Monday, June 16, 2008

GenePython - What’s the Big Idea?

GenePython is exactly what its name suggests! It is the use of Python (www.python.org), a popular and simple, open-source programming language to simulate gene expression in silico. Python has a way to depict real objects in what Pythonspeak is called ‘classes’. Classes can also be formed from other classes thereby inheriting their properties and behavior.

GenePython uses Python classes to depict molecular objects and define their behavior. This allows the flexibility of not just exploring the behavior of a mixture of different objects in-silico but also redefining the response of individual objects to different stimuli.

So in GenePython we have a class defining a sequence, for instance a genome comprising of either DNA or RNA. Similarly, sequences involved in the central dogma of molecular biology as well as the adjunct can all be represented using the class ‘Sequence’ or classes that inherit from class Sequence.

This architecture allows GenePython to facilitate the rapid construction of a virtual cell capable of simulating processes within and similar to the central dogma. This means that it can be used to rapidly create and explore in silico gene expression, understand bio-molecules that can be derived, classify them, create metabolic networks and systems and even design a-life.

In our next blog, we will look at how class ‘Sequence’ works. We’ll get you to use this class and explore the different behavioral patterns possible with the class. Those of you who are new to Python need not fear… we’ll run you through the code in Englishspeak and guide you through installing Python on your computer.

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