Announcing public availability of Genestack Platform Alpha. Free signup at https://alpha.genestack.com. Genestack Platform is a universal platform for developing bioinformatics applications. It is a complete framework with components for processing genomics data, creating powerful analytical visualisations and delivering them securely to end-users.

1. GENOMICS
APPLICATIONS
PLATFORM
Misha Kapushesky, CEO
Wednesday, 10 April 13

2. OUR DREAM
universal platform for
bioinformatics application
development
Wednesday, 10 April 13

3. WHAT’S A PLATFORM?
Application Development Framework
...
• APIs & SDK • Security Model
• Components • Data Model
• Deployment • Storage & Compute
Why do I need a platform?
Wednesday, 10 April 13

4. ALL THIS
file management storage and
with strong metadata compute engine
data visualisation
public data sets
tools & libraries
target multiple tools SDK with APIs &
and languages data model
Wednesday, 10 April 13

5. OUR PLATFORM
• SDK and APIs for developing computational and
interactive apps
• cloud-based virtual file 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
Wednesday, 10 April 13

6. KEY FEATURES
DATA MODEL
• Files are (ОО) classes
• Everything is a file
• A file is > a file
• Files are everywhere
• Files can be initialised
Wednesday, 10 April 13

7. DATA MANAGEMENT
• Simple model
• Flexible metadata
• Powerful search
• Built-in sharing
Wednesday, 10 April 13

8. ORGANISATIONS
GROUPS & USERS
SECURITY MODEL
Wednesday, 10 April 13

9. ORGANISATIONS
GROUPS & USERS
SECURITY MODEL
Wednesday, 10 April 13

10. ORGANISATIONS
GROUPS & USERS
SECURITY MODEL
Wednesday, 10 April 13

11. ORGANISATIONS
GROUPS & USERS
SECURITY MODEL
Wednesday, 10 April 13

12. GENOMICS APPS
NGS QC
Genome Browser
Aligners
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13. GENOME BROWSER
• Never need to save
• Pages are files
• Sticky notes and rulers
• Formula tracks
• Extensible
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14. 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
Wednesday, 10 April 13

15. 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

16. 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

17. 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

18. 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
Wednesday, 10 April 13

19. 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

20. 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
Wednesday, 10 April 13

21. LOADING DATA
• Data transfer APIs and app
• Import from disk (shipped)
• Direct link to the cloud
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22. OUR MODEL
Create as many accounts as you want
Pay for storage and CPU credits: fixed or PAYG
All public datasets are completely free
Wednesday, 10 April 13

23. 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