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Date and Time:  Wednesday 4th  April 2018, 14:00 – 15:00 GMT Abstract Ola Spjuth, (Uppsala University), in his webinar on Challenges and Opportunities with Virtual Research Environments, will talk about Virtual Research Environments (VREs) and their application to data analysis. In his presentation, Ola,  will explain the motivation and approach taken by the PhenoMeNal consortium when developing a cloud-agnostic on-demand VRE for metabolomics implemented using…
We are pleased to announce the 2018.02 release “Cerebellin” of the PhenoMeNal infrastructure. The new release is the result of half a year of intense developments and represents a major upgrade to the 2017-08 production release Bucetin. The main features of this release are: Improved usability following extensive User experience tests The Infrastructure has improved stability…
Tryggve 2, is  a project within The Nordic e-Infrastructure Collaboration (NeIC), consisting of the Nordic countries such as Sweden, Finland, Norway and Denmark and is hosted by the Nordic ELIXIR nodes. Tryggve develops and facilitates access to secure e-infrastructure for sensitive data, suitable for hosting large-scale cross-border biomedical research studies. With GDPR (General Data Protection Regulation)…
PhenoMeNal partner IPB, is hosting a two day workshop from 4th-5th April 2017, on PhenoMeNal workflows. The objective of the workshop is to showcase and improve existing workflows to achieve broader applicability, improve functionalities and add Findable Accessible Interoperable Re-usable (FAIR) information. For registration, click here.
  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…
The PhenoMeNal Cloud Research Environment (CRE) portal provides an entry point to analysis tools via its open source "App Library" (Application Library) - a service catalogue of all applications (currently 24) that are currently available via Galaxy workflows through the CRE.  Each tool, available in the form of Docker container,  carries a tool description, usage instructions to be…
PhenoMeNal aims to isolate bioinformatics tools as micro services through the use of Docker containers. If you haven't used Docker containers in the past, the official Docker guide is an excellent starting point. Building Docker containers requires the use of so called Dockerfiles. They contain a list of commands needed for installing the application with…
One of the main routes to mzML-formatted data is using Open Source converter msconvert. It can convert to mzML from most of the vendor formats. In PhenoMeNal, we have now succeeded to package msconvert in a Docker container and execute it in the WINE environment (“Run Windows applications on Linux, BSD, Solaris and Mac OS…
We are pleased to announce the availability of our phenomenal docker registry at https://docker-registry.phenomenal-h2020.eu/. This is of course intended for machines, so this is where you point your docker command line to retrieve a docker image. This registry holds all the docker images built through our continuous integration server at https://phenomenal-h2020.eu/jenkins/. So for instance, to pull the…
You can now access the galaxy installation of workflow4metabolomics, just click on http://phenomenal-h2020.eu/galaxy/. Have fun!