TinkerCell 1.2.693

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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:

modeling techniques in biology are still at a developmental stage

experimental techniques are constantly evolving, especially automation and directed evolution methods

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 use-case of the ideal CAD program would be like 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:

mathematical analysis of non-linear systems

stochastic simulations, structural analysis, and other methods from systems biology

prediction of evolutionary trajectories for directed evolution

analysis and optimization of the DNA sequence

database look-up to find suitable components

generate different versions of the same design

load experimental data from database(s) and relate them to the diagram

...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.   The basic idea behind TinkerCell is to represent a diagram that is detailed enough so that it can be mapped to models or experimental results. A human researcher is able to connect models and experiments because they are able to link them using a conceptual understanding of the system. TinkerCell enables that capability in software.