Category Archives : Tools

Home  /  Tools

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…
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…