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In June 2016, the PhenoMeNal project held its first annual consortium meeting, as well as convening meetings for potential stakeholders of the PhenoMeNal e-infrastructure, and for the project’s Scientific Advisory Board. The meetings were held over three days on the historic Dodecanese island of Rhodes, Greece. Stakeholder meeting in Rhodes…

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…

The PhenoMeNal consortium together with experts from the Metabolomics community Prof. Mark Viant, Ralf Weber and Warwick Dunn is hosting a workshop on Computational Workflows and Workflow Engines at the 12th Annual Conference of the Metabolomics Society, June 27-30, 2016 in Dublin. The session includes a series of talks on platforms such as Workflow4Metabolomics, MassCascade-KNIME, Galaxy-M, MetaboAnalyst, PhenoMeNal and MetaSpace followed…

PhenoMeNal has commissioned a survey to collect information on computational and storage requirements, as well as on some aspects of software usage for infrastructures managing metabolomics data. This information will help us  to produce an infrastructure that provides tools effectively useful to the community. We would be grateful if you could contribute to…

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,…

Thursday 12th May 2016, Uppsala. Our partners in Uppsala are organizing a focused discussion and workshop on microservices at Science for Life Laboratory, Uppsala University. Speakers include Steven Borrelli, who is a core committer and architect of MANTL, along with Giacinto Donvito, who is lead developer for INDIGO Datacloud ; Marco…

Our partners in Uppsala successfully provision the PhenoMeNal Virtual Research Environment (VRE) on various platforms: Google Cloud, EBI Embassy Cloud (OpenStack), and SNIC Science Cloud (OpenStack). For more information visit:  https://cloud.snic.se/index.php/2016/04/20/virtual-research-environments-for-clinical-metabolomics/

In this blog post, Dr David Johnson from PhenoMeNal consortium parter The University of Oxford looks back at the PhenoMeNal e-infrastructures training workshop held in March 2016 at SciLifeLab in Uppsala, Sweden. This post was originally published on www.isa-tools.org on 11th March 2016, here. Last week, the Horizon 2020 PhenoMeNal project held a training workshop on…

Friday 27th May 2016, Barcelona. The workshop on Metabolic Phenotyping in Clinical Practice, hosted by the University of Barcelona, Hospital Clinic, IDIBAPS and PhenoMeNal Consortium is intended to define the state-of-the-art in metabolic phenotyping in the clinic. A full day  workshop with lightning talks and discussions led by experts in the…

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…