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 a recipe on metagenomics using QIIME 2. Then, we will infer shared chromosomal segments across individuals using Germline. After that, we will have a look at some recipes using the Global Biodiversity Information Facility (GBIF), a database of worldwide scientific data on biodiversity. Then, we will interface Python with Cytoscape, a powerful software platform that's used for visualizing genomic and proteomic interaction networks.

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