The graph below shows was rendered from the JanaWolfGlycolysis.xml SBML file that comes with the
SBW. The model was written by Jana Wolf and was published by Ruoff et al. in 2003.
PGF/TikZ Output
\documentclass{article}
\usepackage{tikz}
\usepackage{pgf}
\usepackage[total={1000pt,500pt}, centering, a2paper, landscape]{geometry}
\pagestyle{empty}
\begin{document}
\begin{center}
\begin{tikzpicture}[xscale = 1, yscale = -1]
{
% List of colors used:
\definecolor{black}{RGB}{0,0,0};
\definecolor{red}{RGB}{255,0,0};
\definecolor{blue}{RGB}{0,0,255};
\definecolor{green}{RGB}{0,255,0};
{
% Curve for reactionGlyph_ProteinPhosphorylation
\pgftransformshift{\pgfpoint{ 85pt }{ 319pt } }
\draw [line width = 1pt, color = blue!100 ]
(0pt,5pt)--(60pt,5pt);
}
{
% Curve for reactionGlyph_CaMKPhosphorylation
\pgftransformshift{\pgfpoint{ 157pt }{ 59pt } }
\draw [line width = 1pt, color = blue!100 ]
(5pt,0pt)--(5pt,53pt)--(5pt,57pt)--(5pt,86pt);
}
{
% Curve for reactionGlyph_reaction0
\pgftransformshift{\pgfpoint{ 327pt }{ 129pt } }
\draw [line width = 1pt, color = black!100 ]
(5pt,0pt)--(5pt,31pt)--(5pt,35pt)--(5pt,66pt);
}
{
% Curve for reactionGlyph_reaction1
\pgftransformshift{\pgfpoint{ 135pt }{ 181pt } }
\draw [line width = 1pt, color = black!100 ]
(5pt,0pt)--(5pt,33pt)--(5pt,33pt)--(25pt,33pt)--(29pt,33pt)--(67pt,33pt)--(67pt,33pt)--(72pt,28pt)--(72pt,28pt)--(72pt,0pt);
}
{
% Curve for reactionGlyph_reaction1
\pgftransformshift{\pgfpoint{ 135pt }{ 181pt } }
\draw [line width = 1pt, color = black!100 ]
(72pt,28pt)--(77pt,33pt)--(77pt,33pt)--(160pt,33pt);
}
{
% Curve for reactionGlyph_proteinPhosphorilationInhibition
\pgftransformshift{\pgfpoint{ 115pt }{ 212pt } }
\draw [line width = 1pt, color = red!100 ]
(47pt,0pt)--(47pt,27pt)--(47pt,27pt)--(0pt,27pt);
}
{
% Curve for reactionGlyph_CaMKDephosphorylation
\pgftransformshift{\pgfpoint{ 155pt }{ 77pt } }
\draw [line width = 1pt, color = red!100 ]
(125pt,5pt)--(12pt,5pt);
}
{
% Curve for reactionGlyph_bindingInhibition
\pgftransformshift{\pgfpoint{ 164pt }{ 114pt } }
\draw [line width = 1pt, color = red!100 ]
(0pt,0pt)--(76pt,0pt)--(76pt,0pt)--(76pt,125pt)--(76pt,125pt)--(25pt,125pt)--(25pt,125pt)--(25pt,105pt);
}
{
% Curve for reactionGlyph_bindingRequirement
\pgftransformshift{\pgfpoint{ 270pt }{ 162pt } }
\draw [line width = 1pt, color = green!100 ]
(60pt,0pt)--(5pt,0pt)--(5pt,0pt)--(5pt,40pt);
}
{
% Curve for reactionGlyph_phosphorylation
\pgftransformshift{\pgfpoint{ 105pt }{ 179pt } }
\draw [line width = 1pt, color = green!100 ]
(5pt,0pt)--(5pt,130pt);
}
{
% Curve for reactionGlyph_autophosphorylation
\pgftransformshift{\pgfpoint{ 30pt }{ 109pt } }
\draw [line width = 1pt, color = green!100 ]
(80pt,70pt)--(80pt,146pt)--(80pt,146pt)--(75pt,151pt)--(75pt,151pt)--(0pt,151pt)--(0pt,151pt)--(0pt,5pt)--(0pt,5pt)--(65pt,5pt)--(62pt,8pt)--(68pt,2pt)--(77pt,8pt)--(83pt,2pt)--(80pt,5pt)--(115pt,5pt);
}
{
% Rectangle for species10
\pgftransformshift{\pgfpoint{ 285pt }{ 70pt } }
\def \wholeShape {(0pt,0pt) rectangle(104pt,24pt)}
\draw[rounded corners = 10.4pt, fill = none] \wholeShape;
\draw[line width = 2pt, color = black!100, rounded corners = 10.4pt ] \wholeShape;
}
{
% Rectangle for species1
\pgftransformshift{\pgfpoint{ 300pt }{ 200pt } }
\def \wholeShape {(0pt,0pt) rectangle(74pt,24pt)}
\draw[rounded corners = 7.4pt, fill = none] \wholeShape;
\draw[line width = 2pt, color = black!100, rounded corners = 7.4pt ] \wholeShape;
}
{
% Rectangle for species4
\pgftransformshift{\pgfpoint{ 100pt }{ 150pt } }
\def \wholeShape {(0pt,0pt) rectangle(124pt,24pt)}
\draw[rounded corners = 12.4pt, fill = none] \wholeShape;
\draw[line width = 2pt, color = black!100, rounded corners = 12.4pt ] \wholeShape;
}
{
% Rectangle for speciesGlyph_variousSubstrates
\pgftransformshift{\pgfpoint{ 150pt }{ 300pt } }
\def \wholeShape {(0pt,0pt) rectangle(104pt,48pt)}
\draw[rounded corners = 10.4pt, fill = none] \wholeShape;
\draw[line width = 2pt, color = black!100, rounded corners = 10.4pt ] \wholeShape;
}
{
% Ellipses for species2
\pgftransformshift{\pgfpoint{ 330pt }{ 160pt } }
\def \wholeShape {(2pt,2pt) ellipse(2pt and 2pt)}
\fill[color = green!100] \wholeShape;
\draw[line width = 1pt, color = green!100 ] \wholeShape;
}
{
% Ellipses for species3
\pgftransformshift{\pgfpoint{ 160pt }{ 212pt } }
\def \wholeShape {(2pt,2pt) ellipse(2pt and 2pt)}
\fill[color = red!100] \wholeShape;
\draw[line width = 1pt, color = red!100 ] \wholeShape;
}
{
% Ellipses for species6
\pgftransformshift{\pgfpoint{ 160pt }{ 112pt } }
\def \wholeShape {(2pt,2pt) ellipse(2pt and 2pt)}
\fill[color = red!100] \wholeShape;
\draw[line width = 1pt, color = red!100 ] \wholeShape;
}
{
% Group for textGlyph_species9_1
\draw (162pt, 42pt) node[text = blue!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { P };
}
{
% Group for textGlyph_species9_2
\draw (70pt, 324pt) node[text = blue!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { P };
}
{
% Group for textGlyph_species0
\draw (337pt, 112pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { Ca++ };
}
{
% Group for speciesGlyph_species1
\draw (337pt, 212pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { CaM };
}
{
% Group for speciesGlyph_species1
\draw (202pt, 312pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { various };
}
{
% Group for speciesGlyph_species1
\draw (202pt, 332pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { substrates };
}
{
% Group for speciesGlyph_species4
\draw (75pt, 162pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { CaMK };
}
{
% Group for speciesGlyph_species4
\draw (130pt, 162pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { kinase };
}
{
% Group for speciesGlyph_species4
\draw (207pt, 162pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { reg };
}
{
% Group for speciesGlyph_species10
\draw (337pt, 82pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { Ph'tase };
}
{
% Group for textGlyph_number1
\draw (120pt, 272pt) node[text = green!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 1 };
}
{
% Group for textGlyph_number2
\draw (145pt, 244pt) node[text = red!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 2 };
}
{
% Group for textGlyph_number3
\draw (170pt, 202pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 3 };
}
{
% Group for textGlyph_number4
\draw (225pt, 202pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 4 };
}
{
% Group for textGlyph_number5
\draw (300pt, 152pt) node[text = green!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 5 };
}
{
% Group for textGlyph_number6
\draw (345pt, 159pt) node[text = black!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 6 };
}
{
% Group for textGlyph_number7
\draw (75pt, 100pt) node[text = green!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 7 };
}
{
% Group for textGlyph_number8
\draw (255pt, 132pt) node[text = red!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 8 };
}
{
% Group for textGlyph_number9
\draw (260pt, 72pt) node[text = red!100, font = \fontsize{ 12 } { 12 }\fontfamily\sfdefault\selectfont] { 9 };
}
}
\end{tikzpicture}
\end{center}
\end{document}