Cloud Computing in Bioinformatics: Benchmarking, Virtual Cluster, Security

Questions in life sciences can be answered using bioinformatics methods. Most of the used approaches require advanced computing resources due to the complexity or the amount of data to be analyzed. Nowadays, access to powerful computing resources is easier than ever because of the widespread use of cloud computing. Especially in the field of life sciences, the interest in this technology is increasing. For example, the use of modern sequencing equipment generates data in the tera- and petabyte range that can not be analyzed with standard desktop computers anymore. The purchase of high-performance compute hardware is expensive in many aspects. In addition to the acquisition costs, there are also costs for maintenance and operation, which can also include personnel costs. In contrast, using a cloud solution can be a cheaper alternative. From a cloud user's perspective, cloud resources may look endlessly, but this is not the case. Since not all cloud users are familiar with the modern paradigm of cloud computing yet, difficulties can arise in efficient resource management and data security. Especially sensitive data as in the field of personalized medicine, require special protection, which is difficult to achieve without specific knowledge. Besides data security, resource utilization is an important issue. As the efficiency of an application has an impact on the resource usage it is advisable to evaluate an application regarding their resource sweet spot to avoid wasting resources. The evaluation can be done with the help of benchmarking tools. However, most tools in this area are not tailored to bioinformatics applications or are not very user-friendly. The same applies to the use of cloud resources as virtual compute clusters. The solutions available vary depending on the cloud platform and usually require expert knowledge. This thesis presentation presents new tools and concepts that enable cloud users to use cloud resources efficiently and without special prior knowledge. The presentation covers the implemented benchmark suite BOOTABLE, specifically tailored to bioinformatics and the tool VALET to create and scale virtual clusters in an OpenStack cloud environment in an automated way. Both tools were used to evaluate the scalability of bioinformatic applications as well as the saving potential of virtual cluster resources using a load-based scaling approach. Likewise, a general security concept for a secured analysis of sensitive data is presented. Furthermore, experiences regarding a certification process in the field of IT security are presented with a focus on the selection of the appropriate standard as well as the implementation in an academic environment with a small number of employees

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

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