de.NBI Cloud Storage Tübingen. A federated and georedundant solution for large scientific data

The »German Network for Bioinformatics Infrastructure«, or in short »de.NBI«, is a national research infrastructure providing bioinformatics services to users in life sciences research, biomedicine and related fields. At five sites across Germany, cloud sites were established to host the bioinformatics services. In Tübingen an extension of the storage capabilites of the cloud was planned, implemented and brought into production. We here report about the motivation, requirements, design decisions and experiences which might serve as inspiration for other large scale storage endeavours in the academic domain

CiTAR – Citing and Archiving Research

While the institutional introduction of infrastructure for the collection and conservation of primary scientific data is currently under construction or already exists, a parallel problem awareness arises for the associated models and methods, in particular for data evaluation. However, there is hardly any usable infrastructure and service offerings yet. Although the DFG recommendations on "good scientific practice" currently only recommend the retention of primary scientific data, the remainder of the recommendation refers to mandatory records of "materials and methods" that are not only necessary for comprehensible results but also for the publication process. If scientific results are to be reproducible, for example for an independent verification, a reconstruction of the experimental setup is necessary. However, in the digital age, with its extremely short life span (and availability) of hardware and software components, replicating a data processing process that is identical in all components can not be achieved solely on the basis of records. CiTAR (Citing and Archiving Research), a three-year Baden-Württemberg state project, develops infrastructure to support computer assisted research. One major outcome of this project are means to publish, cite and provide long-term access to virtual research environments. The aim of this project is to develop a cooperative, multidisciplinary technical-organizational service in order to support teaching and research in the further development of "good scientific practice". The service should provide data and scientific methods jointly citable and reproducibly in order to meet the requirements of modern journals. CiTAR realizes re-use of research data and long-term availability in terms of a modern research data management. To achieve the project objectives, three of the four bwFor HPC operators have joined forces to prototype a broader scope in the natural sciences, especially the computational and data-intensive scientific disciplines. The developed service provides automated import of virtual machines and popular container formats like Docker and Singularity. CiTAR assigns persistent identifiers to the imported research environments and provides ressources to re-run the archived objects with external data

de.NBI Cloud federation through ELIXIR AAI

Belmann P, Fischer B, Krüger J, et al. de.NBI Cloud federation through ELIXIR AAI. F1000Research. 2019;8: 842.The academic de.NBI Cloud offers compute resources for life science research in Germany.  At the beginning of 2017, de.NBI Cloud started to implement a federated cloud consisting of five compute centers, with the aim of acting as one resource to their users. A federated cloud introduces multiple challenges, such as a central access and project management point, a unified account across all cloud sites and an interchangeable project setup across the federation. In order to implement the federation concept, de.NBI Cloud integrated with the ELIXIR authentication and authorization infrastructure system (ELIXIR AAI) and in particular Perun, the identity and access management system of ELIXIR. The integration solves the mentioned challenges and represents a backbone, connecting five compute centers which are based on OpenStack and a web portal for accessing the federation.This article explains the steps taken and software components implemented for setting up a federated cloud based on the collaboration between de.NBI Cloud and ELIXIR AAI. Furthermore, the setup and components that are described are generic and can therefore be used for other upcoming or existing federated OpenStack clouds in Europe

Proceedings of the 4th bwHPC Symposium

The bwHPC Symposium 2017 took place on October 4th, 2017, Alte Aula, Tübingen. It focused on the presentation of scientific computing projects as well as on the progress and the success stories of the bwHPC realization concept. The event offered a unique opportunity to engage in an active dialogue between scientific users, operators of bwHPC sites, and the bwHPC support team

Containerization of Galaxy Workflows increases Reproducibility

Published scientific findings supported by computational experiments should be reproducible by following the methodical description in the publication. Because this is often not the case, we present a method to containerize Galaxy workflows within Singularity containers. These containers are executable such that other researchers can reproduce computational experiments or run their own experiments using the containerized workflows