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[sbml-svn] SF.net SVN: sbml:[21165] trunk/specifications/sbml-level-3/version-2/dyn/ spec
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From: <hgo...@us...> - 2014-09-29 18:34:52
|
Revision: 21165
http://sourceforge.net/p/sbml/code/21165
Author: hgomez87
Date: 2014-09-29 18:34:48 +0000 (Mon, 29 Sep 2014)
Log Message:
-----------
Changes introduced include:
1)The spec is compliant with SBML L3V1.
2) Optional tag was added to optional attributes.
3) Newly introduced classes now define their own id and name attributes.
4)Aside from id and name, the DynElement class now has a idRef and metaIdRef to point to objects' id or metaid, so that all SBML objects can be referenced.
5)Examples/Validation rules were updated to reflect new data model.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-2/dyn/spec/apdx-validation.tex
trunk/specifications/sbml-level-3/version-2/dyn/spec/cbo.tex
trunk/specifications/sbml-level-3/version-2/dyn/spec/examples.tex
trunk/specifications/sbml-level-3/version-2/dyn/spec/images/UMLExtendedCompartment.pdf
trunk/specifications/sbml-level-3/version-2/dyn/spec/images/UMLExtendedEvent.pdf
trunk/specifications/sbml-level-3/version-2/dyn/spec/images/UMLExtendedSBase.pdf
trunk/specifications/sbml-level-3/version-2/dyn/spec/intro.tex
trunk/specifications/sbml-level-3/version-2/dyn/spec/macros.tex
trunk/specifications/sbml-level-3/version-2/dyn/spec/sbml-l3v2-dyn-v1.pdf
trunk/specifications/sbml-level-3/version-2/dyn/spec/syntax.tex
Modified: trunk/specifications/sbml-level-3/version-2/dyn/spec/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-2/dyn/spec/apdx-validation.tex 2014-09-29 09:36:42 UTC (rev 21164)
+++ trunk/specifications/sbml-level-3/version-2/dyn/spec/apdx-validation.tex 2014-09-29 18:34:48 UTC (rev 21165)
@@ -3,7 +3,7 @@
\section{Validation Rules}
\label{validation}
-This section summarizes all the conditions that must (or in some cases,at least \emph{should}) be true of an SBML Level~3 Version~2 model that uses the Dynamic Structures package. We use the same conventions as are used in the SBML Level~3 Version~2 Core specification document. In particular, there are different degrees of rule strictness. Formally, the differences are expressed in the statement of a rule: either a rule states that a condition \emph{must} be true, or a rule states that it \emph{should} be true. Rules of the former kind are strict SBML validation rules---a model encoded in SBML must conform to all of them in order to be considered valid. Rules of the latter kind are consistency rules. To help highlight these differences, we use the following three symbols next to the rule numbers:
+This section summarizes all the conditions that must (or in some cases, at least \emph{should}) be true of an \sbmlthree model that uses the Dynamic Structures package. We use the same conventions as are used in the \sbmlthreecore specification document. In particular, there are different degrees of rule strictness. Formally, the differences are expressed in the statement of a rule: either a rule states that a condition \emph{must} be true, or a rule states that it \emph{should} be true. Rules of the former kind are strict SBML validation rules---a model encoded in SBML must conform to all of them in order to be considered valid. Rules of the latter kind are consistency rules. To help highlight these differences, we use the following three symbols next to the rule numbers:
\begin{description}
@@ -49,24 +49,23 @@
\subsubsection*{General rules about the Dynamic Structures package}
\validRule{dyn-10101}{To conform to Version~1 of the Dynamic Structures package
specification for SBML Level~3, an SBML document must declare the
- use of the following XML Namespace: \\ \textls[-25]{\uri{http://www.sbml.org/sbml/level3/version2/dyn/version1}}. (Reference: \sbmlthreedynamic, \sec{subsec:xml-namespace}.)}
+ use of the following XML Namespace: \\ \textls[-25]{\uri{http://www.sbml.org/sbml/level3/version1/dyn/version1}}. (Reference: \sbmlthreedynamic, \sec{subsec:xml-namespace}.)}
\validRule{dyn-10102}{Wherever they appear in an SBML document,
elements and attributes from the Dynamic Structures
package must be declared either implicitly or explicitly to be in the
XML namespace: \\
- \textls[-25]{\uri{http://www.sbml.org/sbml/level3/version2/dyn/version1}}.
+ \textls[-25]{\uri{http://www.sbml.org/sbml/level3/version1/dyn/version1}}.
(Reference: \sbmlthreedynamic, \sec{subsec:xml-namespace}.) }
\subsubsection*{Rules for the extended \class{SBML} class}
-\validRule{dyn-10201} {In all SBML documents using the Dynamic Structures package, the \SBML object must include a value for the attribute \token{dyn:required} attribute. (Reference: SBML Level~3 Version~2 Core, Section~4.1.3.)}
-
-\validRule{dyn-10202} {The value of attribute \token{dyn:required} on the \SBML object must be of the data type \primtype{boolean}. (Reference: SBML Level~3 Version~2 Core, Section~4.1.3.) }
-
+\validRule{dyn-10201} {In all SBML documents using the Dynamic Structures package, the \SBML object must include a value for the attribute \token{dyn:required} attribute. (Reference: \sbmlthreecore, Section~4.1.2.)}
+%L3V2 Section~4.1.3.
+\validRule{dyn-10202} {The value of attribute \token{dyn:required} on the \SBML object must be of the data type \primtype{boolean}. (Reference: \sbmlthreecore, Section~4.1.2.) }
+%L3V2 Section~4.1.3.
\validRule{dyn-10203} {The value of attribute \token{dyn:required} on
the \SBML object must be set to \val{true} (Reference: \sbmlthreedynamic, \sec{subsec:xml-namespace}.) }
-
\subsubsection*{General rules for CBO usage}
\consistencyRule{dyn-10301} {The value of the attribute \token{dyn:cboTerm} on a \Model object should be a full CBO identifier referring to a model qualifier defined under the \textbf{CBO\textunderscore Object} branch. The value must be a term derived from the \textbf{System\textemdash model} and \textbf{SystemQuality\textemdash model} hierarchies. (Reference: \sbmlthreedynamic, \sec{sec:CBO}.)}
@@ -101,6 +100,10 @@
\consistencyRule{dyn-10316} {The value of the attribute \token{dyn:cboTerm} on a \LocalParameter object should be a full CBO identifier of a quantitative parameter from the \textbf{CBO\textunderscore Object} branch. (Reference: \sbmlthreedynamic, \sec{sec:CBO}.)}
+\consistencyRule{dyn-10317} {The value of the attribute \token{dyn:cboTerm} on a \DynElement object is that of the referenced object. If not set, it should be a full CBO identifier from the \textbf{CBO\textunderscore Object} branch. (Reference: \sbmlthreedynamic, \sec{sec:CBO}.)}
+
+\consistencyRule{dyn-10318} {The value of the attribute \token{dyn:cboTerm} on a \SpatialComponent object is that of the referenced \Parameter. If not set, it should be a full CBO identifier from the \textbf{CBO\textunderscore Object} branch. (Reference: \sbmlthreedynamic, \sec{sec:CBO}.)}
+
\subsubsection*{Rules for extended \class{SBase} abstract class }
\validRule{comp-20101}{Any object derived from the extended \SBase class (defined in the Dynamic Structures package) may contain a \token{dyn:cboTerm} attribute. (References: \sbmlthreedynamic, \sec{subsec:extSBase}.) }
@@ -113,26 +116,31 @@
\validRule{dyn-20202}{ The value of an \token{dyn:applyToAll} attribute on a \Event object must be of the data type \primtype{boolean}. (References: \sbmlthreedynamic, \sec{attr:applyToAll}.) }
-\validRule{dyn-20203}{There may be at most one instance of a \ListOfElements subobject within an \Event object that uses the Dynamic Structures package. (References: \sbmlthreedynamic, \sec{subsec:extEvent}.) }
+\validRule{dyn-20203}{There may be at most one instance of a \ListOfDynElements subobject within an \Event object that uses the Dynamic Structures package. (References: \sbmlthreedynamic, \sec{subsec:extEvent}.) }
-\validRule{dyn-20204}{The \ListOfElements subobject within an \Event object is optional, but if present, this container object must not be empty. (References: \sbmlthreedynamic, \sec{subsec:ListOfElements}.) }
+\validRule{dyn-20204}{The \ListOfDynElements subobject within an \Event object is optional, and it may contain 0 or more \DynElement objects. (References: \sbmlthreedynamic, \sec{subsec:ListOfDynElements}.) }
-\validRule{dyn-20205}{Apart from the general notes and annotation subobjects permitted on all SBML objects, a \ListOfElements container object may only contain \Element objects. (References:\sbmlthreedynamic, \sec{subsec:ListOfElements}.) }
+\validRule{dyn-20205}{Apart from the general notes and annotation subobjects permitted on all SBML objects, a \ListOfDynElements container object may only contain \DynElement objects. (References: \sbmlthreedynamic, \sec{subsec:ListOfDynElements}.) }
-\validRule{dyn-20206}{A \ListOfElements object may have the optional attributes \token{id}, \token{name}, \token{metaid} and \token{sboTerm} defined by SBML Level~3 Core. No other attributes from the SBML Level~3 Core namespace or the Dynamic Structures namespace are permitted on a \ListOfElements object. (References: SBML Level~3 Version~2 Core, Section~4.2.7.) }
+\validRule{dyn-20206}{A \ListOfDynElements object may have the optional attributes \token{metaid} and \token{sboTerm} defined by SBML Level~3 Core. No other attributes from the SBML Level~3 Core namespace or the Dynamic Structures namespace are permitted on a \ListOfDynElements object. (References: \sbmlthreecore, Section~4.2.8.) }
+%L3V2 Section~4.2.7. \token{id}, \token{name},
-\subsubsection*{Rules for \class{Element} objects }
+\subsubsection*{Rules for \class{DynElement} objects }
-\validRule{dyn-20301}{An \Element object must have the attribute \token{dyn:element} because it is required. No other attributes from the Dynamic Structures namespace are permitted on an \Element object. (References: \sbmlthreedynamic, \sec{subsec:Element}.) }
+\validRule{dyn-20301}{A \DynElement object may have the optional SBML Level~3 Core attributes \token{metaid} and \token{sboTerm}. No other attributes from the \sbmlthreecore namespace are permitted on a \DynElement object (References: \sbmlthreecore, Section~4.2.)}
-\validRule{dyn-20302}{An \Element object may have the optional SBML Level~3 Core attributes \token{id}, \token{name}, \token{metaid} and \token{sboTerm}. (References: SBML Level~3 Version~2 Core, Section~4.2.)}
+\validRule{dyn-20302}{A \DynElement object must have a value for one (and exactly one) of the attributes \token{dyn:idRef} or \token{dyn:metaIdRef}, and may additionally have the attributes \token{dyn:id} and \token{dyn:name}. No other attributes from the Dynamic Structures namespace are permitted on a \DynElement object. (References:\sbmlthreedynamic, \sec{subsec:DynElement}.)}
-\validRule{dyn-20303}{An \Element object may have the optional SBML Level~3 Core subobjects for notes and annotation. No other elements from the SBML Level 3 Core namespace are permitted on an \Element object. (References: SBML Level~3 Version~2 Core, Section~4.2.)}
+\validRule{dyn-20303}{A \DynElement object may have the optional SBML Level~3 Core subobjects for notes and annotation. No other elements from the SBML Level 3 Core namespace are permitted on an \DynElement object. (References: \sbmlthreecore, Section~4.2.)}
-\validRule{dyn-20304}{The value of an \token{dyn:element} attribute on an \Element object must always conform to the syntax of the SBML data type \primtype{SIdRef}. (References: \sbmlthreedynamic, \sec{attr:element}.)}
+\validRule{dyn-20304}{The value of an \token{dyn:idRef} attribute on a \DynElement object must always conform to the syntax of the SBML data type \primtype{SIdRef}. (References: \sbmlthreedynamic, \sec{attr:idRef}.)}
-\validRule{dyn-20305}{The value of an \token{dyn:element} attribute on an \Element object must be the identifier of an SBML component whose token{id} is of type SId. (References:\sbmlthreedynamic, \sec{attr:element}.)}
+\validRule{dyn-20305}{The value of a \token{dyn:metaIdRef} attribute on a \DynElement object must always conform to the syntax of the SBML data type \primtype{IDREF}. (References: \sbmlthreedynamic, \sec{attr:metaIdRef}.)}
+\validRule{dyn-20306}{The value of an \token{dyn:idRef} attribute, if set on a given \DynElement object, must be the value of an \token{id} attribute on an existing object in the \primtype{SId} namespace of the parent \Model. (References: \sbmlthreedynamic, \sec{attr:idRef}.)}
+
+\validRule{dyn-20307}{The value of a \token{dyn:metaIdRef} attribute, if set on a given \DynElement object, must be the value of a \token{metaid} attribute on an existing object in the parent \Model. (References: \sbmlthreedynamic, \sec{attr:metaIdRef}.)}
+
\subsubsection*{Rules for extended \class{Compartment} objects }
\validRule{dyn-20401}{There may be at most one instance of a \ListOfSpatialComponents subobject within a \Compartment object that uses the Dynamic Structures package. (References: \sbmlthreedynamic, \sec{subsec:extCompartment}.) }
@@ -141,15 +149,17 @@
\validRule{dyn-20403}{Apart from the general notes and annotation subobjects permitted on all SBML objects, a \ListOfSpatialComponents container object may only contain \SpatialComponent objects. (References:\sbmlthreedynamic, \sec{subsec:listSpatialComp}.)}
-\validRule{dyn-20404}{A \ListOfSpatialComponents object may have the optional attributes \token{id}, \token{name}, \token{metaid} and \token{sboTerm} defined by SBML Level~3. No other attributes from the SBML Level~3 Core namespace or the Dynamic Structures namespace are permitted on a \ListOfSpatialComponents object. (References: SBML Level~3 Version~2 Core, Section~4.2.7.) }
+\validRule{dyn-20404}{A \ListOfSpatialComponents object may have the optional attributes \token{metaid} and \token{sboTerm} defined by SBML Level~3. No other attributes from the SBML Level~3 Core namespace or the Dynamic Structures namespace are permitted on a \ListOfSpatialComponents object. (References: \sbmlthreecore, Section~4.2.8.) }
+%L3V2 Section~4.2.7. \token{id}, \token{name},
\subsubsection*{Rules for \class{SpatialComponent} objects }
-\validRule{dyn-20501}{A \SpatialComponent object must have the attributes \token{dyn:spatialIndex} and \token{dyn:variable} because they are required. No other attributes from the Dynamic Structures namespace are permitted on a \SpatialComponent object. (References: \sbmlthreedynamic, \sec{subsec:spatialComp}.) }
+\validRule{dyn-20501}{A \SpatialComponent object must have the attributes \token{dyn:spatialIndex} and \token{dyn:variable} because they are required, and may additionally have the attributes \token{dyn:id} and \token{dyn:name}. No other attributes from the Dynamic Structures namespace are permitted on a \SpatialComponent object. (References: \sbmlthreedynamic, \sec{subsec:spatialComp}.) }
-\validRule{dyn-20502}{A \SpatialComponent object may have the optional SBML Level~3 Core attributes \token{id}, \token{name}, \token{metaid} and \token{sboTerm}. (References: SBML Level~3 Version~2 Core, Section~4.2.)}
+\validRule{dyn-20502}{A \SpatialComponent object may have the optional SBML Level~3 Core attributes \token{metaid} and \token{sboTerm}. (References: \sbmlthreecore, Section~4.2.)}
+%\token{id}, \token{name},
-\validRule{dyn-20503}{A \SpatialComponent object may have the optional SBML Level 3 Core subobjects for notes and annotation. No other elements from the SBML Level 3 Core namespace are permitted on a \SpatialComponent object. (References: SBML Level~3 Version~2 Core, Section~4.2.)}
+\validRule{dyn-20503}{A \SpatialComponent object may have the optional SBML Level~3 Core subobjects for notes and annotation. No other elements from the \sbmlthreecore namespace are permitted on a \SpatialComponent object. (References: \sbmlthreecore, Section~4.2.)}
\validRule{dyn-20504}{The value of a \token{dyn:spatialIndex} attribute on a \SpatialComponent object must always conform to the syntax and allowed values of the newly defined \primtype{SpatialKind}. Permitted values for this attribute include: \val{cartesianX}, \val{cartesianY}, and \val{cartesianZ} for position; \val{alpha}, \val{beta}, and \val{gamma} for rotational angles; and \val{F\textunderscore x}, \val{F\textunderscore y}, and \val{F\textunderscore z} for force in case of movement. (References: \sbmlthreedynamic, \sec{attr:spatialIndex}.)}
Modified: trunk/specifications/sbml-level-3/version-2/dyn/spec/cbo.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-2/dyn/spec/cbo.tex 2014-09-29 09:36:42 UTC (rev 21164)
+++ trunk/specifications/sbml-level-3/version-2/dyn/spec/cbo.tex 2014-09-29 18:34:48 UTC (rev 21165)
@@ -82,35 +82,36 @@
\begin{itemize}
- \item A \textbf{\textit{Cell Division}} term as value for the \token{cboTerm} attribute indicates that the \Event defines, by means of a \Trigger subobject, the mathematical conditions under which cellular division is to take place. When the \token{applyToAll} \Event attribute is set to \val{false}, the presence of this CBO term also dictates that model components whose \token{id} is referenced by an \Element in the \ListOfElements subobject have to be duplicated into a daughter cell. Quantities of the respective species and size of the compartments are set to half of the original in the case of symmetric cell division. When the value of \token{applyToAll} is \val{true}, all model elements are duplicated.
+ \item A \textbf{\textit{Cell Division}} term as value for the \token{cboTerm} attribute indicates that the \Event defines, by means of a \Trigger subobject, the mathematical conditions under which cellular division is to take place. When the \token{applyToAll} \Event attribute is set to \val{false}, the presence of this CBO term also dictates that model components whose \token{id} or \token{metaid} is referenced by a \DynElement in the \ListOfDynElements subobject have to be duplicated into a daughter cell. Quantities of the respective species and size of the compartments are set to half of the original in the case of symmetric cell division. When the value of \token{applyToAll} is \val{true}, all model elements are duplicated.
- \item A CBO term for \textbf{\textit{Cell Death}} as value for a \token{cboTerm} attribute indicates that the \Event defines, by means of a \Trigger subobject, the mathematical conditions under which cell death is to take place. When the \token{applyToAll} \Event attribute is set to \val{false}, the presence of this CBO term also dictates that SBML model components whose \token{id} is referenced by an \Element in the \ListOfElements subobject have to be removed from the model. When the value of \token{applyToAll} is \val{true}, all model elements are removed.
+ \item A CBO term for \textbf{\textit{Cell Death}} as value for a \token{cboTerm} attribute indicates that the \Event defines, by means of a \Trigger subobject, the mathematical conditions under which cell death is to take place. When the \token{applyToAll} \Event attribute is set to \val{false}, the presence of this CBO term also dictates that SBML model components whose \token{id} or \token{metaid} is referenced by a \DynElement in the \ListOfDynElements subobject have to be removed from the model. When the value of \token{applyToAll} is \val{true}, all model elements are removed.
- \item A CBO term for \textbf{\textit{Movement}} as value for a \token{cboTerm} attribute indicates that the \Event defines, by means of its \Trigger suboject, the mathematical conditions under which cell movement is to take place. When the \token{applyToAll} \Event attribute is set to \val{false}, the presence of this CBO term also dictates that SBML model \Compartments whose \token{id} is referenced by an \Element in the \ListOfElements subobject will have their position updated according to the force vector defined as a \SpatialComponent. When the value of \token{applyToAll} is \val{true}, the spatial location of all model \Compartments is also updated.
+ \item A CBO term for \textbf{\textit{Movement}} as value for a \token{cboTerm} attribute indicates that the \Event defines, by means of its \Trigger suboject, the mathematical conditions under which cell movement is to take place. When the \token{applyToAll} \Event attribute is set to \val{false}, the presence of this CBO term also dictates that SBML model \Compartments whose \token{id} or \token{metaid} is referenced by a \DynElement in the \ListOfDynElements subobject will have their position updated according to the force vector defined as a \SpatialComponent. When the value of \token{applyToAll} is \val{true}, the spatial location of all model \Compartments is also updated.
\end{itemize}
Although the use of CBO can be beneficial on elucidating the role of modeling elements, it is critical to keep in mind that the presence of a \token{cboTerm} value on an object does not change the fundamental mathematical meaning of the model. SBML models must be defined in a way, so that they stand on their own without depending on additional information added by CBO terms for a correct mathematical interpretation. In the case of labeled \Event elements, CBO term definitions will only imply alternative simulation semantics. Though tools not supporting these specific \Event semantics will not be able to reproduce dynamic behaviors as intended, they will be able to understand the meaning of said \Event. Allowing the use of \token{cboTerm} in \Event elements to alter the mathematical meaning of a model would allow too much leeway to slip inconsistent concepts into SBML objects, ultimately reducing model interoperability.
-\subsubsection{Tradeoffs in using CBO terms}
-\label{subsec:tradeoffCBO}
+\subsubsection{Benefits of using CBO terms}
+\label{subsec:benefitsCBO}
-The presented CBO-based approach to annotating SBML \Event components with controlled terms has, just like the SBO-based approach presented in \sbmlthreecore, the following strengths:
+The presented CBO-based approach to annotating SBML \SBase-derived components with controlled terms has, just like the SBO-based approach presented in \sbmlthreecore, the following strengths:
\begin{enumerate}
\item The syntax required is very straight-forward and requires a single \primtype{string} containing the \primtype{id} of a supported CBO term.
\item Supported CBO terms cover a relevant portion of the cellular behaviors required by the community.
- \item It does not interfere with already-existing annotation schemes implemented by either Core and SBML extensions.
+ \item It does not interfere with already-existing annotation schemes implemented by either Core or other available SBML extensions.
+ \item It may be expanded to accommodate further SBML community input without considerable changes to the \token{ids} of the terms themselves or the hierarchical taxonomy of the ontology.
\end{enumerate}
-The following list illustrates some of the weaknesses of the proposed approach:
+%The following list illustrates some of the weaknesses of the proposed approach:
+%
+%\begin{enumerate}
+% \item The Cell Behavior Ontology is a recent and evolving ontology. As such, it is susceptible to minor changes in its hierarchical taxonomy. These however, should not affect the \token{ids} of the terms themselves but rather the structure of the ontology itself.
+%\end{enumerate}
-\begin{enumerate}
- \item The Cell Behavior Ontology is a recent and evolving ontology. As such, it is susceptible to minor changes in its hierarchical taxonomy. These however, should not affect the \token{ids} of the terms themselves but rather the structure of the ontology itself.
-\end{enumerate}
+%{\color{red} Harold: \notice Can we think of any other benefits or weaknesses?}
-{\color{red} Harold: \notice Can we think of any other benefits or weaknesses?}
-
\subsubsection{Relationships to the SBML annotation element}
\label{subsubsec:CBO&Annot}
Modified: trunk/specifications/sbml-level-3/version-2/dyn/spec/examples.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-2/dyn/spec/examples.tex 2014-09-29 09:36:42 UTC (rev 21164)
+++ trunk/specifications/sbml-level-3/version-2/dyn/spec/examples.tex 2014-09-29 18:34:48 UTC (rev 21165)
@@ -11,8 +11,8 @@
\begin{example}
<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2"
- xmlns:dyn="http://www.sbml.org/sbml/level3/version2/dyn/version1" dyn:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
+ xmlns:dyn="http://www.sbml.org/sbml/level3/version1/dyn/version1" dyn:required="true">
<model id="singleCell">
<listOfCompartments>
@@ -21,16 +21,20 @@
<compartment id="Cytosol" spatialDimensions="3" size= "523" constant= "true"/>
</listOfCompartments>
<listOfSpecies>
- <species id="C_EC" compartment="Extracellular" hasOnlySubstanceUnits="false"
+ <species id="C_EC" compartment="Extracellular" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false"/>
<species id="RTR_M" compartment="PlasmaMembrane" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false"/>
<species id="RCC_M" compartment="PlasmaMembrane" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false"/>
- <species id="A_C" compartment="Cytosol" hasOnlySubstanceUnits="false"
+ <species id="A_C" compartment="Cytosol" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false"/>
- <species id="AA_C" compartment="Cytosol" hasOnlySubstanceUnits="false"
+ <species id="AA_C" compartment="Cytosol" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false"/>
+ <species id="T" compartment="Cytosol" initialConcentration="10" hasOnlySubstanceUnits="false"
+ boundaryCondition="false" constant="false"/>
+ <species id="S" compartment="Cytosol" initialConcentration="5" hasOnlySubstanceUnits="false"
+ boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="r1" reversible="true" fast="false" compartment="Extracellular">
@@ -64,7 +68,7 @@
</trigger>
</event>
<event useValuesFromTriggerTime="true" dyn:applyToAll= "true"
- dyn:cboTerm="http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_0.owl#CellDivision">
+ dyn:cboTerm="http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_0.owl#CellDivision">
<trigger initialValue="false" persistent="true">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply> <lt/> <ci> AA_C </ci> <ci> S </ci> </apply>
@@ -84,10 +88,10 @@
\begin{example}
<?xml version="1.0" encoding="UTF-8"?>
- <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"
+ <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1"
- xmlns:dyn="http://www.sbml.org/sbml/level3/version2/dyn/version1"
- comp:required="true" dyn:required="true" level="3" version="2">
+ xmlns:dyn="http://www.sbml.org/sbml/level3/version1/dyn/version1"
+ comp:required="true" dyn:required="true" level="3" version="1">
<model id="grid2x2">
<listOfCompartments>
@@ -194,10 +198,10 @@
\begin{example}
<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"
- xmlns:dyn="http://www.sbml.org/sbml/level3/version2/dyn/version1"
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
+ xmlns:dyn="http://www.sbml.org/sbml/level3/version1/dyn/version1"
xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"
- level="3" version="2" groups:required="false" dyn:required="true" >
+ level="3" version="1" groups:required="false" dyn:required="true" >
<model id="Cell">
<listOfCompartments>
@@ -210,6 +214,8 @@
boundaryCondition="false" constant="false"/>
<species id="EP" compartment="C" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false"/>
+ <species id="T" compartment="C" initialConcentration="5" hasOnlySubstanceUnits="false"
+ boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="Association" compartment="C" reversible="false" fast="false">
@@ -251,9 +257,9 @@
<apply> <lt/> <ci> EP </ci> <ci> T </ci> </apply>
</math>
</trigger>
- <dyn:listOfElements>
- <dyn:element dyn:element="cellGroup"/>
- </dyn:listOfElements>
+ <dyn:listOfDynElements>
+ <dyn:dynElement dyn:idRef="cellGroup"/>
+ </dyn:listOfDynElements>
</event>
</listOfEvents>
</model>
Modified: trunk/specifications/sbml-level-3/version-2/dyn/spec/images/UMLExtendedCompartment.pdf
===================================================================
--- trunk/specifications/sbml-level-3/version-2/dyn/spec/images/UMLExtendedCompartment.pdf 2014-09-29 09:36:42 UTC (rev 21164)
+++ trunk/specifications/sbml-level-3/version-2/dyn/spec/images/UMLExtendedCompartment.pdf 2014-09-29 18:34:48 UTC (rev 21165)
@@ -1,15 +1,16 @@
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@@ Diff output truncated at 100000 characters. @@
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