5th de.NBI Cloud User Meeting

Dec 6, 2022, 8:00 AM → Dec 7, 2022, 8:30 PM Europe/Berlin

Forschungszentrum Jülich, Central Library

Welcome to the 5th de.NBI Cloud User Meeting.

Registration is currently closed!

 

For almost 5 years the de.NBI Cloud has provided free of charge computing resources to the life sciences community in Germany. Scientists involved in various research topics, such as metagenomics, medical imaging, epigenetics, and plant biology benefit from the opportunities provided by the de.NBI Cloud.

With our annual user meeting we would like to highlight topics of interest for our growing community.

We provide the opportunity for our current users to learn more about best practices in cloud computing and present newcomers and possible future users the capabilities provided by the de.NBI Cloud that could help accelerate their research in future projects. Talks and workshops will be given covering topics in cloud computing, such as container orchestration using Kubernetes, the application of infrastructure as code technologies but also bioinformatics related workshops such as an introduction to Bioconda and BioContainers.

The de.NBI Cloud User Meeting supports the interaction with our growing community. Thus, we would like to hear from you the needs of the scientific life sciences community allowing us to shape the future of the de.NBI Cloud according to specific use cases.

This year, we are organizing the de.NBI Cloud user meeting as an on-site, in person event at the Forschungszentrum Jülich from December 6th - 7th. 

The scope of this meeting includes:

• Talks of experienced users in different research areas
• Workshops for new and already experienced users
• Chance to talk to experts on various cloud computing topics

We are looking forward to welcoming interested researchers from many different bioinformatics and life-science research areas to learn more about cloud computing and the de.NBI Cloud.

Please see the registration for more details. 
Registration has closed on November 27th 2022.

Further Information

Feel free to visit our homepages for further information on de.NBI and the de.NBI Cloud:

www.denbi.de                             cloud.denbi.de

 

All times are given in the timetable and the scientific program representing Central European Time (CET)!

Datenschutzerklärung.Kompakt.Digitale.Veranstaltung.ENG_aktualisiert.pdf

Tuesday, December 6

8:00 AM → 8:25 AM Bus Transfer to FZJ Campus

Bus transfer from Dorint Hotel Düren to FZJ Campus

8:30 AM → 9:00 AM Arrival & Registration

9:00 AM → 10:00 AM Opening Session: Welcome and Introduction

9:00 AM Welcome & Introduction

10:00 AM → 10:30 AM Cloud Use Case Presentations

10:00 AM Cloud Use Case Presentation I

Speaker: Alexander Sczyrba (Bielefeld University)

10:30 AM → 6:00 PM Track A

10:30 AM Simple access to de.NBI Cloud resources for life science researchers via SimpleVM

In this hands-on workshop, we introduce participants to SimpleVM, a de.NBI Cloud project type that offers easy, point and-click-style configuration of virtual machines and data volumes. SimpleVM offers preconfigured environments for RStudio, Jupyter Notebooks, virtual Desktop environments and more.
The workshop will first give a basic introduction to the Linux command line and then demonstrate a typical workflow of a SimpleVM user on a metagenomics use case.

Requirements: Linux terminal;

Speakers: David Weinholz (de.NBI), Nils Hoffmann (Cloud and Interoperability Platform Coordinator - ELIXIR-DE, de.NBI - Deutsches Netzwerk für Bioinformatik-Infrastruktur), Peter Belmann (CAU)

3:00 PM Common Workflow Language - CWL

Speaker: Mr Michael Crusoe (CIBI)

Introductory lecture

Setup instructions

10:30 AM → 6:00 PM Track B

10:30 AM Kubernetes I

Requirements: Basic coding (Java, Python, …), Container (Docker), Basic software engineering experience

Part 1 of 2

Speakers: Marius Dieckmann (JLU Gießen), Sebastian Beyvers

10:30 AM → 6:00 PM Track C

10:30 AM Ask an Admin I

3:00 PM OpenStack

OpenStack is the underlying infrastructure of the de.NBI Cloud.
Participants of this workshop will learn how to start one or multiple
virtual machines by using a graphical interface or via an API and get
familiar with basic principles how-to use OpenStack for their projects
e.g. assign floating ips, mount volumes, setup security groups, etc.

Requirements: basic terminal knowledge, Linux/OSX Terminal or Windows
10 PowerShell, Browser

Speakers: Martin Braun, Martin Lang (DKFZ Heidelberg)

12:30 PM → 1:30 PM Lunch

2:30 PM → 3:00 PM Coffee Break

6:15 PM → 6:40 PM Bus Transfer to Düren

Bus transfer from FZJ Campus to Dorint Hotel Düren

7:00 PM → 10:00 PM Dinner

The workshop dinner will take place at Dorint Hotel Düren:
https://hotel-dueren.dorint.com/de/
Participation at the dinner is free of charge for participants but requires registration.
Please indicate special dietary requirements in the event registration form.

Wednesday, December 7

8:15 AM → 8:40 AM Bus Transfer to FZJ Campus

Bus transfer from Dorint Hotel Düren to FZJ

9:00 AM → 9:30 AM Cloud Use Case Presentations

9:00 AM Cloud Use Case Presentation II

Speaker: Leyla Jael Castro (ZB MED Information Centre for Life Sciences)

9:30 AM → 5:30 PM Track A

9:30 AM Ansible & Bibigrid

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.

Estimated length: ~3 hours
Requirements: basic terminal knowledge, Python3 and ssh/ssh-keygen locally installed, Linux/OSX Terminal or Linux for Windows (WSL2) , Browser
Trainers: Xaver Stiensmeier (Universität Bielefeld, CeBitec), Christian Henke, Alex Walender and Jan Krüger (Forschungszentrum Jülich, IBG-5)

Speakers: Alex Walender, Jan Krüger (Forschungszentrum Jülich, IBG-5), Xaver Stiensmeier (Universität Bielefeld)

2:30 PM Bioconda & Biocontainers

Bioinformatic tools running in Containers 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 and workflow management systems. Topics of this workshop are virtualization, packaging and the handling of BioContainers and Bioconda packages.

If you ever wanted to learn how Bioconda works, how to create a BioContainer, this workshop is for you!

Requirements: Linux terminal;

Speaker: Björn Grüning (Uni-Freiburg)

9:30 AM → 5:30 PM Track B

9:30 AM Kubernetes II

Requirements: Basic coding (Java, Python, …), Container (Docker), Basic software engineering experience

Part 2 of 2

Speakers: Marius Dieckmann (JLU Gießen), Sebastian Beyvers

9:30 AM → 5:30 PM Track C

9:30 AM Ask an Admin II

12:00 PM → 1:00 PM Lunch

2:00 PM → 2:30 PM Coffee Break

5:30 PM → 6:00 PM Closing Session

6:15 PM → 6:40 PM Bus Transfer to Düren

Bus Transfer from FZJ Campus to Düren Main Station