Bioinformatics with Python Cookbook

Chapter 8. Other Topics in Bioinformatics

In this chapter, we will cover the following recipes:

• Accessing the Global Biodiversity Information Facility via REST
• Georeferencing GBIF datasets
• Accessing molecular interaction databases with PSIQUIC
• Plotting protein interactions with Cytoscape the hard way

Introduction

In this chapter, we will address some topics that are well within the remit of computational biology and deserve at least some reference. We will start with two recipes using the Global Biodiversity Information Facility (GBIF), a database of worldwide scientific data on biodiversity. After this, we will interface Python with Cytoscape, a powerful software platform to visualize genomic and proteomic interaction networks. To perform visualization ...