4th de.NBI Cloud User Meeting

Scientific Program

Disclaimer

All times are given in Central European Time (CET)!

All Workshops will start at the given times s.t.!

Friday, 12th November

• 9:00am - 9:45am - Presentation: Introduction to the de.NBI Cloud

  The presentation will cover an introduction to the de.NBI Cloud, its features and projects.

  Speaker: Nils Hoffman - Cloud and Interoperability coordinator, ELIXIR-DE, de.NBI

• 10:00am - 12:00pm - Workshop: SimpleVM and Linux Command Line Introduction

  SimpleVM streamlines the launch of Virtual Machines (VMs). It takes care of the network setup, SSH access and other tasks like e.g. volume mounts and provides the user with quick access to the machine. Once you have configured your VM to your liking it can be shared simply by creating a snapshot and providing this snapshot to other users. The workshop is targeted at absolute beginners in command line usage. We will use common shell commands to navigate the system, do file operations and run programs.

  https://cloud.denbi.de/simpleVM/
  https://cloud.denbi.de/project-types/

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

Monday, 15th November

• 10:00am-3:00pm - Workshop: 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: Organizer: Martin Lang (DKFZ), Martin Braun (Charité / BIH)
  Estimated length: 5 hours
  Requirements: basic terminal knowledge, ssh/ssh-keygen locally installed, Linux/OSX Terminal, Windows 10 PowerShell, Browser

Tuesday, 16th November

• 1:00pm-4:00pm - Workshop: 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
  Estimated length: ~3 hours
  Requirements: Linux terminal

Wednesday, 17th November

• 9:00am-9:45am - Presentation: Virtual Research Environment

  The Virtual Research Environment (VRE) is an open-source data management platform that enables medical researchers to store, process and share data in compliance with data protection requirements such as the European Union (EU) General Data Protection Regulations (GDPR). The VRE addresses the present lack of digital research data infrastructures fulfilling the need for a) data protection for sensitive data, b) capability to process complex data such as radiologic imaging, c) flexibility for using own processing workflows, d) access to high performance computing. The platform promotes FAIR data principles and reducing barriers to biomedical research and innovation. Features include a web portal, a segregated Green Room zone to capture and pre-process sensitive data, analytics workbench tools for processing, analyzing, and visualizing datasets, automated ingestion of data from hospital-based data capture sources, a project-specific Data Warehouse for ingestion and query of structured datasets, a metadata repository and graph database for capture and query of metadata and lineage tracking, and support for ontologies and automated extraction and indexing of standard metadata fields to make data findable. The VRE is conceptualized as a portable and extendable framework that comes with a Software Development Kit (SDK), open API endpoints, open developers’ meetings, hackathons, and comprehensive documentation for users, developers, and administrators. Our solution of concerted technical and organizational measures can be adopted by other research communities and thus facilitates the development of a co-evolving interoperable platform ecosystem with an active research software community.
  Speaker: Petra Ritter (Charité Universitätsmedizin Berlin)

• 10:00am-1:00pm - Workshop: Deploying a compute cluster in OpenStack via Terraform

  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: Gianmauro Cuccuru
  Estimated length: ~3 hours
  Requirements: Linux terminal

Thursday, 18th November

• 9:00am-9:45am - Presentation: ESPACE-cloud - a data sharing and analysis platform for an international research project in the de.NBI cloud

  The ESPACE (Expression and Spatial analysis Pancreas Atlas Consortium Europe) consortium builds a first version of the Human Cell Atlas (HCA) of the pancreas by combining methods and standards for sample procurement single cell profiling, spatial proteomics, and computational pipelines. Having many separated project partners involved, the consortium requires a cloud solution for gathering, sharing, integration of data as well as sharing of code and analysis pipelines. In this talk we present the ESPACE cloud and how it is used in the ESPACE consortium for sharing, integration and analysis of research data.
  Speaker: Sven Twardziok (Charité)

• 10:00am-5:00pm - Workshop: Kubernetes Introduction I

  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.

  This workshop is a consecutive course. You will need to hear Kubernetes Introduction I to attend Kubernetes Introduction II.

  Organizer: Marius Dieckmann (JLU Gießen), Sebastian Beyvers (JLU Gießen)
  Estimated length: 2 days, 7 hours per day
  Requirements: Basic coding (Java, Python, …), Container (Docker), Basic software engineering experience

Monday, 22nd November

• 10:00am -5:00pm - Workshop: Kubernetes Introduction II

  his 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.

  This workshop is a consecutive course. You will need to hear Kubernetes I to attend Kubernetes II.

  Organizer: Marius Dieckmann (JLU Gießen), Sebastian Beyvers (JLU Gießen)
  Estimated length: 2 days, 7 hours per day
  Requirements: Basic coding (Java, Python, …), Container (Docker), Basic software engineering experience

• 9:00am-9:45am - Presentation: GHGA at the de.NBI Cloud

  A growing body of research connects genomics data to improvement of clinical diagnosis. However, the decreasing cost of technologies that ease access to sequencing on both research and clinical studies pose a challenge for storing, searching, and accessing these datasets. The German Human Genome-Phenome Archive (www.ghga.de/) is setting up a federated data network in Germany to provide harmonized services to enable data sharing in collaboration with international partners like the European Genome Archive. de.NBI Cloud sites at the two largest German nodes - Heidelberg and Tübingen - will speed up the start-up phase by providing the required efficient and secure infrastructure.
  Speakers: Kersten Breuer (DKFZ) , Koray Kirli (DKFZ)

Tuesday, 23rd November

• 9:00am-9:45am - Presentation: HuMAGs - Recovery of metagenome-assembled genomes from over 10 thousand human Microbiomes

  This presentation will discuss how you can use the de.NBI cloud infrastructure to analyze thousands of human metagenomes. Data on the prevalence of antimicrobial resistance genes in different diet preferences will be presented as an example.
  Speaker: Ulisses Nunes da Rocha (Helmholtz Centre for Environmental Research - UFZ)

• 10:00am-3pm - Workshop: BiBiGrid Cluster Setup

  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:
  Estimated length: ~3 hours
  Requirements: basic terminal knowledge, JRE/JDK 11 and ssh/ssh-keygen locally installed, Linux/OSX Terminal, Windows 10 PowerShell, Browser
  Speaker: Tim Dilger (CeBitec, NBI-BiGi assistance (BiBiGrid))

Wednesday, 24th November

• 9:00am-9:45am - Presentation: The SARS-CoV-2 Genomics Data Portal - CoGDat

  In the beginning of 2021, Germany added viral genome surveillance to their established measures to better monitor the ongoing SARS-CoV-2 pandemic. CoGDat aims to improve the availability of this data, in particular of the sequencing raw data, for research purposes. The CoGDat team has developed both a technical and a data privacy and legal framework to collect and process the sequencing data provided by participating sequencing laboratories.
  Speaker: Léon Kuchenbecker (Universität Tübingen)

• 10:00am-12:00pm: Closing Session and Final Remarks