Thursday, September 23, 2010


TinkerCell now uses "Themes" to categorize graphics object. Each Theme is defined by a set of Nodes, Arrows, and Decorators. Each theme rests in a folder. There are three themes as of today:

Fancy1, Bio1, Blocks1

These themes are located inside the Graphics folder. In TinkerCell Options->"Select Theme" is used to switch between themes. TinkerCell searches the home folder (i.e. Documents/TinkerCell) first, which means that users can make new Themes and place them in the home folder.

Here is how to make a new Theme:

1. Create a folder in the Documents/TinkerCell folder called "Graphics"

2. Inside Graphics, create a folder with any name. The folder name is the name of your theme

3. Make three folders inside your theme folder: Nodes, Arrows, Decorators (case sensitive, I think)

4. Use the NodeGraphics program to make nodes, arrows, and decorators xml and PNG files, and put those files in the appropriate folders. Note that the NodeGraphics program creates an xml file (the vector graphics) and a PNG file (used to draw buttons).

5. Make sure that the names are correct. Eg. the .xml and .PNG file for drawing "Protein" types should be names Protein.xml, and the arrow for EnzymeCatalysis reactions should be names EnzymeCatalysis.xml. The Decorators should also use process family names, e.g. EnzymeCatalysis. You may want to look at the existing TinkerCell/Graphics folder.

6. Once you are done with your Theme, create a drawing in TinkerCell using your theme. Take a screenshot and save the "screenshot.png" file in your Theme folder. The Options->"Select Theme" dialog will display this file.

Tuesday, September 21, 2010

Thursday, September 16, 2010

Wednesday, September 8, 2010

New C/Python/Octave functions


Name change in the C/Python/Octave API

Classes for embedding Python and Octave are now included inside the TinkerCellCore library.

Names of the base classes have changed to avoid confusion with the existing Octave classes. All data structures now have a tc_ prefix to avoid collisions. Here is the detailed documentation:

All the function names available in the link above can be called from C, Python, or Octave.