packages-table.tex

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\begin{sidewaystable}
  \centering
  \rowcolors{0}{}{rowgray}
  \renewcommand{\tabcolsep}{4pt}
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  \caption{Summary of SBML Level~3 Package statuses.  Symbols: \protect\released = released; \protect\notreleased = not released; \protect\done = complete; \protect\inprogress = in progress; \protect\notapplicable = not applicable.}
  \begin{tabular}{m{0.12in}>{\raggedright}m{1.9in}>{\raggedright}m{0.46in}>{\raggedright}m{3.9in}>{\hspace*{3pt}}>{\hspace*{-5pt}}c>{\hspace*{-4pt}}c>{\hspace*{-4pt}}c>{\hspace*{-6pt}}>{\hspace*{1pt}}c>{\hspace*{1pt}}m{1.35in}}
    \toprule
    & \textbf{Package name} & \textbf{Label} & \textbf{Purpose} & \rot{\textbf{Specification}} & \rot{\textbf{libSBML Support}} & \rot{\textbf{JSBML Support}} & \rot{\textbf{Test Suite}} & \textbf{Reference} \\
    \midrule
\released
& Flux Balance Constraints
    & fbc
    & Define constraint-based models (a.k.a.\ steady-state models).
    & \done
    & \done
    & \done
    & \done
    & \textls[-50]{\cite{Olivier2018a}}
    \\    
\released
& Groups
    & groups
    & Collect elements together for annotation purposes.  Groups have no mathematical meaning and do not affect simulations.
    & \done
    & \done
    & \done
    & \notapplicable
    & \textls[-50]{\cite{hucka2016sbml}}
    \\
\released
& Hierarchical Model Composition
    & comp
    & Define models composed of other models. The ``submodels'' can be stored in the same file or as separate files.
    & \done
    & \done
    & \done
    & \done
    & \textls[-50]{\cite{Smith2015}}
    \\
\released
& Layout
    & layout
    & Store positions and sizes of model components in network diagrams of SBML models. (Cf.\ the Rendering package.)
    & \done
    & \done
    & \done
    & \notapplicable
    & \textls[-50]{\cite{Gauges2015}}
    \\
\released
& Multistate, Multicomponent, \& Multicompartment Species
    & multi
    & Define features such as states or binding sites on molecular species, optionally in combination with rule-based processes.
    & \done
    & \done
    & \done
    & \inprogress
    & \textls[-50]{\cite{zhang2018multi}}
    \\
\released
& Qualitative Models
    & qual
    & Allow model where SBML species' values represent qualitative activity levels rather than amounts or concentrations.
    & \done
    & \done
    & \done
    & \inprogress
    & \textls[-50]{\cite{Chaouiya2015sbml}}
    \\
\released
& Rendering
    & render
    & Extend the Layout package to enable storing graphical symbols and styles, curves, colors, and gradients in network diagrams.
    & \done
    & \done
    & \done
    & \notapplicable
    & \textls[-50]{\cite{Bergmann2018sbml}}
    \\
\hline
\notreleased
& Arrays
    & arrays
    & Define arrays of elements, such as arrays of compartments. (Core SBML Level~3 supports only scalar values.)
    & \inprogress
    & \done
    & \done
    & \inprogress
    & 
    \\
\notreleased
& Distributions
    & distrib
    & Define statistical distributions for quantitative values. (Core SBML does not enable indicating value ranges or distributions.)
    & \inprogress
    & \done
    & \done
    & \inprogress
    & 
    \\
\notreleased
& Dynamical Processes
    & dyn
    & Describe the creation, destruction, and movement of model elements during simulation.
    & \inprogress
    & \done
    & \done
    & \inprogress
    & 
    \\
\notreleased
& Extended math
    & math
    & Additional constructs not included in the subset of MathML used by SBML Level~3 Core for mathematical expressions.
    & \inprogress
    & \inprogress
    & \inprogress
    & \inprogress
    & 
    \\    
\notreleased
& Spatial Processes
    & spatial
    & Define spatially-inhomogeneous compartment geometries and processes such as diffusion.
    & \inprogress 
    & \done
    & \done
    & \inprogress
    & 
    \\
    \bottomrule
  \end{tabular}
  \label{packages}
\end{sidewaystable}