OpenTox gadget on Garuda

Garuda OpenTox

Details

DC Role: 
Software development
Duration: 
Ongoing
Client: 
Open to market

ABOUT THIS PROJECT

About OpenTox gadget on Garuda

EwC, together with its partner SBX are developing OpenTox Garuda Gadgets to provide access to multiple sources of toxicology data socialised to systems biology and bioinformatics applications. Garuda is a connectivity and automation platform for various tools and applications (called Gadgets) developed by The Systems Biology Institute, Tokyo with custom services provided by SBX Corporation, Tokyo. The platform hosts an array of gadgets with diverse GUIs and functionalities on a connective platform. Garuda aims to be “the way biology connects”. Garuda has both a community edition with options for customized gadgets for commercial use and is being used both in academia and industry.

 

Inside Garuda, gadgets can communicate with each other by sending data through the platform. The following image visualises gadget connectivity.

       

 

Providing Data Gadgets and Interoperability

DC is working together with SBX as a strategic partner to add OpenTox data gadgets to Garuda. This will allow data from OpenTox APIs to be accessed and analysed through a diverse set of Garuda gadgets.

The Open TG-GATEs sample finder gadget allows the user to search for samples in Open TG-GATEs using the OpenTox API for this database.

 

The Open TG-GATEs Data Fetcher allows the user to fetch data from the Open TG-GATEs API and either export it, or pass it to other gadgets. Genes may be filtered by p-value for relevance.

 

The genes can immediately be used in other gadgets on Garuda through the platform’s connectivity, by sending a gene set. In this way, we can discover significant pathways, analyse the same genes in other databases (such as Percellome) and so on. The two gadgets mentioned above have been published on the Garuda gateway and may be downloaded for free by anyone with a Garuda installation.

DC is working continuously with SBX to make more OpenTox data and APIs available on the Garuda platform.

We describe our recent seminar and hackathon in Tokyo and Seoul on this work in the following blog post: https://wwwedelweissconnect.com/blog/2016-meetings-tokyo-and-seoul and in video tutorials:

OpenTox-Garuda :

1. Basics

2. Gene set Analysis

3. Pathway Analysis

 

For more information about Garuda, please see the official web site http://www.garuda-alliance.org.

 

Contents will be updated with more details

 

 

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