SBML2TikZ

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The figure below describes a feedback loop where a downstream inhibitor represses an upstream species. The figure was originally generated by JDesigner but has had its rendering and layout information replaced with SBGN using the "useSBGN" option on the SBML2TikZ user interface.
 

PGF/TikZ Output

\documentclass{article}
\usepackage{tikz}
\usepackage{pgf}
\usepackage[total={471.503471374512pt,376.5pt}, centering, a4paper, 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{white}{RGB}{255,255,255};
\definecolor{transparent}{RGB}{255,255,255};
\definecolor{EmptySetOutline}{RGB}{128,128,128};
\definecolor{EmptySetGradientStart}{RGB}{255,255,255};
\definecolor{EmptySetGradientEnd}{RGB}{211,211,211};
\definecolor{CompartmentBorder}{RGB}{102,102,102};
\definecolor{CompartmentGradientStart}{RGB}{204,204,204};
\definecolor{CompartmentGradientEnd}{RGB}{204,204,255};
\definecolor{CloneMarkerColor}{RGB}{255,165,0};
\definecolor{EPNGradientStart}{RGB}{255,255,255};
\definecolor{EPNGradientEnd}{RGB}{192,192,192};

% List of gradients used:
\definecolor{color0}{RGB}{255,255,255};
\definecolor{color1}{RGB}{192,192,192};
\pgfdeclareverticalshading {EPNBackgroundGradient} { 70pt } {color(0pt)=(color0!100); color(73.96073pt)=(color1!100)}

\definecolor{color0}{RGB}{255,255,255};
\definecolor{color1}{RGB}{255,255,255};
\definecolor{color2}{RGB}{255,165,0};
\definecolor{color3}{RGB}{255,165,0};
\definecolor{color4}{RGB}{255,165,0};
\pgfdeclareverticalshading {cloneMarker} { 70pt } {color(0pt)=(color0!0); color(0.375pt)=(color1!0); color(0.38pt)=(color2!100); color(0.5pt)=(color3!100); color(50pt)=(color4!100)}

\definecolor{color0}{RGB}{255,255,255};
\definecolor{color1}{RGB}{211,211,211};
\pgfdeclareverticalshading {EmptySetGradient} { 70pt } {color(0pt)=(color0!100); color(73.96073pt)=(color1!100)}

\definecolor{color0}{RGB}{204,204,204};
\definecolor{color1}{RGB}{204,204,255};
\pgfdeclareverticalshading {CompartmentGradient} { 70pt } {color(0pt)=(color0!100); color(73.96073pt)=(color1!100)}

{
   % Group for J0
   \draw[line width = 2pt, color = black!100,  ] (64pt, 80.0285714285714pt) -- (131pt, 107.971428571429pt);
   {
      \pgftransformshift{\pgfpoint{ 131pt }{ 107.9714pt } }
      \pgftransformcm { 0.9229488 }{ 0.3849228 }{ -0.3849228 }{ 0.9229488 }{\pgfpoint{ 0pt }{ 0pt } }
      {
         % LineEnding for S1
         {
            % Polygon for S1
            \pgftransformshift{\pgfpoint{ -8pt }{ -4pt } }
            \draw [line width = 2pt, color = black!100, fill = black!100 ]
            (0pt,0pt)--(8pt,4pt)--(0pt,8pt)--(2.64pt,4pt)--(0pt, 0pt) -- cycle;
         }
      }
   }
   \draw[line width = 2pt, color = black!100,  ] (404pt, 229.257142857143pt) -- (353pt, 243pt);
   \draw[line width = 2pt, color = black!100,  ] (353pt, 243pt) -- (69pt, 127pt);
   \draw[line width = 2pt, color = black!100,  ] (69pt, 127pt) -- (84pt, 101pt);
   {
      \pgftransformshift{\pgfpoint{ 84pt }{ 101pt } }
      \pgftransformcm { 0.4997225 }{ -0.8661855 }{ 0.8661855 }{ 0.4997226 }{\pgfpoint{ 0pt }{ 0pt } }
      {
         % LineEnding for S4
         {
            % Curve for S4
            \pgftransformshift{\pgfpoint{ -0.5pt }{ -5pt } }
            \draw [line width = 2pt, color = black!100 ]
            (-0.5pt,0pt)--(1.5pt,10pt);
         }
      }
   }
   \draw[line width = 2pt, color = black!100,  ] (97.5pt, 94pt) -- (97.5pt, 94pt);
   {
      \pgftransformshift{\pgfpoint{ 97.5pt }{ 94pt } }
      {
         % LineEnding for J0
         {
            % Rectangle for J0
            \pgftransformshift{\pgfpoint{ -4pt }{ -4pt } }
            \def \wholeShape {(0pt,0pt) rectangle(8pt,8pt)}
            \fill[fill = white!100] \wholeShape;
            \draw[line width = 2pt, color = black!100 ] \wholeShape;
         }
      }
   }
}
{
   % Group for J1
   \draw[line width = 2pt, color = black!100,  ] (169pt, 123.875pt) -- (227pt, 147.125pt);
   {
      \pgftransformshift{\pgfpoint{ 227pt }{ 147.125pt } }
      \pgftransformcm { 0.9282005 }{ 0.3720804 }{ -0.3720803 }{ 0.9282005 }{\pgfpoint{ 0pt }{ 0pt } }
      {
         % LineEnding for S2
         {
            % Polygon for S2
            \pgftransformshift{\pgfpoint{ -8pt }{ -4pt } }
            \draw [line width = 2pt, color = black!100, fill = black!100 ]
            (0pt,0pt)--(8pt,4pt)--(0pt,8pt)--(2.64pt,4pt)--(0pt, 0pt) -- cycle;
         }
      }
   }
   \draw[line width = 2pt, color = black!100,  ] (198pt, 135.5pt) -- (198pt, 135.5pt);
   {
      \pgftransformshift{\pgfpoint{ 198pt }{ 135.5pt } }
      {
         % LineEnding for J1
         {
            % Rectangle for J1
            \pgftransformshift{\pgfpoint{ -4pt }{ -4pt } }
            \def \wholeShape {(0pt,0pt) rectangle(8pt,8pt)}
            \fill[fill = white!100] \wholeShape;
            \draw[line width = 2pt, color = black!100 ] \wholeShape;
         }
      }
   }
}
{
   % Group for J2
   \draw[line width = 2pt, color = black!100,  ] (265pt, 163pt) -- (311pt, 182pt);
   {
      \pgftransformshift{\pgfpoint{ 311pt }{ 182pt } }
      \pgftransformcm { 0.9242614 }{ 0.3817602 }{ -0.3817601 }{ 0.9242614 }{\pgfpoint{ 0pt }{ 0pt } }
      {
         % LineEnding for S3
         {
            % Polygon for S3
            \pgftransformshift{\pgfpoint{ -8pt }{ -4pt } }
            \draw [line width = 2pt, color = black!100, fill = black!100 ]
            (0pt,0pt)--(8pt,4pt)--(0pt,8pt)--(2.64pt,4pt)--(0pt, 0pt) -- cycle;
         }
      }
   }
   \draw[line width = 2pt, color = black!100,  ] (288pt, 172.5pt) -- (288pt, 172.5pt);
   {
      \pgftransformshift{\pgfpoint{ 288pt }{ 172.5pt } }
      {
         % LineEnding for J2
         {
            % Rectangle for J2
            \pgftransformshift{\pgfpoint{ -4pt }{ -4pt } }
            \def \wholeShape {(0pt,0pt) rectangle(8pt,8pt)}
            \fill[fill = white!100] \wholeShape;
            \draw[line width = 2pt, color = black!100 ] \wholeShape;
         }
      }
   }
}
{
   % Group for J3
   \draw[line width = 2pt, color = black!100,  ] (349pt, 196.387096774194pt) -- (404pt, 217.612903225806pt);
   {
      \pgftransformshift{\pgfpoint{ 404pt }{ 217.6129pt } }
      \pgftransformcm { 0.9329361 }{ 0.3600421 }{ -0.3600421 }{ 0.932936 }{\pgfpoint{ 0pt }{ 0pt } }
      {
         % LineEnding for S4
         {
            % Polygon for S4
            \pgftransformshift{\pgfpoint{ -8pt }{ -4pt } }
            \draw [line width = 2pt, color = black!100, fill = black!100 ]
            (0pt,0pt)--(8pt,4pt)--(0pt,8pt)--(2.64pt,4pt)--(0pt, 0pt) -- cycle;
         }
      }
   }
   \draw[line width = 2pt, color = black!100,  ] (376.5pt, 207pt) -- (376.5pt, 207pt);
   {
      \pgftransformshift{\pgfpoint{ 376.5pt }{ 207pt } }
      {
         % LineEnding for J3
         {
            % Rectangle for J3
            \pgftransformshift{\pgfpoint{ -4pt }{ -4pt } }
            \def \wholeShape {(0pt,0pt) rectangle(8pt,8pt)}
            \fill[fill = white!100] \wholeShape;
            \draw[line width = 2pt, color = black!100 ] \wholeShape;
         }
      }
   }
}
{
   % Group for J4
   \draw[line width = 2pt, color = black!100,  ] (423.6pt, 243pt) -- (426.4pt, 285pt);
   {
      \pgftransformshift{\pgfpoint{ 426.4pt }{ 285pt } }
      \pgftransformcm { 0.06651872 }{ 0.9977852 }{ -0.9977853 }{ 0.06651773 }{\pgfpoint{ 0pt }{ 0pt } }
      {
         % LineEnding for X1
         {
            % Polygon for X1
            \pgftransformshift{\pgfpoint{ -8pt }{ -4pt } }
            \draw [line width = 2pt, color = black!100, fill = black!100 ]
            (0pt,0pt)--(8pt,4pt)--(0pt,8pt)--(2.64pt,4pt)--(0pt, 0pt) -- cycle;
         }
      }
   }
   \draw[line width = 2pt, color = black!100,  ] (425pt, 264pt) -- (425pt, 264pt);
   {
      \pgftransformshift{\pgfpoint{ 425pt }{ 264pt } }
      {
         % LineEnding for J4
         {
            % Rectangle for J4
            \pgftransformshift{\pgfpoint{ -4pt }{ -4pt } }
            \def \wholeShape {(0pt,0pt) rectangle(8pt,8pt)}
            \fill[fill = white!100] \wholeShape;
            \draw[line width = 2pt, color = black!100 ] \wholeShape;
         }
      }
   }
}
{
   % Ellipses for S1
   \pgftransformshift{\pgfpoint{ 138pt }{ 104pt } }
   \def \wholeShape {(12pt,12pt) ellipse(12pt and 12pt)}
   \fill[shading = EPNBackgroundGradient, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = black!100 ] \wholeShape;
}
{
   % Ellipses for S2
   \pgftransformshift{\pgfpoint{ 234pt }{ 143pt } }
   \def \wholeShape {(12pt,12pt) ellipse(12pt and 12pt)}
   \fill[shading = EPNBackgroundGradient, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = black!100 ] \wholeShape;
}
{
   % Ellipses for S3
   \pgftransformshift{\pgfpoint{ 318pt }{ 178pt } }
   \def \wholeShape {(12pt,12pt) ellipse(12pt and 12pt)}
   \fill[shading = EPNBackgroundGradient, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = black!100 ] \wholeShape;
}
{
   % Ellipses for S4
   \pgftransformshift{\pgfpoint{ 411pt }{ 212pt } }
   \def \wholeShape {(12pt,12pt) ellipse(12pt and 12pt)}
   \fill[shading = EPNBackgroundGradient, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = black!100 ] \wholeShape;
}
{
   % Ellipses for X0
   \pgftransformshift{\pgfpoint{ 33pt }{ 60pt } }
   \def \wholeShape {(12pt,12pt) ellipse(12pt and 12pt)}
   \fill[shading = EPNBackgroundGradient, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = black!100 ] \wholeShape;
}
{
   % Ellipses for X1
   \pgftransformshift{\pgfpoint{ 415pt }{ 292pt } }
   \def \wholeShape {(12pt,12pt) ellipse(12pt and 12pt)}
   \fill[shading = EPNBackgroundGradient, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = black!100 ] \wholeShape;
}
{
   % Group for sGlyph_0
   \draw (150pt, 116pt) node[text = black!100, font = \fontsize{ 10 } { 10 }\fontfamily\sfdefault\selectfont] { S1 };
}
{
   % Group for sGlyph_1
   \draw (246pt, 155pt) node[text = black!100, font = \fontsize{ 10 } { 10 }\fontfamily\sfdefault\selectfont] { S2 };
}
{
   % Group for sGlyph_2
   \draw (330pt, 190pt) node[text = black!100, font = \fontsize{ 10 } { 10 }\fontfamily\sfdefault\selectfont] { S3 };
}
{
   % Group for sGlyph_3
   \draw (423pt, 224pt) node[text = black!100, font = \fontsize{ 10 } { 10 }\fontfamily\sfdefault\selectfont] { S4 };
}
{
   % Group for sGlyph_4
   \draw (45pt, 72pt) node[text = black!100, font = \fontsize{ 10 } { 10 }\fontfamily\sfdefault\selectfont] { X0 };
}
{
   % Group for sGlyph_5
   \draw (427pt, 304pt) node[text = black!100, font = \fontsize{ 10 } { 10 }\fontfamily\sfdefault\selectfont] { X1 };
}
}
\end{tikzpicture}
\end{center}
\end{document}