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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…
BATMAN: Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra Bayesian automated metabolite analyzer for NMR (BATMAN) is an open source R-package for estimation of concentration of metabolites from Nuclear Magnetic Resonance spectral data. The software uses a Bayesian model of 1D NMR spectra to automatically deconvolve and quantify metabolites in complex mixtures.…
MetFrag: Annotation of high precision tandem mass spectra of metabolites MetFrag, one of the popular metabolomic analysis tools in the PhenoMeNal App library, is an insilico fragmenter used in the annotation of high precision tandem mass spectra of metabolites. Launched in 2010, the tool has grown in the past 7 years with new functions that…
The CloudMet2017 summer school organised by CRS4 in Sardinia, brought  together participants and trainers from eight different countries. The event proved to be an opportunity for participants to learn a lot about metabolomics data analysis in the cloud, and the PhenoMeNal consoritum  was also glad to see that our infrastructure(s) were chugging along while 30+…
The recent application for establishing Metabolomics as a use case for ELIXIR has recently been approved by the Heads of Nodes of ELIXIR. Together with Proteomics and Galaxy, Metabolomics will be added to the portfolio of ELIXIR use cases, or "communities" as this will be called in the work programme of ELIXIR 2019-2023. For details…
The PhenoMeNal project is developing a Virtual Research Environment (VRE) also known as the Cloud Research Environment (CRE) for interoperable and scalable metabolomics data analysis. It is designed as a microservice architecture with services being implemented as virtual machines and Docker containers, orchestrated using Kubernetes. The main workflow system in PhenoMeNal is Galaxy, which also…
  Date: 30th October - 2nd November 2017; Venue: European Bioinformatics Institute (EMBL-EBI), Cambridge,  CB10 1SD, United Kingdom The participants will learn about metabolomics data analysis using publicly available softwares and tools. The training course includes hand-on tutorials on data submissions and using the PhenoMeNal compute platform for a workflow based approach to data analysis. For registration and details click here.
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…