Software

The complexity of biology calls for the aid of computers in a synthetic biology design process. Over the summer we have created a range of useful applications to make the life of the synthetic biologist easier. One of them, the Logbook Designer, is directly related to our project. Others have been designed for general usage in synthetic biology, iGEM and modeling.

Logbook Designer

The Logbook Designer is a webtool that allows for easy and quick Cellular Logbook plasmid design. Upon parts selection it gives all the related genbank files, a graphical overview of the plasmids and an algorithm that can compute which sensors have come to expression given the gel electrophoresis band sizes.

The Logbook Designer can be found here
Information about the Logbook Designer setup can be found here
A manual about the Logbook Designer can be found here
The future perspective for the Logbook Designer can be found here

MDL2LaTeX

MDL2LaTeX (MDL-to-LaTeX) converts MDL stochastic model description files used by the stochastic simulation package [1] to LaTeX representations, so they become more human-readable and can be easily integrated into reports.