The GINML format

The GINML format is used by GINsim. It extends the GXL (Graph eXchange Language) format to integrate an encoding of the logical functions as logical parameters in the node elements. GINML supports documentation, as well as layout information and styles. Note that in GINsim, the GINML file is usually part of a ZGINML archive, which can contain separate files for associated information, such as perturbations or simulation parameters.

BioLQM supports only export of the GINML format, but GINsim now uses bioLQM internally, and can export its models to SBML-qual or other bioLQM-supported format directly.

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE gxl SYSTEM "http://ginsim.org/GINML_2_2.dtd">
<gxl xmlns:xlink="http://www.w3.org/1999/xlink">
  <graph class="regulatory" id="toy_3" nodeorder="G0 G1 G2">

    <nodestyle background="#ffffff" foreground="#000000" text="#000000" shape="RECTANGLE" width="45" height="25"/>
    <edgestyle color="#000000" pattern="SIMPLE" line_width="1" properties="positive:#00c800 negative:#c80000 dual:#0000c8"/>

    <node id="G0" maxvalue="1" input="true">
      <nodevisualsetting x="297" y="138" style=""/>
    </node>
    <node id="G1" maxvalue="1">
      <parameter idActiveInteractions=" G0:G1" val="1"/>
      <nodevisualsetting x="250" y="270" style=""/>
    </node>
    <node id="G2" maxvalue="1">
      <parameter idActiveInteractions=" G1:G2" val="1"/>
      <nodevisualsetting x="439" y="271" style=""/>
    </node>

    <edge id="G1:G2" from="G1" to="G2" minvalue="1" sign="positive" />
    <edge id="G0:G1" from="G0" to="G1" minvalue="1" sign="positive" />
    <edge id="G0:G2" from="G0" to="G2" minvalue="1" sign="negative" />

    <annotation>
      <linklist>
        <link xlink:href="www.ginsim.org"/>
      </linklist>
      <comment>Documentation can be added to the model itself, nodes, or edges</comment>
    </annotation>
  </graph>
</gxl>