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 with Cytoscape, we will first set the stage by accessing the PSIQUIC service, a common query interface to several molecular interaction databases.

We will take the opportunity to indirectly introduce other topics, such as more bioinformatics databases, graph processing, and geo-referencing that are relevant in our context (one way or another). To interface, we will use only REST APIs to all databases and services, making the code in all recipes here quite streamlined. You may want to refresh your knowledge of REST architectures. We will...