From: <luc...@us...> - 2017-02-07 22:53:33
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Revision: 23806 http://sourceforge.net/p/sbml/code/23806 Author: luciansmith Date: 2017-02-07 22:53:30 +0000 (Tue, 07 Feb 2017) Log Message: ----------- Fix for issue 341 (https://sourceforge.net/p/sbml/sbml-specifications/341/): section added but not made red; extra paragraph fragment that shouldn't be there (a direct copy of an earlier section). Modified Paths: -------------- trunk/specifications/sbml-level-3/version-2/core/spec/components.tex Modified: trunk/specifications/sbml-level-3/version-2/core/spec/components.tex =================================================================== --- trunk/specifications/sbml-level-3/version-2/core/spec/components.tex 2017-02-07 14:42:20 UTC (rev 23805) +++ trunk/specifications/sbml-level-3/version-2/core/spec/components.tex 2017-02-07 22:53:30 UTC (rev 23806) @@ -4155,15 +4155,11 @@ In \ref{sec:bp:reactions}, we present some recommendations for how to encode rate laws and models in SBML. -\paragraph{Species with negative or zero values} +\paragraphRelChange{Species with negative or zero values} \label{sec:neg-species} -In many models, a \Species will represent an amount of a physical entity. In those cases, the level of that species should never go negative. Similarly, many reactions represent physical conversion of physical entities. In those cases, if the entities to be converted have reached a level of zero, no conversion can take place. However, in both cases, it is the duty of the modeler to ensure that the \KineticLaw of the \Reaction is encoded in such a way that these physical restrictions are obeyed. Other systems and models use the \Species construct to represent quantities that can go negative, such as charge. Thus, mathematically, if a model dictates that a \Species level goes negative, or if a \Reaction process acts on zero- or negative-level \Species, proper interpretation of that model requires that to happen. +\relchange{In many models, a \Species will represent an amount of a physical entity. In those cases, the level of that species should never go negative. Similarly, many reactions represent physical conversion of physical entities. In those cases, if the entities to be converted have reached a level of zero, no conversion can take place. However, in both cases, it is the duty of the modeler to ensure that the \KineticLaw of the \Reaction is encoded in such a way that these physical restrictions are obeyed. Other systems and models use the \Species construct to represent quantities that can go negative, such as charge. Thus, mathematically, if a model dictates that a \Species level goes negative, or if a \Reaction process acts on zero- or negative-level \Species, proper interpretation of that model requires that to happen.} -A consequence of the approach to ``kinetic laws'' discussed in the -previous section is this: when constructing equations describing -the time-rates of change of different species defined by an SBML - \subsubsection{Use of reaction identifiers in mathematical expressions} \label{subsec:reaction-as-symbol} |