SimpleVM Workshop

This workshop demonstrates a typical workflow of a SimpleVM user. In this workshop your goal will be to identify pathogenic bacteria that were classified as "greatest threat to human health" by the World Health Organisation (WHO) in 2017: https://www.who.int/news/item/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-urgently-needed

You will search for those microbes in publicly available metagenomic datasets that are stored in the Sequence Read Archive (SRA). In metagenomics, microbial genetic material is extracted from environmental samples like human gut, soil, freshwater or biogas plants in order to investigate the functions and interactions of the microbial community.

In order to find those microbes, you will have to interact with the de.NBI Cloud via SimpleVM. This workshop is divided into three parts.

Section 1: Big things start small

In the first part you will learn the basic concept of virtual machines and how to configure them.

Go to the first section

Section 2: Verify your VM properties and tools

In the second section you will test whether SimpleVM correctly provisioned your VM with all your tools installed on it.

Go to the second section

Section 3: Scale up your analysis

In the third section you will learn about object storage and the Sequence Read Archive. Further, you will run your analysis pipeline.

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Section 4: Inspect your generated data via a research environment

In the fourth section you will start a virtual machine with a RStudio research environment installed.

Go to the fourth section

Section 5: Use a cluster setup to further scale up your analysis

In this part you will use a SimpleVM Cluster to distribute your analysis on multiple machines instead of just one.

Go to the fifth section (Part 1)

Go to the fifth section (Part 2)