GENOMICS APPLICATIONS PLATFORM

Misha Kapushesky, CEO

Wednesday, 10 April 13

OUR DREAM

universal platform for bioinformatics application

development

Wednesday, 10 April 13

WHAT’S A PLATFORM?Application Development Framework

• APIs & SDK

• Components

• Deployment

• Security Model

• Data Model

• Storage & Compute

. . .

Why do I need a platform?

Wednesday, 10 April 13

ALL THIS!le management

with strong metadatastorage and

compute engine

target multiple tools and languages

SDK with APIs &data model

data visualisation tools & librariespublic data sets

Wednesday, 10 April 13

OUR PLATFORM• SDK and APIs for developing computational and

interactive apps

• cloud-based virtual !le system for data storage and sharing

• format-independent object model for functional genomics data types

• free pre-loaded curated public datasets and integrated core NGS tools

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KEY FEATURES

• Files are (ОО) classes

• Everything is a "le

• A "le is > a "le

• Files are everywhere

• Files can be initialised

DATA MODEL

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DATA MANAGEMENT

• Simple model

• Flexible metadata

• Powerful search

• Built-in sharing

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ORGANISATIONSGROUPS & USERS

SECURITY MODEL

Wednesday, 10 April 13

ORGANISATIONSGROUPS & USERS

SECURITY MODEL

Wednesday, 10 April 13

ORGANISATIONSGROUPS & USERS

SECURITY MODEL

Wednesday, 10 April 13

ORGANISATIONSGROUPS & USERS

SECURITY MODEL

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GENOMICS APPSNGS QC

Aligners

Genome Browser

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GENOME BROWSER

• Never need to save

• Pages are "les

• Sticky notes and rulers

• Formula tracks

• Extensible

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WRITING AN APP• Computational: Python, R, binary

• Interactive: Java + Javascript

• Application versioning, test framework, OO model

public class SimpleApplication extends Application implements IFileApplication { @Override public boolean accepts(IFile ... files) { return files.length == 1 && files[0] instanceof ISequencingAssay; }

public List<SequenceRead> head(final String accession, final int n) { final ISequencingAssay assay = getFileSystemFacade().getFileByAccession(accession, ISequencingAssay.class, true); return assay.head(n); }} Java

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ROLL YOUR OWN

function head(n) {G$.invokeMethod('head', [G$.accession, n], function(reads) { $.each(reads, function(i, read) { var readDiv = $('<div class="well"/>');

var spark = $('<div/>'); $('#display').append(readDiv); readDiv.append('<pre>' + read.sequences[0].sequence + '</pre>'); readDiv.prepend(spark); var q = phredToNumeric(read.sequences[0].quality); spark.sparkline(q, {type: 'line', width: '500px', height: '2em'}); }); });} Javascript

Wednesday, 10 April 13

ROLL YOUR OWN

function head(n) {G$.invokeMethod('head', [G$.accession, n], function(reads) { $.each(reads, function(i, read) { var readDiv = $('<div class="well"/>');

var spark = $('<div/>'); $('#display').append(readDiv); readDiv.append('<pre>' + read.sequences[0].sequence + '</pre>'); readDiv.prepend(spark); var q = phredToNumeric(read.sequences[0].quality); spark.sparkline(q, {type: 'line', width: '500px', height: '2em'}); }); });} Javascript

Wednesday, 10 April 13

ROLL YOUR OWN

function head(n) {G$.invokeMethod('head', [G$.accession, n], function(reads) { $.each(reads, function(i, read) { var readDiv = $('<div class="well"/>');

var spark = $('<div/>'); $('#display').append(readDiv); readDiv.append('<pre>' + read.sequences[0].sequence + '</pre>'); readDiv.prepend(spark); var q = phredToNumeric(read.sequences[0].quality); spark.sparkline(q, {type: 'line', width: '500px', height: '2em'}); }); });} Javascript

Wednesday, 10 April 13

MORE ON APPS• Quick resource allocation and scheduling

• Format conversion on demand

• Isolated deployment infrastructure

• Secure app delivery to end-user

• Detailed event logging

• Every method in your app is an API endpoint

• Love and support from Genestack team

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PUBLIC DATA

Different technologies, different contexts, aim for correct minimal metadata and full data

• Expression – RNA-seq & Arrays

• Genotypes – WGS, Exome, SNP Chips

• Epigenetics – ChIP-seq, ChIP-chip, etc.

• Microbial genomes

• 1000 Genomes, ENCODE, GEUVADIS

Wednesday, 10 April 13

GETTING STARTED

• Genestack Platform Alpha is out today

• Completely free for alpha users, discounted rates for early adopters

• Full platform user access

• Developer access coming soon

https://alpha.genestack.com

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LOADING DATA

• Data transfer APIs and app

• Import from disk (shipped)

• Direct link to the cloud

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OUR MODELCreate as many accounts as you want

Pay for storage and CPU credits: !xed or PAYGAll public datasets are completely free

Wednesday, 10 April 13

WHERE DO I START?

Sign up now to test the platform Genestack Platform Alpha

alpha.genestack.com

Follow us: @genestackltd, genestack.com/blog

Wednesday, 10 April 13