Genestack BioIT-World-2013

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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.

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Genestack BioIT-World-2013

  1. 1. GENOMICS APPLICATIONS PLATFORM Misha Kapushesky, CEOWednesday, 10 April 13
  2. 2. OUR DREAM universal platform for bioinformatics application developmentWednesday, 10 April 13
  3. 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. 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 modelWednesday, 10 April 13
  5. 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 toolsWednesday, 10 April 13
  6. 6. KEY FEATURES DATA MODEL • Files are (ОО) classes • Everything is a file • A file is > a file • Files are everywhere • Files can be initialisedWednesday, 10 April 13
  7. 7. DATA MANAGEMENT • Simple model • Flexible metadata • Powerful search • Built-in sharingWednesday, 10 April 13
  8. 8. ORGANISATIONS GROUPS & USERS SECURITY MODELWednesday, 10 April 13
  9. 9. ORGANISATIONS GROUPS & USERS SECURITY MODELWednesday, 10 April 13
  10. 10. ORGANISATIONS GROUPS & USERS SECURITY MODELWednesday, 10 April 13
  11. 11. ORGANISATIONS GROUPS & USERS SECURITY MODELWednesday, 10 April 13
  12. 12. GENOMICS APPS NGS QC Genome Browser AlignersWednesday, 10 April 13
  13. 13. GENOME BROWSER • Never need to save • Pages are files • Sticky notes and rulers • Formula tracks • ExtensibleWednesday, 10 April 13
  14. 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); } } JavaWednesday, 10 April 13
  15. 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/>); $(#display).append(readDiv); readDiv.append(<pre> + read.sequences[0].sequence + </pre>); readDiv.prepend(spark); var q = phredToNumeric(read.sequences[0].quality); spark.sparkline(q, {type: line, width: 500px, height: 2em}); }); }); } JavascriptWednesday, 10 April 13
  16. 16. ROLL YOUR OWN function head(n) { G$.invokeMethod(head, [G$.accession, n], function(reads) { $.each(reads, function(i, read) { var readDiv = $(<div class="well"/>); var spark = $(<div/>); $(#display).append(readDiv); readDiv.append(<pre> + read.sequences[0].sequence + </pre>); readDiv.prepend(spark); var q = phredToNumeric(read.sequences[0].quality); spark.sparkline(q, {type: line, width: 500px, height: 2em}); }); }); } JavascriptWednesday, 10 April 13
  17. 17. ROLL YOUR OWN function head(n) { G$.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}); }); }); } JavascriptWednesday, 10 April 13
  18. 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 teamWednesday, 10 April 13
  19. 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, GEUVADISWednesday, 10 April 13
  20. 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.comWednesday, 10 April 13
  21. 21. LOADING DATA • Data transfer APIs and app • Import from disk (shipped) • Direct link to the cloudWednesday, 10 April 13
  22. 22. OUR MODEL Create as many accounts as you want Pay for storage and CPU credits: fixed or PAYG All public datasets are completely freeWednesday, 10 April 13
  23. 23. WHERE DO I START? Sign up now to test the platform Genestack Platform Alpha alpha.genestack.com Follow us: @genestackltd, genestack.com/blogWednesday, 10 April 13

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