Deploying PhenoMeNal virtual research environments on the EGI Federated Cloud

Ola Spjuth and Anders Larsson on the successes of the PhenoMeNal project

What is PhenoMeNal?

The PhenoMeNal e-infrastructure supports data processing and analysis workflows for large datasets generated in metabolomics research. The computational services provided within PhenoMeNal enable researchers to build, share and run reproducible data processing workflows in cloud environments. They aim to improve the understanding of the causes and mechanisms underlying health and disease, and to render the generated data and metadata more traceable as demanded by reproducible research. PhenoMeNal’s services can enhance a wide range of metabolomics applications in biological, agricultural and environmental sciences.

PhenoMeNal services

  • The PhenoMeNal Virtual Research Environment (VRE) is implemented as a microservice architecture with Docker containers orchestrated in a Kubernetes environment. The containers can be connected into analysis pipelines using scientific workflow platforms, such as Galaxy. For deployment, PhenoMeNal has developed the KubeNow cloud deployment software that simplifies instantiation of complete virtual infrastructures with Kubernetes, including storage, network and other required services readily available.
  • The PhenoMeNal Gateway provides a web-based Graphical User Interface (GUI) on top of KubeNow. The use of Galaxy as the main workflow system provides a user friendly GUI for workflow authoring, and execution of tools and workflows.
  • The PhenoMeNal App library is a service catalogue of all open source metabolomics tools available through the VRE. The library also provides an online training featuring tutorials and technical documentation on the developed tools and workflows.

Deployment on the EGI Federated Cloud

PhenoMeNal has worked closely with the EGI Federated Cloud to harness EGI’s strategy for provision of a secure and reliable infrastructure. PhenoMeNal VREs are now successfully deployed on EGI Federated Cloud resources (Cloud provider IN2P3-IRES). This achievement was a joint effort between the two consortia and covered the extension of the PhenoMeNal deployment engine (KubeNow) to include OpenStack Virtual Organization Management System (VOMS) authentication methods. The work was carried out on EGI cloud resources provided by IN2P3-IRES within the ELIXIR-FR virtual organisation. Technical details can be found in the PhenoMeNal wiki.

Deployment of PhenoMeNal VRE on the EGI Federated Cloud.

Cloud resources

The PhenoMeNal VRE uses EGI Federated Cloud resources provided by IN2P3-IRES within the ELIXIR-FR virtual organisation.

More information

Ola Spjuth and Anders Larsson are members of the PhenoMeNal consortium based at Uppsala University.

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