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Friday, July 30, 2010

JarnacLite – Helping with Kinetics!

The new version of JarnacLite, that is distributed with SBW 2.8.1 finally helps out in the arduous task of entering the kinetics. By using a customizable list of kinetic rate laws, it is now rather easy to construct models in this simple script format.

There are two steps to using this assistance:

  1. Enter the reaction scheme: In order to be able to filter the available rate laws, a reaction scheme needs to be present. Special note should be given to the reversible notation:

    S1 –> S2

    would mean that a species S1 is converted to S2, while

    S1 => S2

    would mean that this reaction is reversible. Different kinetics will be suggested.
  2. Once the reaction scheme is entered, pressing CTRL+SPACE or clicking the ‘Edit kinetic’ button will bring up the rate law selection dialog.
  3. All that is left to do after selecting a rate law is to adjust the parameters.

And here an example of how this looks in practice:

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