Introduction to artificial intelligence and deep learning using interactive electronic programming notebooks.

Artificial intelligence (AI), or deep learning (DL), approaches have already found their way into our everyday lives. Furthermore, these methods are a central part of research in the life and natural sciences and have been applied in the form of machine learning for decades. In pharmaceutical and medicinal chemistry, and in computer-aided drug discovery, current developments are also changing the way drugs are developed. It is essential to familiarize students with AI methods already during their studies and prepare them for future tasks and challenges. We developed a set of interactive learning materials based on cheminformatics examples that can be used to establish such introductory AI courses in the life and natural sciences. These interactive notebooks are easily accessible without the need for installation, and no prior programming knowledge is required. Through these notebooks, students can easily study how AI/DL works and how these methods can be applied. This knowledge will foster a general competence when interacting with and evaluating future DL applications later in their career. The materials are freely available and publicly accessible through a GitHub repository in German and English.

Mango: Exploratory Data Analysis for Large-Scale Sequencing Datasets.

The decreasing cost of DNA sequencing over the past decade has led to an explosion of sequencing datasets, leaving us with petabytes of data to analyze. However, current sequencing visualization tools are designed to run on single machines, which limits their scalability and interactivity on modern genomic datasets. Here, we leverage the scalability of Apache Spark to provide Mango, consisting of a Jupyter notebook and genome browser, which removes scalability and interactivity constraints by leveraging multi-node compute clusters to allow interactive analysis over terabytes of sequencing data. We demonstrate scalability of the Mango tools by performing quality control analyses on 10 terabytes of 100 high-coverage sequencing samples from the Simons Genome Diversity Project, enabling capability for interactive genomic exploration of multi-sample datasets that surpass the computational limitations of single-node visualization tools. Mango is freely available for download with full documentation at https://bdg-mango.readthedocs.io/en/latest/.