Activity for Systems Biology Markup Language (SBML)

Systems Biology Markup Language (SBML) updated /test-suite/README.md

Systems Biology Markup Language (SBML) — Wed, 13 Mar 2024 13:35:05 -0000

Lucian Smith posted a comment on ticket #189

Lucian Smith — Fri, 15 Sep 2023 17:36:13 -0000

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

Lucian Smith created ticket #26

Lucian Smith — Wed, 13 Jul 2022 20:59:14 -0000

DO NOT POST NEW ISSUES HERE

Lucian Smith modified ticket #14

Lucian Smith — Wed, 13 Jul 2022 20:57:54 -0000

Add NSF/Google/Volkswagen to Acknowledgements of Funding

Lucian Smith posted a comment on ticket #14

Lucian Smith — Wed, 13 Jul 2022 20:57:54 -0000

Moved to https://github.com/sbmlteam/sbml-org-website/issues/42

Lucian Smith modified ticket #25

Lucian Smith — Wed, 13 Jul 2022 20:54:21 -0000

Multiple entries for SBSCL within the Simulation Database

Lucian Smith posted a comment on ticket #25

Lucian Smith — Wed, 13 Jul 2022 20:54:21 -0000

Moved to https://github.com/sbmlteam/sbml-org-website/issues/41

Michael Hucka modified ticket #22

Michael Hucka — Wed, 13 Jul 2022 20:46:54 -0000

images and javascript not found for latest (1.5) JSBML API docs

Michael Hucka modified ticket #17

Michael Hucka — Wed, 13 Jul 2022 20:45:32 -0000

Dead link in sbml.org/News

Michael Hucka modified ticket #18

Michael Hucka — Wed, 13 Jul 2022 20:44:52 -0000

Tool conversion SBML level 3 to SBML level 2

Michael Hucka modified ticket #19

Michael Hucka — Wed, 13 Jul 2022 20:44:36 -0000

Image not loading on SBML software guide

Michael Hucka modified ticket #20

Michael Hucka — Wed, 13 Jul 2022 20:44:17 -0000

libSBML Example Program page for printSupported.pl is broken

Michael Hucka modified ticket #21

Michael Hucka — Wed, 13 Jul 2022 20:43:56 -0000

sbml validator webpage is down

Michael Hucka modified ticket #23

Michael Hucka — Wed, 13 Jul 2022 20:43:13 -0000

update reference to homepage

Lucian Smith created ticket #8

Lucian Smith — Wed, 13 Jul 2022 18:15:49 -0000

DO NOT POST NEW ISSUES HERE

Lucian Smith created ticket #36

Lucian Smith — Wed, 13 Jul 2022 18:15:10 -0000

DO NOT POST NEW ISSUES HERE

Lucian Smith created ticket #14

Lucian Smith — Wed, 13 Jul 2022 18:13:10 -0000

DO NOT POST NEW ISSUES HERE

Lucian Smith modified ticket #10

Lucian Smith — Wed, 13 Jul 2022 18:10:42 -0000

SBML validator registration for API key not working

Lucian Smith posted a comment on ticket #10

Lucian Smith — Wed, 13 Jul 2022 18:10:42 -0000

I think this has been addressed? If not, please file a new issue at https://github.com/sbmlteam/libsbml/issues/

Lucian Smith modified ticket #11

Lucian Smith — Wed, 13 Jul 2022 18:09:16 -0000

libsbml doesn't work with vckpg libraries

Lucian Smith posted a comment on ticket #11

Lucian Smith — Wed, 13 Jul 2022 18:09:16 -0000

Moved to https://github.com/sbmlteam/libsbml/issues/245

Lucian Smith modified ticket #12

Lucian Smith — Wed, 13 Jul 2022 18:06:43 -0000

Issue with installation of R interface of libSBML 5.18.0

Lucian Smith posted a comment on ticket #12

Lucian Smith — Wed, 13 Jul 2022 18:06:43 -0000

This has been addressed. Note that any new tickets should be posted to the new github site, at https://github.com/sbmlteam/libsbml/issues

Lucian Smith created ticket #371

Lucian Smith — Wed, 13 Jul 2022 18:05:10 -0000

DO NOT POST NEW ISSUES HERE

Lucian Smith posted a comment on ticket #289

Lucian Smith — Wed, 13 Jul 2022 18:03:51 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/289

Lucian Smith modified ticket #289

Lucian Smith — Wed, 13 Jul 2022 18:03:51 -0000

FBC V2 typos section 2

Lucian Smith modified ticket #293

Lucian Smith — Wed, 13 Jul 2022 18:00:14 -0000

wrong namespace used for the protein modification ontology

Lucian Smith posted a comment on ticket #293

Lucian Smith — Wed, 13 Jul 2022 18:00:14 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/291

Lucian Smith modified ticket #294

Lucian Smith — Wed, 13 Jul 2022 17:58:49 -0000

MathML package: Allow n-ary function definitions?

Lucian Smith posted a comment on ticket #294

Lucian Smith — Wed, 13 Jul 2022 17:58:49 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/292

Lucian Smith modified ticket #333

Lucian Smith — Wed, 13 Jul 2022 17:57:56 -0000

Layout: no validation rule for must-be-positive attributes

Lucian Smith posted a comment on ticket #333

Lucian Smith — Wed, 13 Jul 2022 17:57:56 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/331

Lucian Smith posted a comment on ticket #350

Lucian Smith — Wed, 13 Jul 2022 17:57:26 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/348

Lucian Smith modified ticket #350

Lucian Smith — Wed, 13 Jul 2022 17:57:26 -0000

Render: UML diagram for GraphicalPrimitive2D class incorrect

Lucian Smith modified ticket #351

Lucian Smith — Wed, 13 Jul 2022 17:56:52 -0000

Render: Style is abstract base class: should be italicized in UML

Lucian Smith posted a comment on ticket #351

Lucian Smith — Wed, 13 Jul 2022 17:56:52 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/349

Lucian Smith modified ticket #352

Lucian Smith — Wed, 13 Jul 2022 17:56:12 -0000

Render: Figure 2 doesn't say versionMajor and versionMinor are optional

Lucian Smith posted a comment on ticket #352

Lucian Smith — Wed, 13 Jul 2022 17:56:12 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/350

Lucian Smith modified ticket #354

Lucian Smith — Wed, 13 Jul 2022 17:55:40 -0000

Layout: Figure 5 has a 'ListOfLineSegments' class, which should be 'ListOfCurveSegments'.

Lucian Smith posted a comment on ticket #354

Lucian Smith — Wed, 13 Jul 2022 17:55:40 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/352

Lucian Smith modified ticket #355

Lucian Smith — Wed, 13 Jul 2022 17:54:48 -0000

Render: fix examples that switch namespaces.

Lucian Smith posted a comment on ticket #355

Lucian Smith — Wed, 13 Jul 2022 17:54:48 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/353

Lucian Smith modified ticket #359

Lucian Smith — Wed, 13 Jul 2022 17:54:03 -0000

Multi: Syntax errors in the examples

Lucian Smith posted a comment on ticket #359

Lucian Smith — Wed, 13 Jul 2022 17:54:03 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/357

Lucian Smith modified ticket #360

Lucian Smith — Wed, 13 Jul 2022 17:53:21 -0000

Allow l3v1 packages in l3v2 documents to inherit 'id' and 'name'?

Lucian Smith posted a comment on ticket #360

Lucian Smith — Wed, 13 Jul 2022 17:53:12 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/358

Lucian Smith modified ticket #364

Lucian Smith — Wed, 13 Jul 2022 17:51:26 -0000

spatial spec example problematic

Lucian Smith posted a comment on ticket #364

Lucian Smith — Wed, 13 Jul 2022 17:51:26 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/362

Lucian Smith modified ticket #365

Lucian Smith — Wed, 13 Jul 2022 17:50:41 -0000

Possible typo in the value of the "persistent" attribute

Lucian Smith posted a comment on ticket #365

Lucian Smith — Wed, 13 Jul 2022 17:50:41 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/363

Lucian Smith modified ticket #366

Lucian Smith — Wed, 13 Jul 2022 17:50:02 -0000

Suggested change to SBML multi-compartment model example

Lucian Smith posted a comment on ticket #366

Lucian Smith — Wed, 13 Jul 2022 17:50:02 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/364

Lucian Smith modified ticket #367

Lucian Smith — Wed, 13 Jul 2022 17:49:13 -0000

Update identifiers.org URLs

Lucian Smith posted a comment on ticket #367

Lucian Smith — Wed, 13 Jul 2022 17:49:13 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/365

Lucian Smith posted a comment on ticket #368

Lucian Smith — Wed, 13 Jul 2022 17:48:26 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/366

Lucian Smith modified ticket #368

Lucian Smith — Wed, 13 Jul 2022 17:48:26 -0000

qual: Input Species not in FunctionTerm

Lucian Smith modified ticket #369

Lucian Smith — Wed, 13 Jul 2022 17:46:23 -0000

SBML L3V2 units UML is incorrect (arrow direction)

Lucian Smith posted a comment on ticket #369

Lucian Smith — Wed, 13 Jul 2022 17:46:23 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/367

Lucian Smith modified ticket #370

Lucian Smith — Wed, 13 Jul 2022 17:45:10 -0000

Extensive/Intensive reversed

Lucian Smith posted a comment on ticket #370

Lucian Smith — Wed, 13 Jul 2022 17:45:10 -0000

Moved to https://github.com/sbmlteam/sbml-specifications/issues/368

Lucian Smith committed [r26322]

Lucian Smith — Wed, 13 Jul 2022 17:10:44 -0000

Remove everything and point to new locations on github.

Lucian Smith committed [r26321]

Lucian Smith — Wed, 13 Jul 2022 17:06:10 -0000

Remove everything and point to new locations on github.

Lucian Smith committed [r26320]

Lucian Smith — Wed, 13 Jul 2022 17:04:04 -0000

Remove everything and point to new locations on github.

Lucian Smith committed [r26319]

Lucian Smith — Wed, 13 Jul 2022 17:00:24 -0000

Remove everything and point to new locations on github.

Lucian Smith committed [r26318]

Lucian Smith — Wed, 13 Jul 2022 16:54:57 -0000

Remove everything and leave a note pointing people to the new source repository.

Lucian Smith committed [r26317]

Lucian Smith — Sat, 23 Oct 2021 00:01:21 -0000

Change non-ASCII character to double dash.

Frank Bergmann modified ticket #13

Frank Bergmann — Thu, 05 Aug 2021 11:26:52 -0000

Installation in MATLAB

Frank Bergmann posted a comment on ticket #476

Frank Bergmann — Thu, 05 Aug 2021 11:24:50 -0000

thanks for letting us know, i've applied the fix to the git repo, so it will be part of the next release.

smoretti posted a comment on ticket #476

smoretti — Thu, 05 Aug 2021 08:43:24 -0000

It also concerns libSBML-5.19.0

smoretti posted a comment on ticket #476

smoretti — Thu, 05 Aug 2021 08:42:30 -0000

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)

Joel Mhaske posted a comment on ticket #13

Joel Mhaske — Mon, 26 Jul 2021 08:13:36 -0000

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...

Frank Bergmann posted a comment on ticket #13

Frank Bergmann — Mon, 26 Jul 2021 07:46:00 -0000

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...

Joel Mhaske created ticket #13

Joel Mhaske — Sun, 25 Jul 2021 23:03:12 -0000

Installation in MATLAB

Brett Olivier posted a comment on ticket #370

Brett Olivier — Wed, 12 May 2021 09:31:41 -0000

Seconded. Jannie Hofmeyr also noted this and suggested the change in a personal communication.

Lucian Smith created ticket #370

Lucian Smith — Tue, 11 May 2021 16:51:44 -0000

Extensive/Intensive reversed

Andreas Dräger posted a comment on ticket #25

Andreas Dräger — Sat, 08 May 2021 10:15:29 -0000

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...

Frank Bergmann posted a comment on ticket #10

Frank Bergmann — Mon, 03 May 2021 09:58:56 -0000

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.

Radoslav Doktor posted a comment on ticket #10

Radoslav Doktor — Fri, 30 Apr 2021 22:29:30 -0000

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

Frank Bergmann posted a comment on ticket #25

Frank Bergmann — Fri, 30 Apr 2021 11:50:06 -0000

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.

Andreas Dräger posted a comment on ticket #25

Andreas Dräger — Fri, 30 Apr 2021 11:21:48 -0000

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...

Frank Bergmann posted a comment on ticket #25

Frank Bergmann — Fri, 30 Apr 2021 10:17:34 -0000

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

Andreas Dräger created ticket #25

Andreas Dräger — Fri, 30 Apr 2021 06:53:42 -0000

Multiple entries for SBSCL within the Simulation Database

Michael Hucka modified ticket #24

Michael Hucka — Tue, 23 Feb 2021 22:28:19 -0000

SBML Packages links dead

Michael Hucka posted a comment on ticket #24

Michael Hucka — Tue, 23 Feb 2021 22:28:02 -0000

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.

Matthias König posted a comment on ticket #24

Matthias König — Sun, 21 Feb 2021 08:36:35 -0000

@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.

Michael Hucka posted a comment on ticket #24

Michael Hucka — Thu, 18 Feb 2021 04:45:40 -0000

Yes, Fengkai is right; it seems to be an https issue. I'll ask Nico if he has any ideas.

Fengkai Zhang posted a comment on ticket #24

Fengkai Zhang — Tue, 09 Feb 2021 14:17:57 -0000

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...

Frank Bergmann posted a comment on ticket #24

Frank Bergmann — Tue, 09 Feb 2021 10:16:17 -0000

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

Samuel Pastva created ticket #24

Samuel Pastva — Thu, 04 Feb 2021 12:58:48 -0000

SBML Packages links dead

Matthias König created ticket #369

Matthias König — Tue, 02 Feb 2021 09:10:06 -0000

SBML L3V2 units UML is incorrect (arrow direction)

Lucian Smith modified ticket #362

Lucian Smith — Wed, 02 Dec 2020 18:23:09 -0000

Clarify use of bvar in lambda element of FunctionDefinition

Lucian Smith posted a comment on ticket #362

Lucian Smith — Wed, 02 Dec 2020 18:23:09 -0000

Released.

Lucian Smith modified ticket #346

Lucian Smith — Wed, 02 Dec 2020 18:17:30 -0000

Be explicit about rateOf at times < 0

Lucian Smith posted a comment on ticket #346

Lucian Smith — Wed, 02 Dec 2020 18:17:30 -0000

Released.

Lucian Smith modified ticket #348

Lucian Smith — Wed, 02 Dec 2020 18:14:42 -0000

l3v1r2 mentions 'rateOf' in validation rule 10205

Lucian Smith posted a comment on ticket #348

Lucian Smith — Wed, 02 Dec 2020 18:14:42 -0000

Released.

Lucian Smith modified ticket #349

Lucian Smith — Wed, 02 Dec 2020 18:13:55 -0000

Min and max are not generally discouraged, only no-argument

Lucian Smith posted a comment on ticket #349

Lucian Smith — Wed, 02 Dec 2020 18:13:55 -0000

Released.

Lucian Smith modified ticket #353

Lucian Smith — Wed, 02 Dec 2020 18:11:25 -0000

Update unit validation rules for compartments

Lucian Smith posted a comment on ticket #353

Lucian Smith — Wed, 02 Dec 2020 18:11:25 -0000

Released.