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COVID-19: Greek collaborations on infrastructures and Galaxy installation for data analysis to detect mutations

Galaxy-COVID-workshop-rev

The focus: Athena Research Center (ARC) continues the series of informative and educational workshops related to important practices, tools and contact points for COVID-19 research in Greece. In December, a joint workshop on Galaxy, the infrastructure for biological data analysis was organised with the Biomedical Sciences Research Center "Alexander Fleming" and the Institute of Applied Biosciences of the Centre for Research and Technology Hellas.

The workshop informed about the Greek Node of the European Research Infrastructure for Life Science (ELIXIR-GR) and its Cloud Infrastructure (EG-CI) developed to support services provided by ELIXIR-GR such as the Galaxy platform.

Distributed Infrastructure for Biological Data: Presentations kicked off with Alexandros Dimopoulos from Biomedical Sciences Research Center "Alexander Fleming", who concentrated on the ELIXIR research infrastructure. ELIXIR is an intergovernmental entity that collects Europe's life science resources from databases and software tools to computing resources. The aim is to integrate and coordinate resources into one single centralized infrastructure in support of researchers activities in the following pillars: Tools, Data, Compute, Interoperability and Training. Alexandros, also, highlighted the contribution of the Greek National Node, ELIXIR-GR, to install Galaxy in the EG-CI Cloud Infrastructure by exploiting its clusters and VMs.

ELIXIR GR Cloud Infrastructure: Thanasis Vergoulis, from Athena Research Center, provided more insight on EG-CI, a Cloud infrastructure developed to support the ELIXIR-GR community and to run Galaxy. Two platforms enable access to computing resources: a. CLIMA for managing cloud resources, and b. SCHeMa for managing non-demand computations. Also, the infrastructure offers three types of services:

  • "24/7 services" projects providing private virtual servers,
  • "on-demand computation" projects for the execution of computational tasks,
  • cold-storage projects for datasets backup.

Thanasis noted that, currently, EG-CI is in beta and will be fully operational by 2021. New functionalities include automatic workflows' visualisation and interconnection with data repositories, namely Hellenic Data Service - HELIX and Zenodo.

Use cases on COVID data: Fotis Psomopoulos demonstrated the use of Galaxy, an open source, web-based platform for accessible, reproducible, transparent computational and data intensive biomedical research. He showcased Galaxy's main functionalities and described all the necessary steps to be followed for a successful data analysis based on a COVID-19 scenario. More specifically, among the tools he used were Mark Duplicates to check duplicates, Insert indel qualities to optimize quality for reliable information and LoFreqs to detect mutations. The platform allows for workflow to be visualised and saved for future use.

In dialogue: Participants engaged in discussions with speakers and expressed their interest to equally use and get more actively involved in the aforementioned infrastructures through technical and non-technical contributions. Participants were also informed about the 5-day Galaxy Training event that takes place in 2021 for they can learn more about the use of Galaxy in a wide range of scientific topics (e.g. Proteomics and Machine Learning).

Next on the COVID-19 series in January 20201 is Argos, OpenAIRE's tool for Data Management Planning. 

You may find the recordings and presentations here.

Contact details:

OpenAIRE:

ELIXIR-GR : link to contact

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15 Jun 2021

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