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Data management and analysis is often cumbersome and requires investment of lot of time by researchers. Cloud computing has opened up new avenues and offers solutions for these challenges. Ola Spjuth,  Associate Professor at Uppsala University, in his presentation "The case for cloud computing in Life Sciences" talks about the ongoing work in his laboratory…
  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…
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.
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…
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 e-infrastructures for metabolomics. It was…