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[SOSlib-devel] [ sbmlsolver-Bugs-1951462 ] Compartment size could be absent
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From: SourceForge.net <no...@so...> - 2008-05-06 09:54:09
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Bugs item #1951462, was opened at 2008-04-25 10:24 Message generated for change (Comment added) made by ch_li You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1951462&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: solver malfunction Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chen (ch_li) Assigned to: Nobody/Anonymous (nobody) Summary: Compartment size could be absent Initial Comment: Hello, I have a model, which compartment was not used by any species or reactions. For instance, in the model I attached, its species has intialAmount and hasOnlySubstanceUnits is TRUE. The whole model's reactions doesn't nothing with the compartment. For this model, it should be able to be simulated without given compartment size. Regards, Chen ---------------------------------------------------------------------- >Comment By: Chen (ch_li) Date: 2008-05-06 10:54 Message: Logged In: YES user_id=1712101 Originator: YES Hi, James, > Looks like SOSlib returns a fatal error message "No value found for > compartment cell" in this case? Yes, I got that error. In this model, all reactions do nothing with that compartment. It was there, only because species need to be defined in at least one compartment according to SBML spec. So in this case, my humble opinion is, SOSlib should not throw that error. Regards, Chen ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2008-04-28 09:50 Message: Logged In: NO hi Chen: Looks like SOSlib returns a fatal error message "No value found for compartment cell" in this case? BTW, it seems MathSBML integrates the model correctly, but it does so with the complaint that value for compartment is absent. James ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1951462&group_id=139893 |
