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Monday, June 27 • 9:00am - 11:30am
Dynamic prototyping of tools with Galaxy ProTo

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In addition to being a feature-rich framework for biomedical research, Galaxy can also be thought of as a simple way to provide web access to locally developed functionality. Galaxy can for instance be used by master students to showcase their developed functionality to the supervisors and examiners, or it can be used by researchers to easily provide access to their ad hoc developed scripts. For such use, however, Galaxy poses some limitations. For one, the developer needs to learn the XML format used by Galaxy, with all the twists and turns inherent in the format. Also, the format itself has limited support for dynamics in the parameter option boxes, e.g. for providing the user with direct feedback based upon dynamic calculations within the interface itself.

The Galaxy Prototyping Tool API (Galaxy ProTo) is a new tool building methodology introduced by the Genomic HyperBrowser project. Galaxy ProTo is an unofficial alternative for defining Galaxy tools. Instead of XML files, Galaxy ProTo supports defining the user interface of a tool as a Python class. There are no limitations to what kind of code that can be executed to generate the interface. For instance one could read the beginning of an input file and provide dynamic options based on the file contents. When developing a ProTo tool, results of changes in the code can be witnessed on-the-fly in a web browser; there is no need to reload the tool or restart the Galaxy server. When development is finished, a ProTo tool can be easily be installed into the Galaxy tool menu alongside the standard Galaxy tools. Galaxy ProTo thus empowers developers without Galaxy experience to easily develop Galaxy tools, both for prototyping purposes, but also for developing fully functional, interactive tools.

This session will cover a number of example for creating Galaxy ProTo-based tools using different options and various levels of dynamicity. The participants will try developing their own ProTo tools on-the-fly, on VMs

Session document

Prerequisites:
  • Python programming experience
  • A wi-fi enabled laptop with a modern web browser.  Google Chrome, Firefox and Safari will work best. 
  • VirtualBox as a VM manager

Instructors
avatar for Abdulrahman Azab

Abdulrahman Azab

Head Engineer, University of Oslo
avatar for Boris Simovski

Boris Simovski

University of Oslo



Attendees (8)