okay or if there are any mistakes or you would prefer anything to be changed. Thank you again, and I hope all is well with you and your family during these difficult times. Best regards, Mike -- Mike Hucka, Ph.D. mh...@ca... -- http://www.cds.caltech.edu/~mhucka California Institute of Technology On 12 May 2020, at 3:35, MEDHA BHATTACHARYA wrote: > Hello everyone! > > I am Medha Bhattacharya, a second-year undergraduate student pursuing > a > Bachelor of Technology (Computer Science and Engineering) at Indira > Gandhi > Delhi Technical University for Women, India. I am glad to inform you > all of > my selection in the Google Summer of Code 2020 program with National > Resource for Network Biology. > > Project title: Development of a system that generates spatial SBML > models > using deep learning. > > (Issue: https://github.com/nrnb/GoogleSummerOfCode/issues/140) > > This project aims at creating and implementing a software tool that > automatically generates various spatial SBML models via XitoSBML by > comprehensively segmenting microscopic images of cells using deep > learning. > Consequently, my project will create a large number of spatial SBML > models. > Furthermore, as XitoSBML uses JSBML to write spatial SBML models, it > will > be used throughout. > > Since the development of the SBML Version 3 spatial package is > currently > under progress, a large number of test models are required. These can > be > provided as deliverables via this project to the SBML repository. > Additionally, the provision of several spatial SBML models will enable > testing the compatibility of software tools that deal with spatial > SBML > models. > > The link to my blog-post: https://gsoc2020mb.blogspot.com/ > > I am hoping to be able to contribute towards the development of the > SBML > spatial package this summer! > > Cheers! > > Medha > _______________________________________________ > sbml-spatial mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-spatial |
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From: Lucian S. <luc...@gm...> - 2020-10-06 22:42:26
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Hello! I apologize for not getting this set up earlier, but would people be up for a breakout session during COMBINE? The timezones may well be a problem, as usual, but hopefully we can get at least a few of us together to try to exchange some models and iron out any remaining ambiguities/problems in the spec itself. Is there a time we should aim for? Should I set up a doodle poll or the like? -Lucian |
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From: MEDHA B. <me1...@gm...> - 2020-09-05 09:15:59
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Hello everyone! My project, "Development of a system that generates spatial SBML models using deep learning" under Google Summer of Code 2020, is now complete. As a result, I have been able to generate a few hundred spatial SBML models, which can contribute to the development of the SBML Version 3 spatial package. I am enclosing the link to a sample folder containing 20 microscopic cellular images, corresponding ground truth images and, spatial SBML models generated via this project. https://drive.google.com/drive/folders/1z83_pUTlI7eYKL9J9iV-EV6lLAEqC7pG?usp=sharing Kindly inform me whether these are suitable as test models for the spatial package; I would be glad to contribute many more such models. Cheers! Medha Bhattacharya. On Tue, May 12, 2020 at 4:05 PM MEDHA BHATTACHARYA <me1...@gm...> wrote: > Hello everyone! > > I am Medha Bhattacharya, a second-year undergraduate student pursuing a > Bachelor of Technology (Computer Science and Engineering) at Indira Gandhi > Delhi Technical University for Women, India. I am glad to inform you all of > my selection in the Google Summer of Code 2020 program with National > Resource for Network Biology. > > Project title: Development of a system that generates spatial SBML models > using deep learning. > > (Issue: https://github.com/nrnb/GoogleSummerOfCode/issues/140) > > This project aims at creating and implementing a software tool that > automatically generates various spatial SBML models via XitoSBML by > comprehensively segmenting microscopic images of cells using deep learning. > Consequently, my project will create a large number of spatial SBML models. > Furthermore, as XitoSBML uses JSBML to write spatial SBML models, it will > be used throughout. > > Since the development of the SBML Version 3 spatial package is currently > under progress, a large number of test models are required. These can be > provided as deliverables via this project to the SBML repository. > Additionally, the provision of several spatial SBML models will enable > testing the compatibility of software tools that deal with spatial SBML > models. > > The link to my blog-post: https://gsoc2020mb.blogspot.com/ > > I am hoping to be able to contribute towards the development of the SBML > spatial package this summer! > > Cheers! > > Medha > |
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From: Lucian S. <luc...@gm...> - 2020-06-19 00:05:30
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Hey, everyone! We had a successful meeting about a month ago, so let's meet again to figure out what the next steps are: https://doodle.com/poll/8wrbh5z2d4b3iv8g The agenda: * Any models newly imported? Any problems doing so? * Any new models to share/exchange? * Any issues with validation? * Spec examples now fixed. * Any other spec clarifications ('hasOnlySubstanceUnits', 'isLocal'). Thank you, everyone! -Lucian |
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From: Luke W. <lwh...@gm...> - 2020-06-18 17:20:50
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Okay, thanks for that suggestion. That might be a way I can hack it. Cheers! Luke On Thu, Jun 18, 2020 at 11:19 AM Herbert M Sauro <hs...@uw...> wrote: > You could fake a spatial model by creating a series of connected > compartments or species but it would be tedious to construct, although one > could write some software that would build it for you. I've done this > before to simulate simple one diffusion. > > Herbert > > On Thu, Jun 18, 2020 at 9:20 AM Lucian Smith <luc...@gm...> > wrote: > >> Neither antimony nor Tellurium support spatial modeling at present, >> unfortunately. The tools I know of that support spatial modeling include: >> >> * VCell (though it's a little out of date) >> * XitoSBML >> * CellOrganizer >> * CellBlender/MCell >> >> You might get a better response from the sbml-spatial list, at >> sbm...@li... >> >> -Lucian >> >> On Thu, Jun 18, 2020 at 8:50 AM Luke Wheeler <lwh...@gm...> wrote: >> >>> Hello, >>> >>> I was wondering if it is possible to encode a spatial concentration >>> gradient within a compartment in the antimony language? I am hoping to >>> create a spatially-resolved model that can be simulated with Tellurium. >>> >>> Thanks, >>> >>> Luke >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "tellurium-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to tel...@go.... >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/tellurium-discuss/8409f668-be51-4ad3-831f-b0698644c24do%40googlegroups.com >>> <https://groups.google.com/d/msgid/tellurium-discuss/8409f668-be51-4ad3-831f-b0698644c24do%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> You received this message because you are subscribed to the Google Groups >> "tellurium-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to tel...@go.... >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/tellurium-discuss/CAHLmBr36oVK%2BWpYcwcyZrei-Hte7kCceGT%2BooN%3DUCwDs50nbyw%40mail.gmail.com >> <https://groups.google.com/d/msgid/tellurium-discuss/CAHLmBr36oVK%2BWpYcwcyZrei-Hte7kCceGT%2BooN%3DUCwDs50nbyw%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > > > -- > Herbert Sauro, Professor > University of Washington, Bioengineering > 206-685-2119, www.sys-bio.org > hs...@uw... > Books: http://books.analogmachine.org/ > |
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From: Herbert M S. <hs...@uw...> - 2020-06-18 17:20:15
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You could fake a spatial model by creating a series of connected compartments or species but it would be tedious to construct, although one could write some software that would build it for you. I've done this before to simulate simple one diffusion. Herbert On Thu, Jun 18, 2020 at 9:20 AM Lucian Smith <luc...@gm...> wrote: > Neither antimony nor Tellurium support spatial modeling at present, > unfortunately. The tools I know of that support spatial modeling include: > > * VCell (though it's a little out of date) > * XitoSBML > * CellOrganizer > * CellBlender/MCell > > You might get a better response from the sbml-spatial list, at > sbm...@li... > > -Lucian > > On Thu, Jun 18, 2020 at 8:50 AM Luke Wheeler <lwh...@gm...> wrote: > >> Hello, >> >> I was wondering if it is possible to encode a spatial concentration >> gradient within a compartment in the antimony language? I am hoping to >> create a spatially-resolved model that can be simulated with Tellurium. >> >> Thanks, >> >> Luke >> >> -- >> You received this message because you are subscribed to the Google Groups >> "tellurium-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to tel...@go.... >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/tellurium-discuss/8409f668-be51-4ad3-831f-b0698644c24do%40googlegroups.com >> <https://groups.google.com/d/msgid/tellurium-discuss/8409f668-be51-4ad3-831f-b0698644c24do%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- > You received this message because you are subscribed to the Google Groups > "tellurium-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to tel...@go.... > To view this discussion on the web visit > https://groups.google.com/d/msgid/tellurium-discuss/CAHLmBr36oVK%2BWpYcwcyZrei-Hte7kCceGT%2BooN%3DUCwDs50nbyw%40mail.gmail.com > <https://groups.google.com/d/msgid/tellurium-discuss/CAHLmBr36oVK%2BWpYcwcyZrei-Hte7kCceGT%2BooN%3DUCwDs50nbyw%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hs...@uw... Books: http://books.analogmachine.org/ |
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From: Lucian S. <luc...@gm...> - 2020-06-18 16:19:56
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Neither antimony nor Tellurium support spatial modeling at present, unfortunately. The tools I know of that support spatial modeling include: * VCell (though it's a little out of date) * XitoSBML * CellOrganizer * CellBlender/MCell You might get a better response from the sbml-spatial list, at sbm...@li... -Lucian On Thu, Jun 18, 2020 at 8:50 AM Luke Wheeler <lwh...@gm...> wrote: > Hello, > > I was wondering if it is possible to encode a spatial concentration > gradient within a compartment in the antimony language? I am hoping to > create a spatially-resolved model that can be simulated with Tellurium. > > Thanks, > > Luke > > -- > You received this message because you are subscribed to the Google Groups > "tellurium-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to tel...@go.... > To view this discussion on the web visit > https://groups.google.com/d/msgid/tellurium-discuss/8409f668-be51-4ad3-831f-b0698644c24do%40googlegroups.com > <https://groups.google.com/d/msgid/tellurium-discuss/8409f668-be51-4ad3-831f-b0698644c24do%40googlegroups.com?utm_medium=email&utm_source=footer> > . > |
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From: Lucian S. <luc...@gm...> - 2020-05-20 21:32:09
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OK! I've now investigated the example with the invalid reference, and it's a little more complicated than I thought it would be. The issue is that we are assigning an initial value of 'img/2+3' to 'ATP_nuc'. 'img' turns out to be the spatial ID of a SampledFieldGeometry. According to the spec, a SampledFieldGeometry has no mathematical value. Therefore, even if I created a spatialSymbolReference to the 'img', it would still be illegal, for a different reason. However, the 'img' SampledFieldGeometry has a SampledField with the id 'imgvals'. 'imgvals' already has a spatialSymbolReference, and therefore my *guess* is that the formula in question should actually be: 'imgvals/2+3'. Does this match other peoples' interpretation of the situation? -Lucian |
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From: Lucian S. <luc...@gm...> - 2020-05-20 15:15:12
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Thanks to everyone who participated in the meeting today! It looks like the spec is indeed about ready for release; we just need to do a few things. Here's the plan: * People with sbml-spatial interpreters: * If you can import models at https://github.com/sbmlteam/sbml-spatial-models, indicate that you can on the new wiki page, https://github.com/sbmlteam/sbml-spatial-models/wiki * If you don't already have a model or two on the site, please create a simple model and upload it and add it to the wiki (or send it to me, and I can do that). * If you haven't tried the validator yet, please do so. If you don't have access to libsbml's validator (which is more comprehensive than jsbml's right now), send it to me and I can validate it and send you the report. If you disagree with any validation message, let me know! * Lucian: * Investigate why libsbml complains about one of the examples in the spec. Either fix the example, or fix libsbml. * Consider writing a clarification on the 'hasOnlySubstanceUnits' attribute in relation to spatial models. * Bob Murphy's group: * After the above is done, take point on an applications note (or similar) describing the tools involved and how they exchanged models. I think that's about it! Keep in touch, and I'll try to schedule a meeting about once a month or so, to make sure everyone has what they need to move forward. Thanks again! -Lucian |
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From: Lucian S. <luc...@gm...> - 2020-05-18 22:14:50
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Also, here's a page we can use for information beforehand, and for recording the minutes: https://docs.google.com/document/d/1ZwXZe18ZoNACBT04ErqSSFR8Ivk527-x5yGVhXIUurA/edit?usp=sharing If any of you have more information you'd like to share, feel free to edit. Thank you! -Lucian On Mon, May 18, 2020 at 2:42 PM Lucian Smith <luc...@gm...> wrote: > Thanks everyone for replying: we have a time where everyone who replied > can make it. Feel free to attend whether you signed up or not. (And feel > free to forward this message to anyone who might not be on the list--I'm > not sure if Liam is or not.) > > I've created a Zoom meeting for us for this Wednesday at 6:00 AM Pacific > time; local times available at the Doodle poll: > > https://doodle.com/poll/n5w48ut52iqcdrd3 > > Here's the information for the meeting itself. Thank you again! > > -Lucian > > > https://washington.zoom.us/j/91707205826 > > > Topic: SBML Spatial > Time: May 20, 2020 06:00 AM Pacific Time (US and Canada) > > Join Zoom Meeting > https://washington.zoom.us/j/91707205826 > > Meeting ID: 917 0720 5826 > One tap mobile > +12532158782,,91707205826# US (Tacoma) > +16027530140,,91707205826# US (Phoenix) > > Dial by your location > +1 253 215 8782 US (Tacoma) > +1 602 753 0140 US (Phoenix) > +1 669 219 2599 US (San Jose) > +1 669 900 6833 US (San Jose) > +1 720 928 9299 US (Denver) > +1 971 247 1195 US (Portland) > +1 213 338 8477 US (Los Angeles) > +1 346 248 7799 US (Houston) > +1 651 372 8299 US (St. Paul) > +1 786 635 1003 US (Miami) > +1 267 831 0333 US (Philadelphia) > +1 301 715 8592 US (Germantown) > +1 312 626 6799 US (Chicago) > +1 470 250 9358 US (Atlanta) > +1 470 381 2552 US (Atlanta) > +1 646 518 9805 US (New York) > +1 646 876 9923 US (New York) > Meeting ID: 917 0720 5826 > Find your local number: https://washington.zoom.us/u/adMWhSOy4V > > Join by SIP > 917...@zo... > > Join by H.323 > 162.255.37.11 (US West) > 162.255.36.11 (US East) > 221.122.88.195 (China) > 115.114.131.7 (India Mumbai) > 115.114.115.7 (India Hyderabad) > 213.19.144.110 (EMEA) > 103.122.166.55 (Australia) > 209.9.211.110 (Hong Kong SAR) > 64.211.144.160 (Brazil) > 69.174.57.160 (Canada) > 207.226.132.110 (Japan) > Meeting ID: 917 0720 5826 > |
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From: Lucian S. <luc...@gm...> - 2020-05-18 21:43:19
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Thanks everyone for replying: we have a time where everyone who replied can make it. Feel free to attend whether you signed up or not. (And feel free to forward this message to anyone who might not be on the list--I'm not sure if Liam is or not.) I've created a Zoom meeting for us for this Wednesday at 6:00 AM Pacific time; local times available at the Doodle poll: https://doodle.com/poll/n5w48ut52iqcdrd3 Here's the information for the meeting itself. Thank you again! -Lucian https://washington.zoom.us/j/91707205826 Topic: SBML Spatial Time: May 20, 2020 06:00 AM Pacific Time (US and Canada) Join Zoom Meeting https://washington.zoom.us/j/91707205826 Meeting ID: 917 0720 5826 One tap mobile +12532158782,,91707205826# US (Tacoma) +16027530140,,91707205826# US (Phoenix) Dial by your location +1 253 215 8782 US (Tacoma) +1 602 753 0140 US (Phoenix) +1 669 219 2599 US (San Jose) +1 669 900 6833 US (San Jose) +1 720 928 9299 US (Denver) +1 971 247 1195 US (Portland) +1 213 338 8477 US (Los Angeles) +1 346 248 7799 US (Houston) +1 651 372 8299 US (St. Paul) +1 786 635 1003 US (Miami) +1 267 831 0333 US (Philadelphia) +1 301 715 8592 US (Germantown) +1 312 626 6799 US (Chicago) +1 470 250 9358 US (Atlanta) +1 470 381 2552 US (Atlanta) +1 646 518 9805 US (New York) +1 646 876 9923 US (New York) Meeting ID: 917 0720 5826 Find your local number: https://washington.zoom.us/u/adMWhSOy4V Join by SIP 917...@zo... Join by H.323 162.255.37.11 (US West) 162.255.36.11 (US East) 221.122.88.195 (China) 115.114.131.7 (India Mumbai) 115.114.115.7 (India Hyderabad) 213.19.144.110 (EMEA) 103.122.166.55 (Australia) 209.9.211.110 (Hong Kong SAR) 64.211.144.160 (Brazil) 69.174.57.160 (Canada) 207.226.132.110 (Japan) Meeting ID: 917 0720 5826 |
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From: MEDHA B. <me1...@gm...> - 2020-05-12 10:35:48
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Hello everyone! I am Medha Bhattacharya, a second-year undergraduate student pursuing a Bachelor of Technology (Computer Science and Engineering) at Indira Gandhi Delhi Technical University for Women, India. I am glad to inform you all of my selection in the Google Summer of Code 2020 program with National Resource for Network Biology. Project title: Development of a system that generates spatial SBML models using deep learning. (Issue: https://github.com/nrnb/GoogleSummerOfCode/issues/140) This project aims at creating and implementing a software tool that automatically generates various spatial SBML models via XitoSBML by comprehensively segmenting microscopic images of cells using deep learning. Consequently, my project will create a large number of spatial SBML models. Furthermore, as XitoSBML uses JSBML to write spatial SBML models, it will be used throughout. Since the development of the SBML Version 3 spatial package is currently under progress, a large number of test models are required. These can be provided as deliverables via this project to the SBML repository. Additionally, the provision of several spatial SBML models will enable testing the compatibility of software tools that deal with spatial SBML models. The link to my blog-post: https://gsoc2020mb.blogspot.com/ I am hoping to be able to contribute towards the development of the SBML spatial package this summer! Cheers! Medha |
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From: Lucian S. <luc...@gm...> - 2020-05-07 16:48:40
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Hey, everyone! As far as I can tell, the spatial specification is just about ready to release. In fact, some software has already been published that has SBML spatial support, so it would be nice if the spec itself was official. To that end, I've set up a doodle poll to see if we can meet to hammer out what needs to be done to finish everything. We have people in the US, Japan, and Europe, so this may be a little difficult, but let's see what we can do: https://doodle.com/poll/n5w48ut52iqcdrd3 The goal of the meeting is to figure out: * If there's anything in the spec that has no implementations, and should be removed. * If we can demonstrate that some tools can exchange models. * If there are any other obstacles to groups implementing support for any part of spatial. Thank you all for all the work you've invested in spatial over the years! -Lucian |
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From: Frank T. B. <fbe...@ca...> - 2020-03-02 08:25:22
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It is fine to have it apply only to species (and spatially resolved ones at that), after all we need to know the corresponding compartment information, and that is not available for parameters. Cheers Frank On Sat, Feb 29, 2020 at 12:01 AM Lucian Smith <luc...@gm...> wrote: > > Quick question for anyone using AdvectionCoefficients: you can definitely define one that references a Species, through the 'variable' attribute. > > But could you reference a Parameter as well? Does it make sense for a Parameter to have an associated advection coefficient, in some context? > > Currently, the main body of the spec says you can, and the validation rules say you can't (section 3.11 vs. validation rule 23504). > > -Lucian > _______________________________________________ > sbml-spatial mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-spatial |
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From: Michael H. <mh...@li...> - 2020-02-29 06:25:09
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It is awesome to see activity and progress! MH On 28 Feb 2020, at 15:21, Lucian Smith wrote: > Based on my implementation and analysis of the new validation rules, > and > especially after talking with Frank about compression, we now have a > new > version of the spec at: > > https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.95.pdf > > > Most of the changes here involve the new validation rules, codifying > what > was stated in the main body of the spec, but not previously broken out > into > specific rules. > > Also, the discussion of how to compress/uncompress data has been > updated, > as per discussions with Frank (and his discussions with Robert > Murphy). > The way compression now works is: > > * Data is stored as a string. > * The string is compressed to a char array. > * The char array is converted to integers > * The integers are expressed as a string. > > So, for example, the data: > > "1 2 3 4 5 6 7 8 9 10 11 12 "; > > would be converted to: > > "120 218 5 193 1 1 0 16 16 4 176 42 139 224 30 143 254 197 108 81 166 > 101 > 107 199 245 100 72 164 124 63 21 4 132 " > > Obviously, this particular example doesn't do much actual compressing; > larger examples work better but are worse email examples ;-) Another > advantage of compressing a string means that inconveniences and > ambiguities > like byte order for doubles, etc. goes away: everything is simply > characters. > > I know Frank and I will be at HARMONY in March--will anyone else on > the > list be there? Would anyone be interested in participating in a > remote > session to help finalize this specification? Thank you all! > > -Lucian > _______________________________________________ > sbml-spatial mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-spatial |
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From: Lucian S. <luc...@gm...> - 2020-02-28 23:21:43
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Based on my implementation and analysis of the new validation rules, and especially after talking with Frank about compression, we now have a new version of the spec at: https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.95.pdf Most of the changes here involve the new validation rules, codifying what was stated in the main body of the spec, but not previously broken out into specific rules. Also, the discussion of how to compress/uncompress data has been updated, as per discussions with Frank (and his discussions with Robert Murphy). The way compression now works is: * Data is stored as a string. * The string is compressed to a char array. * The char array is converted to integers * The integers are expressed as a string. So, for example, the data: "1 2 3 4 5 6 7 8 9 10 11 12 "; would be converted to: "120 218 5 193 1 1 0 16 16 4 176 42 139 224 30 143 254 197 108 81 166 101 107 199 245 100 72 164 124 63 21 4 132 " Obviously, this particular example doesn't do much actual compressing; larger examples work better but are worse email examples ;-) Another advantage of compressing a string means that inconveniences and ambiguities like byte order for doubles, etc. goes away: everything is simply characters. I know Frank and I will be at HARMONY in March--will anyone else on the list be there? Would anyone be interested in participating in a remote session to help finalize this specification? Thank you all! -Lucian |
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From: Lucian S. <luc...@gm...> - 2020-02-28 23:01:43
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Quick question for anyone using AdvectionCoefficients: you can definitely define one that references a Species, through the 'variable' attribute. But could you reference a Parameter as well? Does it make sense for a Parameter to have an associated advection coefficient, in some context? Currently, the main body of the spec says you can, and the validation rules say you can't (section 3.11 vs. validation rule 23504). -Lucian |
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From: Lucian S. <luc...@gm...> - 2019-12-17 17:42:41
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Question for everyone, but particularly Bob Murphy... In the spec, the TransformationComponent is described as having a 'components' attribute, which is a 16-entry vector of doubles. This ended up getting implemented incorrectly in libsbml, and is instead implemented as a child, i.e.: spec: <transformationComponent components="1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16"> vs. libsbml: <transformationComponent>1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16</transformationComponent> jsbml implements support as an attribute, matching the spec. It seems like the obvious solution would be to fix libsbml to match the spec, but I did want to check with people to see if anyone was using libsbml in this way first. (The TransformationComponent is part of the CSGHomogeneousTransformation class, and can be used to move, scale, and rotate a CSG object all at once.) -Lucian |
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From: Lucian S. <luc...@gm...> - 2019-11-22 21:46:21
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Hello! Last summer, Google Summer of Code student Bhavye Jain went through the spatial specification and pulled out a large number of validation rules that had not been formalized in the automatic validation generation process. After his project was done, I went through the spec again, and pulled out even more. The result is a new version of the spec, currently available at: https://sourceforge.net/p/sbml/code/26180/tree//trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.94.pdf If you just want to look (and/or comment) on the validation rules themselves, they're available at: https://docs.google.com/document/d/13lIj_KXmGxlI-F2TWkXOnF78erLyPLYrXT-fagnxFvk/edit?usp=sharing Bhavye has implemented support in jsbml for all of the GSOC-discovered rules, I did the same for libsbml, and I've been working through the remaining rules to implement support for them as well. This process isn't finished (it's... a little bit of a slog), but I figured it would be good to go ahead and release a version of the spec with the new rules so everyone could get a look at them before they were finalized in the code. A few of the rules are not going to be able to receive full library support, as they involve a spatial understanding of the model that neither libsbml nor jsbml is prepared to handle. But the rules will be available in the libraries so other tools can correctly flag model violations as needed. Most of the rules will be testable by libsbml, however. Thank you all, and thank you Bhavye in particular! -Lucian Smith |
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From: Lucian S. <luc...@gm...> - 2019-11-21 19:08:06
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minBoundary and maxBoundary are used to set up the axis of the coordinate system itself: Xmin and Xmax; Ymin and Ymax, and Zmin and Zmax (the 'CoordinateComponents', in SBML spatial parlance). I would have guessed that if your entire model is constrained to a single voxel width, you'd be better off modeling it as a 2D geometry instead of a 3D geometry? But maybe it's useful to leave it as 3D anyway, in some cases? This is different from a sampled field geometry, which can indeed have a lower dimensionality than the coordinate system in which it is defined. Thanks for your input! -Lucian -Lucian On Thu, Nov 21, 2019 at 10:35 AM Robert Murphy <mu...@an...> wrote: > I didn’t have a chance to look at where minBoundary and maxBoundary are > used, but for a 3D sampled-field geometry (voxels), an object might have a > one voxel width in one dimension, in which case min=max for that dimension. > > Best, > > Bob > ======================= > Robert F. Murphy, Ph.D. > Ray and Stephanie Lane Professor of Computational Biology and Professor > of Biological Sciences, Biomedical Engineering, and Machine Learning > Head, Computational Biology Department, School of > Computer Science, Carnegie Mellon University > 7723 Gates and Hillman Centers, 5000 Forbes Ave., Pittsburgh, PA 15213 > Phone: 412-268-3480, FAX: 412-268-2977, email: mu...@cm... > <mu...@cm...>, Skype: rfmurphy1953 > Personal: Home Page (http://www.andrew.cmu.edu/user/murphy), Twitter > @murphy2537 > Comp Bio Department: Facebook (cmucbd), Twitter @CMUCompBio > Honorary Professor, University of Freiburg > Senior Fellow, Allen Institute for Cell Science > > > > > > > On Nov 21, 2019, at 9:53 AM, Lucian Smith <luc...@gm...> > wrote: > > Yes, this would be the same error as max<min--it's just a question of > whether the error should trigger if 'max<min' or if 'max<=min'. > > Sounds like I'll make it so that min must be strictly less than max > (unless anyone else has an opposing use-case). Thanks! > > -Lucian > > On Thu, Nov 21, 2019 at 12:29 AM Frank Bergmann <fbe...@ca...> > wrote: > >> Hello Lucian, >> >> >> >> I can see no particular usecase for the minBoundary and maxBoundary being >> the same. It would basically fix the coordinate to a fixed value for when >> it would appear in formulas. >> >> >> >> As for the severity of the error, whether it should be a warning or an >> error, what are you currently doing. Is it an error not to have the max >> boundary defined? What happens if max < min? This seems to be in the same >> category. >> >> >> >> Cheers >> >> Frank >> >> >> >> *From:* Lucian Smith <luc...@gm...> >> *Sent:* Wednesday, November 20, 2019 6:28 PM >> *To:* The SBML L3 Spatial Processes and Geometries package discussion >> list <sbm...@li...> >> *Subject:* [sbml-spatial] Quick question: axis min <= max, or min < max? >> >> >> >> Hello! I'm in the process of adding validation rules to the spatial >> spec, and have a question: When a CoordinateComponent (the Geometry axis) >> has a minBoundary and a maxBoundary, is it OK if the two boundaries are >> equal? This is essentially reducing the dimensionality of the Geometry, >> but perhaps it would be useful in some situations? >> >> >> >> -Lucian >> _______________________________________________ >> sbml-spatial mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-spatial >> > _______________________________________________ > sbml-spatial mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-spatial > > _______________________________________________ > sbml-spatial mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-spatial > |
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