Lecture

An introduction to the Galaxy platform for computational biology
05.11.2018
Speaker: Alexandros Kanterakis, Vangelis Kritsotakis
Date: 05 November 2018 Time: 10:00-13:00
Location: Seminar Room 1, FORTH, Heraklion, Crete
Host: Alexandros Kanterakis

Abstract:

Galaxy is an open source, web-based platform for data intensive biomedical research. It aims in making computational biology accessible to research scientists with limited or absent computer programming experience. Through Galaxy, users can select from a wide variety of bioinformatic tools, upload/download biomedical datasets, compose analysis workflows, insert analysis parameters, submit workflows to computer clusters and visualize/inspect the results. It is accompanied with data editors and visualizers for a large collection of common bioinformatic formats and enables easy management of Big data.

When using Galaxy, the information is captured such that any user can repeat and understand a complete computational analysis. The platform is mainly used for sequence alignment, variant calling, variant annotation, RNA seq, CHIP-seq, 16S rRNA and other common bioinformatics tasks.  Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.

More about Galaxy:

https://galaxyproject.org/
https://usegalaxy.org/

 

Agenda

This three hour tutorial aims at presenting an overview of the Galaxy Platform and the way it can be used by biologists or bioinformaticians for constructing working workflows.

The first part of the event (1st hour) includes:

a) A short introducing the platform and the respective ecosystem

b) A quick description of the provided Web UI

c) Simple guidelines presenting the steps to install Galaxy in a local environment.

The second part (2nd & 3rd hours) of this events includes practical examples, where, the platform will be used in action to construct and execute three indicative workflow examples. These examples are: (1) Alignment and Variant Calling, (2) Variant Filtering and (3) Variant Annotation.

During this part, all the participants will be able to use the platform themselves by reproducing the presented steps and get in touch with the platform. For this purpose you are kindly asked to bring your own laptop.

At the end of the tutorial, a short questionnaire will be handed to you that will provide valuable feedback and will help us improve this tutorial in the future. Also the complete material (notes, slides) will be made available online.

Bio:

Alexandros Kanterakis is a postdoctoral researcher at FORTH-ICS. He owns a PhD in Bioinformatics from the University of Groningen, Netherlands. His research interest are in open science, bioinformatics workflows for genetic analysis, pharmacogenomics, machine learning and web services for data and analysis integration.

Vangelis Kritsotakis is a technical staff member at FORTH-ICS. He received his MSc degree in Internet Computing from the University of Surrey and his BSc degree in Mathematics & Computer Science from the University of Sussex. His research interests lie in the areas of Biomedical Information Systems, Semantic Web, Information Modelling and Data Integration, Service Oriented Technologies and Big Data Processing.

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