ICAR 2015 Workshop - Blake Meyers

transcript

University of Delaware Department of Plant & Soil Sciences, and the Delaware Biotechnology Institute Photo by

Alex Kozik, UC Davis

SMALL RNA INFORMATICS VIA ARAPORT Araport “science apps” for small RNA data

Blake Meyers & Mayumi Nakano

OUR ARABIDOPSIS SMALL RNA WEBSITE

PHASING ANALYSIS TOOL

TAS3a Problem: data is entwined with the app, not an easy

format for external sites/tools to consume; true

for nearly all web apps.

REST INTERFACE (an example from Araport)

JSON output

JSON = JavaScript Object Notation, an open, standard format that uses human-

readable text to transmit data objects

EXPOSING DATA VIA ARAPORT

Original data, different format,

easy to parse

Web page exposes

the data in JSON format

Meyers lab website Araport

Mediator re-exposes

the data

Community API with online

documentation

Science app displays the data

open source, demonstrative

WHY EXPOSE OUR DATA VIA ARAPORT?

• Community: Araport is an open-access online community resource for Arabidopsis research

• Interoperability: Araport is designed to allow users to access and integrate a wide range of Arabidopsis information through a single interface

• Standards: Araport defines standards for data storage, access and interconnectivity

• Scaling: Araport will grow through the contributions of research community (data, computation, visualization tools)

• Security: Araport offers authentication & profiles service that can be shared across different web sites

• Reporting: Araport is maintained by scientists at JCVI, TACC, CSBC and other collaborators

Step 1: Make data accessible in JSON format from our server

Step 2: Build application programing interfaces (APIs) for JSON web services on Araport

Step 3: Build a Science App using JSON API on Araport

Step 4: Encourage others!

PHASING ANALYSIS TOOL: JSON OUTPUTS

MEYERS LAB JSON WEB SERVICES

MEYERS LAB JSON OUTPUT: Phased Loci

Our phasing analysis pipeline identified 37 loci generating phased siRNAs, which aren’t listed together on any of our web pages, but the list of these

loci is available as a JSON web service. These are now exposed via Araport.

ARAPORT API & JSON OUTPUT

ARAPORT ‘SCIENCE APP’

WHAT’S NEXT?

• Display small RNA abundance data as a new track in JBrowse

• Release sPARTA (small RNA-PARE Target Analyzer) as an Araport science app

• Release more datasets & new tools (e.g. target prediction)

• Add more lists of loci that produce other types of regulatory small RNA.

A PREVIEW OF sPARTA AS A SCIENCE APP

ACKNOWLEDGEMENTS

NSF Plant Genome & MCB Awards

https://mpss.udel.edu

Blake Meyers Mayumi Nakano Deepti Ramachandruni Atul Kakrana Rui Xia & others

Meyers Lab JCVI Chris Town Jason Miller Vivek Krishnakumar Erik Ferlanti

TACC Matt Vaughn Walter Moreira Steve Mock

https://www.araport.org