Computer-Aided Design in Synthetic Biology. TinkerCell is a Computer-Aided Design (CAD) tool for synthetic biology. Since synthetic biology is a rapidly evolving field, here are the issues which were taken into consideration when designing TinkerCell:
1. modeling techniques in biology are not robust
2. experimental techniques are constantly evolving, especially automation and directed evolution methods
3. databases of biological components are still maturing

In summary, TinkerCell is designed with the anticipation that the future of synthetic biology will be an intricate interplay between a variety of experimental techniques, databases that store results from experiments, and mathematical models explaining different aspects of the experiments.

The ideal situation of the CAD program is this:
step 1: user draws a biological system
step 2: user performs some analysis
step 3: go back to step 1 if analysis is not satisfactory

The analysis step can potentially include:
1. mathematical analysis of non-linear systems
2. stochastic simulations and other methods from systems biology
3. prediction of evolutionary trajectories for directed evolution
4. analysis and optimization of the sequence
5. database look-up to find suitable components
6. generate different mathematical representations for the same diagram
7. ...more...

It is too much to have all of these functions in TinkerCell from the start. So TinkerCell uses a flexible plug-in framework, which will allow others to contribute new functions to TinkerCell. The plug-ins can be written in C, C++, Python, or Octave. Other languages, e.g. Java, might also get added to this list.

TinkerCell Features:
1. Customizable hierarchy of biological parts
2. Attributes (e.g. sequence) for characterizing parts
3. Drawing program for designing part graphics
4. Multi-threaded simulations for speed
5. Automatic generation of complex reactions with intermediate steps

The license of this software is Free, you can free download and free use this flowchart & diagram software.