diff --git a/specification/level-1-version-4/images/uml/sed-ml.pdf b/specification/level-1-version-4/images/uml/sed-ml.pdf index 578a7d0..094b12b 100644 Binary files a/specification/level-1-version-4/images/uml/sed-ml.pdf and b/specification/level-1-version-4/images/uml/sed-ml.pdf differ diff --git a/specification/level-1-version-4/sed-ml-L1V4.pdf b/specification/level-1-version-4/sed-ml-L1V4.pdf index e941f03..b858661 100644 Binary files a/specification/level-1-version-4/sed-ml-L1V4.pdf and b/specification/level-1-version-4/sed-ml-L1V4.pdf differ diff --git a/specification/level-1-version-4/sources/sedml.tex b/specification/level-1-version-4/sources/sedml.tex index ea2f1cd..e53851a 100644 --- a/specification/level-1-version-4/sources/sedml.tex +++ b/specification/level-1-version-4/sources/sedml.tex @@ -12,13 +12,14 @@ \subsection{\element{SED-ML} top level element} \item \DataGenerator (for the definition of post-processing), \item \hyperref[class:output]{Output} (for the specification of plots and reports). \item \hyperref[class:style]{Style} \changed{(for the specification of plot element styles)}. + \item \AlgorithmParameter \changed{(for the definition of global algorithm parameters)}. \end{itemize} A SED-ML document needs to have the SED-ML namespace defined through the mandatory \hyperref[sec:xmlns]{\element{xmlns}} attribute. In addition, the SED-ML \hyperref[sec:level]{\element{level}} and \hyperref[sec:version]{\element{version}} attributes are required. -The root element of each SED-ML XML file is the \code{sedML} element, encoding \hyperref[sec:level]{\element{level}} and \hyperref[sec:version]{\element{version}} of the file, and setting the necessary namespaces. Nested inside the \code{sedML} element are the six optional lists serving as containers for the encoded information: \hyperref[class:listOfDataDescriptions]{\element{listOfDataDescriptions}} for all external data, \hyperref[class:listOfModels]{\element{listOfModels}} for all models, \hyperref[class:listOfSimulations]{\element{listOfSimulations}} for all simulations, \hyperref[class:listOfTasks]{\element{listOfTasks}} for all tasks, \hyperref[class:listOfDataGenerators]{\element{listOfDataGenerators}} for all post-processing definitions, \hyperref[class:listOfOutputs]{\element{listOfOutputs}} for all output definitions, \changed{and \ListOfStyles for all style definitions}. +The root element of each SED-ML XML file is the \code{sedML} element, encoding \hyperref[sec:level]{\element{level}} and \hyperref[sec:version]{\element{version}} of the file, and setting the necessary namespaces. Nested inside the \code{sedML} element are the six optional lists serving as containers for the encoded information: \hyperref[class:listOfDataDescriptions]{\element{listOfDataDescriptions}} for all external data, \hyperref[class:listOfModels]{\element{listOfModels}} for all models, \hyperref[class:listOfSimulations]{\element{listOfSimulations}} for all simulations, \hyperref[class:listOfTasks]{\element{listOfTasks}} for all tasks, \hyperref[class:listOfDataGenerators]{\element{listOfDataGenerators}} for all post-processing definitions, \hyperref[class:listOfOutputs]{\element{listOfOutputs}} for all output definitions, \changed{\ListOfStyles for all style definitions. and \ListOfAlgorithmParameters for parameters that apply to processing this SED-ML file as a whole}. -\sedfig[width=0.76\textwidth]{images/uml/sed-ml}{The SED-ML class}{fig:sed-mlMain} +\sedfig[width=0.7\textwidth]{images/uml/sed-ml}{The SED-ML class}{fig:sed-mlMain} The basic XML structure of a SED-ML file is shown in listing \vref{lst:sedmlRoot}. @@ -48,6 +49,9 @@ \subsection{\element{SED-ML} top level element} [DEFINITION OF STYLES] + + [PARAMETERS TO APPLY TO THE ENTIRE SIMULATION PROCESS] + \end{myXmlLst} @@ -73,7 +77,7 @@ \subsubsection{\element{version}} % ~~~ LIST OF DATA DESCRIPTIONS ~~~ \subsubsection{\element{listOfDataDescriptions}} \label{class:listOfDataDescriptions} -In order to reference data in a simulation experiment, the data files along with a description on how to access such files and what information to extract from them have to be defined. The \hyperref[class:sed-ml]{SED-ML document} uses the \concept{\element{listOfDataDescriptions}} container to define \hyperref[class:dataDescription]{DataDescription}s for referencing external data (\fig{sed-mlMain}). The \concept{\element{listOfDataDescriptions}} is optional and may contain zero to many \hyperref[class:dataDescription]{DataDescriptions}. +In order to reference data in a simulation experiment, the data files along with a description on how to access such files and what information to extract from them have to be defined. The \hyperref[class:sed-ml]{SED-ML document} uses the \concept{\element{listOfDataDescriptions}} container to define \hyperref[class:dataDescription]{DataDescription}s for referencing external data (\fig{sed-mlMain}). The \concept{\element{listOfDataDescriptions}} is optional and may contain zero or more \hyperref[class:dataDescription]{DataDescriptions}. \lsttext{listOfDataDescriptions}{listOfDataDescriptions} @@ -103,7 +107,7 @@ \subsubsection{\element{listOfDataDescriptions}} % ~~~ LIST OF MODELS ~~ \subsubsection{\element{listOfModels}} \label{class:listOfModels} -The models used in a simulation experiment are defined in the \concept{\element{listOfModels}} container (\fig{sed-mlMain}). The \concept{\element{listOfModels}} is optional and may contain zero to many \Models. However, if a \hyperref[class:sed-ml]{SED-ML document} contains one or more \hyperref[class:abstractTask]{Tasks}, at least one \Model must be defined to which the \hyperref[class:abstractTask]{Task} elements refer (see Section~\ref{sec:modelReference}). +The models used in a simulation experiment are defined in the \concept{\element{listOfModels}} container (\fig{sed-mlMain}). The \concept{\element{listOfModels}} is optional and may contain zero or more \Models. However, if a \hyperref[class:sed-ml]{SED-ML document} contains one or more \hyperref[class:abstractTask]{Tasks}, at least one \Model must be defined to which the \hyperref[class:abstractTask]{Task} elements refer (see Section~\ref{sec:modelReference}). \lsttext{listOfModels}{listOfModels} @@ -120,7 +124,7 @@ \subsubsection{\element{listOfModels}} % ~~~ LIST OF SIMULATIONS ~~ \subsubsection{\element{listOfSimulations}} \label{class:listOfSimulations} -The \concept{\element{listOfSimulations}} element is the container for \Simulation descriptions (\fig{sed-mlMain}). The \concept{\element{listOfSimulations}} is optional and may contain zero to many \Simulations. However, if the \hyperref[class:sed-ml]{SED-ML document} contains one or more \hyperref[class:abstractTask]{Tasks}, at least one \Simulation element must be defined to which the \hyperref[class:abstractTask]{Task} elements refer (see Section \ref{sec:simulationReference}). +The \concept{\element{listOfSimulations}} element is the container for \Simulation descriptions (\fig{sed-mlMain}). The \concept{\element{listOfSimulations}} is optional and may contain zero or more \Simulations. However, if the \hyperref[class:sed-ml]{SED-ML document} contains one or more \hyperref[class:abstractTask]{Tasks}, at least one \Simulation element must be defined to which the \hyperref[class:abstractTask]{Task} elements refer (see Section \ref{sec:simulationReference}). \lsttext{listOfSimulations}{listOfSimulation} \begin{myXmlLst}{The SED-ML \element{listOfSimulations} element, containing two simulation setups}{lst:listOfSimulations} @@ -137,7 +141,7 @@ \subsubsection{\element{listOfSimulations}} % ~~~ LIST OF TASKS ~~~ \subsubsection{\element{listOfTasks}} \label{class:listOfTasks} -The \concept{\element{listOfTasks}} element contains the defined \hyperref[class:task]{tasks} for the simulation experiment (\fig{sed-mlMain}). The \concept{\element{listOfTasks}} is optional and may contain zero to many tasks, each of which is an instance of a subclass of \AbstractTask. +The \concept{\element{listOfTasks}} element contains the defined \hyperref[class:task]{tasks} for the simulation experiment (\fig{sed-mlMain}). The \concept{\element{listOfTasks}} is optional and may contain zero or more tasks, each of which is an instance of a subclass of \AbstractTask. \lsttext{listOfTasks}{listOfTasks} \begin{myXmlLst}{The SED-ML \code{listOfTasks} element, defining one task}{lst:listOfTasks} @@ -151,7 +155,7 @@ \subsubsection{\element{listOfTasks}} % ~~~ LIST OF DATA GENERATORS ~~~ \subsubsection{\element{listOfDataGenerators}} \label{class:listOfDataGenerators} -The \concept{\element{listOfDataGenerators}} container holds the \hyperref[class:dataGenerator]{dataGenerator} definitions of a simulation experiment (\fig{sed-mlMain}). The \concept{\element{listOfDataGenerators}} is optional and in general may contain zero to many \DataGenerators. +The \concept{\element{listOfDataGenerators}} container holds the \hyperref[class:dataGenerator]{dataGenerator} definitions of a simulation experiment (\fig{sed-mlMain}). The \concept{\element{listOfDataGenerators}} is optional and in general may contain zero or more \DataGenerators. In SED-ML, all variable and parameter values used in the \hyperref[class:output]{Output} class need to be defined as a \DataGenerator beforehand. @@ -172,7 +176,7 @@ \subsubsection{\element{listOfDataGenerators}} % ~~ LIST OF OUTPUTS ~~~ \subsubsection{\element{listOfOutputs}} \label{class:listOfOutputs} -The \concept{\element{listOfOutputs}} container holds the \hyperref[class:output]{Output} definitions of a simulation experiment (\fig{sed-mlMain}). The \concept{\element{listOfOutputs}} is optional and may contain zero to many outputs. +The \concept{\element{listOfOutputs}} container holds the \hyperref[class:output]{Output} definitions of a simulation experiment (\fig{sed-mlMain}). The \concept{\element{listOfOutputs}} is optional and may contain zero or more outputs. \lsttext{listOfOutputs}{listOfOutputs} \begin{myXmlLst}{The \concept{listOfOutput} element}{lst:listOfOutputs} @@ -191,10 +195,10 @@ \subsubsection{\element{listOfOutputs}} % ~~ LIST OF STYLES ~~~ \subsubsection{\element{listOfStyles}} \label{class:listOfStyles} -The \concept{\element{listOfStyles}} container holds the \Style definitions of a simulation experiment (\fig{sed-mlMain}). The \concept{\element{listOfStyles}} is optional and may contain zero to many styles. +The \concept{\element{listOfStyles}} container holds the \Style definitions of a simulation experiment (\fig{sed-mlMain}). The \concept{\element{listOfStyles}} is optional and may contain zero or more styles. \lsttext{listOfStyles}{listOfStyles} -\begin{myXmlLst}{The \concept{listOfStyle} element}{lst:listOfStyles} +\begin{myXmlLst}{The \concept{listOfStyles} element}{lst:listOfStyles}