BioCoder #7

Chapter 2. Bioinformatics for Aspiring Synthetic Biologists

Edgar Andrés Ochoa Cruz, Sayane Shome, Pablo Cárdenas, Maaruthy Yelleswarapu, Jitendra Kumar Gupta, Eugenio Maria Battaglia, Alioune Ngom, Pedro L. Fernandes, and Gerd Moe-Behrens

Abstract

For a synthetic biologist or biohacker to be able to hack, design, create, and engineer biological systems, the ability to work with biological data is essential. Basic bioinformatics skills will be required in order to read, interpret, write, and generate files containing DNA, RNA, protein, and other biological information. In this article, we will show the path you need to follow to implement a biological function using online data. As a case study, we are using Imperial College’s 2014 iGEM project, which focused on the optimization of bacterial cellulose production for use in water filtration.

Introduction

There are three requirements for the design of a biological system:

• The specification of the desired system in terms of its functions, inputs, and outputs
• The use of bioinformatics skills to select and combine DNA parts that follow these specifications
• The actual genetic modification of the organism in the wet lab

The design requires more than knowing how to pick bioparts from a catalog; it implies knowing how to create them and how to combine them to achieve the desired system.

Proper bioinformatics skills allow you to extract information within biological data and use it to model the desired system. Therefore, they’re of ...