Registration Deadline: 30.09.2020
What is it about?
We are pleased to announce the third de.NBI Cloud User Meeting. In comparison to preceding meetings, this year`s meeting will be organized as an online conference. Over five days users can watch talks of already experienced users and long running projects and thereby learn about best practices in cloud computing. Same as the last years we will try to cover topics for begin
ners such as virtualization but also topics for software engineers and administrators such as orchestration with Kubernetes. Participants will learn how to scale up their analysis to handle growing input data and how to use workflow managers such as Snakemake in a cloud environment. As every year we are also going to demonstrate the usage of bioinformatics software in the de.NBI Cloud using Docker images or Bioconda packages.
Dates
User Meeting date: 8.10.2020 – 14.10.2020
Registration deadline: 30.09.2020
Confirmed speakers:
Peter Belmann – Bielefeld University, de.NBI Administration Office
Daniel Hübschmann – German Cancer Research Center
Cov-seq: An amplicon sequencing protocol for Sars-CoV-2
Peter Ebert – Heinrich Heine University Düsseldorf, Institute for Medical Biometry and Bioinformatics
Leveraging the deNBI Cloud for large-scale human genome assembly
Martin Zurowietz – Bielefeld University, Biodata Mining
BIIGLE – Large-scale image annotation in the de.NBI Cloud
Kay Schallert – Otto von Guericke University Magdeburg, Institute for Process Engineering
MetaProteomeCloud – Microbial community proteomics using cloud
technologies
Confirmed Workshops:
UNIX/Shell workshop
Each participant gets access to a prepared virtual machine running the Web IDE Theia. Theia-IDE provides a (simplified) file manager, an editor and a terminal. The workshops is targeted at absolute beginners. We will use common shell commands to navigate the system, do file operations and run programs.
Organizer: Jan Krüger (Bielefeld University)
Requirements: web browser
Running Snakemake Workflows in the de.NBI Cloud
Sharing data and execution of workflows via cloud resources will be essential for the work with the increasing amount of data in the field of genomics. This training will introduce the cloud standards from the Global Alliance for Genomics and Health (GA4GH) and give solutions on how to run workflows in the cloud and how to integrate cloud storage systems. Thereby, we will focus on workflow development with the workflow system Snakemake.
Organizer: Sven Olaf Twardziok (sven.twardziok@charite.de) (BIH Berlin)
Estimated length: ~5 hours
Requirements: Python basics, Linux terminal, Conda, OpenStack
OpenStack Introduction
OpenStack is the underlying infrastructure of the de.NBI Cloud. Any service that is provided is set up on top of OpenStack. Participants of this workshop will learn how to start one or multiple virtual machines by using a graphical interface or via an API.
Organizer: Jan Krüger (Bielefeld University)
Estimated length: 4 hours
Requirements: basic terminal knowledge, ssh/ssh-keygen locally installed, Linux/OSX Terminal, Windows 10 PowerShell, Browser
Extensible Cluster Setup in the Cloud with BibiGrid and Ansible
BiBiGrid is an open source tool hosted at Github for an easy cluster setup inside a cloud environment. It provides a HPC like environment, providing a shared filesystem between all nodes, a Grid Batch Scheduler and a monitoring system on top of Ubuntu LTS or Debian. In this hands-on session we will learn how to setup a cluster in the cloud using BiBiGrid and how to adjust it to make it fit our needs using Ansible.
Organizer: Jan Krüger (Bielefeld University)
Estimated length: ~3 hours
Requirements: basic terminal knowledge, JRE/JDK 11 and ssh/ssh-keygen locally installed, Linux/OSX Terminal, Windows 10 PowerShell, Browser
Using Terraform to define infrastructure as code
The goal of this workshop is to give a first overview about how Terraform works and corresponding use cases. Topics that will be covered by Terraform in this workshop are for example, start and stop VMs, configure VMs, set up more complex environments like a virtual HPC cluster The workshop is directed to users that already have some cloud experiences and some programming abilities.
Organizer: Maximillian Hanussek (University of Tübingen), Fabian Paz (University of Tübingen)
Estimated length: ~4 hours
Requirements: Linux terminal
BioConda and BioContainers
Bioinformatic tools running in Container or as part of a Conda environment are provided by Bioinformatic communities such as Bioconda and BioContainers. They are essential for reproducible science and will enable you running tools and workflows in the Cloud. Topics of this workshop are virtualization, packaging and the handling of BioContainers and Bioconda packages.
Organizer: Björn Grüning (University of Freiburg)
Estimated length: ~2 hours
Requirements: Linux terminal
Kubernetes Introduction –
This workshop will introduce Kubernetes as a container orchestration solution. It will focus on concepts and the basic functionality of Kubernetes in order provide a solid background for further exploration of Kubernetes. It will also introduce some best-practices for software development with containers and Kubernetes. A good understand of container technologies like Docker is a prerequisit.
Organizer: Marius Dieckmann (Giessen University)
Estimated length: 2 days
Requirements: Basic coding (Java, Python, …), Container (Docker), Basic software engineering experience
Deploying Web Services in the de.NBI Cloud
Web services can improve collaboration of spatially distinct researchers; e.g. by providing a shared workspace for data analysis or as an application user interface to access data and tools. In our online lecture we will cover the whole process from applying a project in the de.NBI cloud to the deployment of a web service in the de.NBI cloud infrastructure. Thereby, we will focus on scalable deployment via docker swarm. As an example we will create and deploy a small R-Shiny application.
Organizer: Martin Braun (martin.braun@charite.de) (BIH Berlin)
Estimated length: ~4 hours
Requirements: Linux terminal
Agenda
Wednesday (07.10.2020) (User Meeting pre-course)
10:00 – 11:30 Introduction to basic UNIX commands
Thursday (08.10.2020)
09:00 – 09:30 Talk: de.NBI Cloud Introduction – Peter Belmann
09:45 – 12:00 Workshop: BioConda and BioContainers
12:30 – 16:00 Workshop: OpenStack Introduction
Friday (09.10.2020)
09:00 – 09:30 Talk: Martin Zurowietz – BIIGLE – Large-scale image annotation in the de.NBI Cloud
09:45 – 14:00 Workshop: Extensible Cluster Setup in the Cloud with BibiGrid and Ansible
Monday (12.10.2020)
09:00 – 09:30 Talk: Peter Ebert – Leveraging the deNBI Cloud for large-scale human genome assembly
09:45 – 15:00 Workshop: Using Terraform to define infrastructure as code
Tuesday (13.10.2020)
09:00 – 9:30 Talk: Kay Schallert – MetaProteomeCloud – Microbial community proteomics using cloud technologies
09:45 – 15:00 Workhops: Running Snakemake Workflows in the de.NBI Cloud
09:45 – 16:00 Workshop: Kubernetes Introduction (Part 1)
Wednesday (14.10.2020)
09:00 – 09:30 Talk: Daniel Hübschmann – Cov-seq: An amplicon sequencing protocol for Sars-CoV-2
09:45 – 15:00 Workshop: Deploying Web Services in the de.NBI Cloud
09:45 – 16:00 Workshop: Kubernetes Introduction (Part 2)
Questions?
Please contact clum@denbi.de if you have any questions.
Registration
You can register for the meeting and the individual workshops which are explained on this site via the following link:
Please note that there are no free places left for all workshops!
If you still register for a workshop you will be placed on a waiting list.
However you can still register for the presentations.
Registration is closed!
Please contact clum@denbi.de if you want to participate!
Registration Deadline: 30.09.2020