How Do I Use SBML2TikZ?
The easiest way to use SBML2TikZ is via its Graphical User Interface (GUI). This page details how to use SBML2TikZ through this user interface. Alternatively, SBML2TikZ can be accessed via its console application SBML2TikZ_Console through a command line shell. More details on the console application can be found by running:
SBML2TikZ_Console help
The rest of this tutorial will deal solely with the GUI frontend.
For Windows
In Windows, simply run the executable file SBML2TikZ.exe from the command line shell or double click the executable.
For Linux/OSX
For Linux or OSX, you can run SBML2TikZ by going to its directory and typing:
mono SBML2TikZ.exe
in the command line shell of your operating system.
Mono is an open source implementation of the .NET framework which SBML2TikZ relies on for Linux or OSX. You can download mono for the Mac OSX and Linux here.
Regardless of your operating system, running SBML2TikZ.exe should open the following window:
Load SBML
To begin, you can load an SBML file into SBML2TikZ. Clicking on the Load SBML Button will open a file dialogue box from which you can select an SBML file to render in LaTeX:
Select the SBML file you would like to render and press Open. The name of the SBML file should now appear next to the Load SBML button. For instance, if I were to select an SBML file "equilib.xml" in the image above and click Open, this is what I should see at the top of the SBML2TikZ application:
Heights, Widths and Layout
Once you've loaded an SBML file, SBML2TikZ checks the dimensions of the graph stored in SBML, and displays it in the Recommended Height and Recommended Width boxes. The default units for the display are pts, but you can elect to have SBML2TikZ display the dimensions in cm or inches as well.
Desired Height and Desired Width are the dimensions of the graph the user wants SBML2TikZ to generate. The default values for these dimensions are the Recommended dimensions, although you can change the Desired values to match the space constraints of your paper.
Selected Layout allows you to choose between multiple graphs stored in an SBML file if there is more than one graph available in the file.
Convert to *.TeX
Once you are satisfied with the dimensions and the selected layout, you can click Convert to *.TeX. This opens a dialogue box asking you where you would like to write the TeX output. Once you have selected a valid directory, SBML2TikZ generates its TeX output and writes it to the selected output directory.
Additional Options
Use SBGN causes SBML2TikZ to override the rendering information in an SBML file with Systems Biology Graphical Notation. The algorithm used to do this is from the SBMLExtension library written by Frank Bergman.
Show Output Dir causes SBML2TikZ to inform the user of the location of the TeX file after it has generated it.
Compile with pdflatex causes SBML2TikZ to automatically compile its TeX output using pdfLaTeX to generate a PDF file. This is largely for the user's convenience, and only works if the user has pdfLaTeX installed on their system. If this option is not selected, users can always manually compile the TeX document later.
Show PDF causes SBML2TikZ to open a PDF of its output if the Compile with pdflatex option was checked.