PhenoMeNal meets de.NBI

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deNBI logo  The German Network for Bioinformatics Infrastructure – de.NBI is a network of partners that provide bioinformatics services in different areas. Recently, Germany joined the European life-sciences infrastructure for biological information (ELIXIR) as a full member [1], and de.NBI is now busy establishing the German node in ELIXIR by providing high-quality bioinformatics services and training expertise to the scientific user community.

Several of the service centers with experience in cloud computing are currently establishing a de.NBI cloud as basis for a future-oriented compute structure. The German Federal Ministry of Education and Research is supporting the de.NBI cloud with altogether up to 5 Mio. Euro and six positions for scientists [2]. The Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi), was running a Cloud Computing Tutorial at the German Conference on Bioinformatics (GCB 2016) , where PhenoMeNalists Christoph Ruttkies and Steffen Neumann attended.

PhenoMeNal provides Virtual Research Environments (VRE) for interoperable and scalable metabolomics analysis. Users should be able to create, on-demand, an environment of tools, services, and data, supporting their research needs. Hardware setup and software deployment required to operate these facilities are completely transparent to the VRE and hence the users can focus on the analysis and not the technicalities.

With IPB Halle now joining the de.NBI network as partner project of the Center for Integrative Bioinformatics (CIBI), this is a fantastic opportunity to showcase how a PhenoMeNal Galaxy VRE can be bootstrapped on OpenStack clusters like the ones operated by the CeBiTec at Bielefeld University and the Bioinformatics team at Giessen University.

Installing a set of virtual machines, providing all the ingredients (Galaxy, Kubernetes, GlusterFS, …), the network and storage setup manually yourself would be tedious if not impossible for an average user, is error-prone and would certainly take a while. Instead, in PhenoMeNal we are using a number of industrial-strength cloud technologies to automagically provision and set up your own copy of our PhenoMeNal research environment. First, there is Terraform, which you can think of as a scripted remote-control for instantiating (and deleting) resources not only on the de.NBI OpenStacks, but really any of the major cloud providers, including Amazon AWS and the  Google Compute Engine (GCE). After it has done its job, Ansible takes care of installing and configuring all the required software on your freshly instantiated cloud machines.

In the end, you have you own instance of Galaxy, with all tools packaged by the PhenoMeNal team!

Looking forward to hear your feedback, Yours,
The PhenoMeNalists!


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