Connecting Data to Data

Garuda Gadget - Integrated Safety Solutions

 

Garuda is a systems biology platform developed by the Systems Biology Institute (SBI) in Tokyo, Japan. It hosts an array of gadgets with diverse GUIs and functionalities on a connective platform. Garuda aims to be “the way biology connects”. Within Garuda, gadgets can communicate with each other by sending data through the platform. Garuda has both a community edition and commercial version, and is being used both in academia and industry.

Douglas Connect is working together with SBI to add two OpenTox gadgets to Garuda. This will allow data from OpenTox APIs to be accessed and analysed through a diverse set of Garuda gadgets. The two gadgets DC is developing will provide access to multiple sources of toxicology data socialised to systems biology and bioinformatics applications.

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.

Douglas Connect is working continuously with SBI 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://www.douglasconnect.com/blog/2016-meetings-tokyo-and-seoul.

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

 

 

Rok Predan
Community Manager

 

 

 

 

Dr Johan Nyström-Persson
Data Scientist

 

 

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