Activity for Systems Biology Markup Language (SBML)
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Systems Biology Markup Language (SBML) updated /test-suite/README.md
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Lucian Smith posted a comment on ticket #189
For reference, just in case someone finds this issue in the future: FBC package issues can now be found at https://github.com/sbmlteam/sbml-specifications/labels/L3%20Package%3A%20fbc
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DO NOT POST NEW ISSUES HERE
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Add NSF/Google/Volkswagen to Acknowledgements of Funding
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Moved to https://github.com/sbmlteam/sbml-org-website/issues/42
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Multiple entries for SBSCL within the Simulation Database
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Moved to https://github.com/sbmlteam/sbml-org-website/issues/41
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Michael Hucka modified ticket #22
images and javascript not found for latest (1.5) JSBML API docs
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Dead link in sbml.org/News
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Tool conversion SBML level 3 to SBML level 2
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Image not loading on SBML software guide
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libSBML Example Program page for printSupported.pl is broken
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sbml validator webpage is down
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update reference to homepage
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DO NOT POST NEW ISSUES HERE
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DO NOT POST NEW ISSUES HERE
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DO NOT POST NEW ISSUES HERE
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SBML validator registration for API key not working
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I think this has been addressed? If not, please file a new issue at https://github.com/sbmlteam/libsbml/issues/
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libsbml doesn't work with vckpg libraries
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Moved to https://github.com/sbmlteam/libsbml/issues/245
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Issue with installation of R interface of libSBML 5.18.0
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This has been addressed. Note that any new tickets should be posted to the new github site, at https://github.com/sbmlteam/libsbml/issues
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DO NOT POST NEW ISSUES HERE
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FBC V2 typos section 2
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/289
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wrong namespace used for the protein modification ontology
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/291
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MathML package: Allow n-ary function definitions?
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/292
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Layout: no validation rule for must-be-positive attributes
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/331
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Render: UML diagram for GraphicalPrimitive2D class incorrect
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/348
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Render: Style is abstract base class: should be italicized in UML
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/349
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Render: Figure 2 doesn't say versionMajor and versionMinor are optional
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/350
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Layout: Figure 5 has a 'ListOfLineSegments' class, which should be 'ListOfCurveSegments'.
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/352
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Render: fix examples that switch namespaces.
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/353
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Multi: Syntax errors in the examples
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/357
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Allow l3v1 packages in l3v2 documents to inherit 'id' and 'name'?
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/358
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spatial spec example problematic
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/362
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Possible typo in the value of the "persistent" attribute
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/363
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Suggested change to SBML multi-compartment model example
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/364
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Update identifiers.org URLs
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/365
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qual: Input Species not in FunctionTerm
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/366
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SBML L3V2 units UML is incorrect (arrow direction)
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/367
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Extensive/Intensive reversed
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/368
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Remove everything and point to new locations on github.
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Remove everything and point to new locations on github.
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Remove everything and point to new locations on github.
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Remove everything and point to new locations on github.
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Remove everything and leave a note pointing people to the new source repository.
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Change non-ASCII character to double dash.
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Frank Bergmann modified ticket #13
Installation in MATLAB
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thanks for letting us know, i've applied the fix to the git repo, so it will be part of the next release.
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smoretti posted a comment on ticket #476
It also concerns libSBML-5.19.0
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The fix is simple: in src/bindings/perl/CMakeLists.txt, line 233, replace set(PERL_PACKAGE_INSTALL_BIN_DIR ${PERL_PACKAGE_INSTALL_DIR}/auto/libSBML) by set(PERL_PACKAGE_INSTALL_BIN_DIR ${PERL_PACKAGE_INSTALL_DIR}/auto/LibSBML)
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Joel Mhaske posted a comment on ticket #13
Hello there, It seems like I downloaded a completely different version of SBML from the website. It got resolved when I used the one ith MATLAB archive with more specific functions for my use. Thanks very much for the help though. Have a great day, Regards, Joel On Mon, 26 Jul 2021, 08:46 Frank Bergmann, fbergmann@users.sourceforge.net wrote: Hello Joel, to clarify, that we know exactly which steps you took: you downloaded this archive: https://sourceforge.net/projects/sbml/files/libsbml/5.19.0/stable/MATLAB%20interface/libSBML-5.19.0-matlab-binaries.zip/download...
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Hello Joel, to clarify, that we know exactly which steps you took: you downloaded this archive: https://sourceforge.net/projects/sbml/files/libsbml/5.19.0/stable/MATLAB%20interface/libSBML-5.19.0-matlab-binaries.zip/download extracted it, and added the folder into your matlab path? then changing into the folder and calling TranslateSBML('test.xml') gave you which error message? Could we see the complete log? the archive contains the binaries for windows (64bit / 32bit), linux (64bit / 32bit) and...
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Installation in MATLAB
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Brett Olivier posted a comment on ticket #370
Seconded. Jannie Hofmeyr also noted this and suggested the change in a personal communication.
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Extensive/Intensive reversed
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Andreas Dräger posted a comment on ticket #25
Thanks! That would be so helpful if it isn’t too much effort for you! Enjoy the weekend. Best wishes! Andreas Dräger Sent from a phone, please excuse typos and brevity. Am 30.04.2021 um 13:50 schrieb Frank Bergmann fbergmann@users.sourceforge.net: I can change the 1.2 name to 'Systems Biology Simulation Core Library (SBSCL)' (you or whoever created the entry should also be possible to edit / remove it). If you give me the go ahead i will. [sbml-org-website:#25] Multiple entries for SBSCL within...
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Sorry for the inconvenience, we have not yet made a new version of the validator available, so the forwarding problem from before remains. Your registration did go through and i will send you the API key to your registered email address.
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Radoslav Doktor posted a comment on ticket #10
Good evening Frank! I'd love to use the API, but the registration is still broken. I'll try to register with the link and hope for the response. Rado Doktor
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I can change the 1.2 name to 'Systems Biology Simulation Core Library (SBSCL)' (you or whoever created the entry should also be possible to edit / remove it). If you give me the go ahead i will.
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Hi Frank, obviously, a mistake happened here. The names should match but different persons uploaded the results and used diverging names. Is it possible to change the name of one of both to make them merge? Cheers Andreas Am 30.04.2021 um 12:17 schrieb Frank Bergmann fbergmann@users.sourceforge.net: Hello Andreas, I'm not sure how likely it is to change the display at this point. The results should have been grouped, if the names of the simulators are the same (in that case only the latest version...
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Hello Andreas, I'm not sure how likely it is to change the display at this point. The results should have been grouped, if the names of the simulators are the same (in that case only the latest version would appear in the list). Since here the names differ, that would be an issue. you could just let me know which entries you'd like to have removed. Also please drop me a mail, when you want the new results to go public. cheers Frank
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Multiple entries for SBSCL within the Simulation Database
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SBML Packages links dead
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This problem should be fixed now. There was a firewall configuration issue on the server that blocked https. Nicolas Rodriguez kindly fixed it, even though it's not really his responsibility anymore.
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Matthias König posted a comment on ticket #24
@all Encountered the same issue. Could we not just register an identifiers.org resource for the specifications. It would allow to simply update all links and ensure that links are not broken in the future. I.e. use something like https://identifiers.org/combine.specifications/ with https://identifiers.org/combine.specifications/sbml.level-3.version-1.qual.version-1.release-1 resolving to the actual document.
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Yes, Fengkai is right; it seems to be an https issue. I'll ask Nico if he has any ideas.
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Fengkai Zhang posted a comment on ticket #24
It looks like an issue on the combine website for the https links. Currently, the http links are accessible, but the https ones are not. Fengkai From: Frank Bergmann fbergmann@users.sourceforge.net Reply-To: "[sbml:sbml-org-website]" 24@sbml-org-website.sbml.p.re.sourceforge.net Date: Tuesday, February 9, 2021 at 5:16 AM To: "[sbml:sbml-org-website]" 24@sbml-org-website.sbml.p.re.sourceforge.net Subject: [sbml:sbml-org-website] #24 SBML Packages links dead I've just encountered the same issue. For...
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I've just encountered the same issue. For the time you can find all documents also in the SVN repository here: https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/ Sorry for the inconvenience. Frank
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Samuel Pastva created ticket #24
SBML Packages links dead
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SBML L3V2 units UML is incorrect (arrow direction)
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Clarify use of bvar in lambda element of FunctionDefinition
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Released.
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Be explicit about rateOf at times < 0
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Released.
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l3v1r2 mentions 'rateOf' in validation rule 10205
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Released.
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Min and max are not generally discouraged, only no-argument
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Released.
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Update unit validation rules for compartments
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Released.
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