Latest News

PhenoMeNal is participating as a panelist in the session on Virtual Research Environments (VRE) for the Open Science Cloud at the Digital Infrastructures for Research (DI4R2016), 28-30 September 2016, Krákow Poland. Organised by the BlueBRIDGE project, the session will include some lightning talks and discussions on the VRE sector.
EMBL-EBI, 14th-15th November 2016. EMBL-EBI is hosting a two day hackathon intended for the software developers in the consortium. Participants will engage in the establishment of PhenoMeNal testing at different levels including tool unit testing, container testing, workflow and infrastructure testing.
Metabolomics is a key source of experimental information to understand the functional processes ongoing in cells. As such, it is central to systems biology. For this reason, we set up a working group initially involving PhenoMeNal partners and the Wageningen Centre for Systems Biology to explore the state-of-the-art and perspective of metabolomics in systems biology.…
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. https://twitter.com/NuDataScientist/status/742613515786149888 The meetings were extremely productive, and it was…
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…
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 by discussions on the current…
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 the survey by clicking on…
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…
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 Capuccini will present the PhenoMeNal…
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/