IMPORTANT DATES for this Training course:

  • Deadline for applications: 23 June 2017
  • Course date: 03-05 July 2017

VENUE: Department of Electrical and Electronic Engineering (DIEE) of University of Cagliari, via Marengo, 09134 Cagliari

FEE: The course does not include a fee but the participants are expected to pay their own travel, meals and hotel costs (if any).

A maximum of 25 candidates will be accepted in the course. Selection will start on 09/06/2017 and those with an adequate profile will be accepted immediately, especially if they come from other countries (to allow them to find reasonably cheap flight tickets).

Instructors

Organisers

  • Gianmauro Cuccuru (CRS4)
  • Loredana Le Pera (ELIXIR-IIB Training Team)
  • Allegra Via (ELIXIR-IIB Training Coordinator, CNR, Italy)

Course Description

Galaxy is an open source, web-based platform for data intensive biomedical analysis. It is used in a broad range of biomedical research domains to make  accessible bioinformatics applications to users lacking programming skills, and enabling them to easily build analysis workflows for NGS data.  The aim of this course is to make participants familiarize with the Galaxy platform and prepare them to work independently, using best practices guidelines for building, maintaining and installing Galaxy tools.  The course will be delivered using a mixture of lectures and computer based hands-on practical sessions. Lectures will provide an up-to-date overview of the practices for the most successful Galaxy tool development. During this 2 days course participants will learn a modern approach to create, configure and install their own tools into a Galaxy server.

Target audience

PhD students, computer scientists, bioinformaticians and developers who need to maintain/extend existing tools or develop new tools for Galaxy.

Learning outcomes

After this course participants should be able to:

  • use utilities to develop a good Galaxy tool wrapper
  • make a tool ready for publishing on a ToolShed
  • install a tool in a Galaxy instance
  • access tools and workflows through Galaxy API

Course prerequisites

Knowledge in a scripting language (bash, python, …). Working knowledge of  the Unix/Linux command line. Attendees should have access to a personal laptop.


Application Form


Programme

Monday 03th July
14:30 - 15:15 Registration
15:15 - 15:30 Welcome and introduction
15:30 - 16:00 Lecture Paolo Uva Galaxy at Glance
16:00 - 16:30 Lecture Paolo Uva Why Galaxy tools
16:30 - 17:00 Lecture Paolo Uva Help Resources
17:00 - 17:15 Afternoon break
17:15 - 18:00 Lecture Paolo Uva Get a basic Galaxy server up and running
18:00 - 18:30 Close Day 1

Tuesday 04th July
09:00 - 10:00 Lecture Marco Tangaro Everything in a box: Docker and Galaxy
10:00 - 11:00 Practical ALL Hands-on
11:00 - 11:15 Morning break
11:15 - 12:15 Lecture Gianmauro Cuccuru Galaxy Tool XML File
12:15 - 13:00 Practical ALL Hands-on
13:00 - 14:00 Lunch break
14:00 - 15:00 Lecture Gianmauro Cuccuru Building Galaxy Tools
15:00 - 16:00 Practical ALL Hands-on
16:00 - 16:15 Afternoon break
16:15 - 18:00 Practical ALL Hands-on
18:00 - 18:30 Close Day 2

Wednesday 05th July
09:00 - 09:30 Lecture Rossano Atzeni Galaxy Interactive Tour
09:30 - 11:00 Lecture Rossano Atzeni BioBlend API
11:00 - 11:15 Morning break
11:15 - 12:45 Practical ALL Hands-on
12:45 - 13:30 Wrap-up and close


ELIXIR-IIB member institutions

  • CNR (ELIXIR-IIB coordinator)
  • CRS4
  • CINECA
  • Fondazione Edmund Mach, Trento
  • INFN
  • GARR
  • Sapienza Università di Roma
  • Università di Bari
  • Università di Bologna
  • Università di Firenze
  • Università di Milano
  • Università di Milano Bicocca
  • Università di Padova
  • Università di Parma
  • Università di Roma "Tor Vergata"
  • Università di Salerno
  • Università della Tuscia