Analyze Genomes: A Federated In-memory Database Computing Platform enabling real-time Analysis of...

Analyze Genomes: A Federated In-Memory Database Computing Platform Enabling Real-time Analysis of Big Medical Data

Dr. Matthieu-P. Schapranow SAPPHIRE, Orlando, USA

May 17, 2016

■  Online: Visit we.analyzegenomes.com for latest research results, slides, videos, tools, and publications

■  Offline: High-Performance In-Memory Genome Data Analysis: In-Memory Data Management Research, Springer,

ISBN: 978-3-319-03034-0, 2014

■  In Person: Join us for Intel Tech Talks at SAPPHIRE booth 625 daily!

□  May 17 12.30pm: A Federated In-Memory Database Computing Platform Enabling Real-time Analysis of Big Medical Data

□  May 18 12.30pm: In-Memory Apps for Next Generation Life Sciences Research

□  May 19 11.30am: In-Memory Apps Supporting Precision Medicine

Where to find additional information?

Schapranow, SAPPHIRE, May 17, 2016

A Federated In-Memory Database Computing Platform for Big Medical Data

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Ind irect In te raction

D irect In te raction

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Intelligent Healthcare Networks in the 21st Century?



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Intelligent Healthcare Networks in the 21st Century?



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Intelligent Healthcare Networks in the 21st Century!



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■  Patients

□  Individual anamnesis, family history, and background

□  Require fast access to individualized therapy

■  Clinicians

□  Identify root and extent of disease using laboratory tests

□  Evaluate therapy alternatives, adapt existing therapy

■  Researchers

□  Conduct laboratory work, e.g. analyze patient samples

□  Create new research findings and come-up with treatment alternatives

The Setting Actors in Oncology


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IT Challenges Distributed Heterogeneous Data Sources

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Human genome/biological data 600GB per full genome 15PB+ in databases of leading institutes

Prescription data 1.5B records from 10,000 doctors and 10M Patients (100 GB)

Clinical trials Currently more than 30k recruiting on ClinicalTrials.gov

Human proteome 160M data points (2.4GB) per sample >3TB raw proteome data in ProteomicsDB

PubMed database >23M articles

Hospital information systems Often more than 50GB

Medical sensor data Scan of a single organ in 1s creates 10GB of raw data Cancer patient records

>160k records at NCT A Federated In-Memory Database Computing Platform for Big Medical Data



Our Approach Analyze Genomes: Real-time Analysis of Big Medical Data

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In-Memory Database

Extensions for Life Sciences

Data Exchange, App Store

Access Control, Data Protection

Fair Use

Statistical Tools

Real-time Analysis

App-spanning User Profiles

Combined and Linked Data

Genome Data

Cellular Pathways

Genome Metadata

Research Publications

Pipeline and Analysis Models

Drugs and Interactions


Drug Response Analysis

Pathway Topology Analysis

Medical Knowledge Cockpit Oncolyzer

Clinical Trial Recruitment

Cohort Analysis

...

Indexed Sources

Combined column and row store

Map/Reduce Single and multi-tenancy

Lightweight compression

Insert only for time travel

Real-time replication

Working on integers

SQL interface on columns and rows

Active/passive data store

Minimal projections

Group key Reduction of software layers

Dynamic multi-threading

Bulk load of data

Object-relational mapping

Text retrieval and extraction engine

No aggregate tables

Data partitioning Any attribute as index

No disk

On-the-fly extensibility

Analytics on historical data

Multi-core/ parallelization

Our Technology In-Memory Database Technology

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Where are all those Clouds go to?



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Gartner's 2014 Hype Cycle for Emerging Technologies

■  Requirements

□  Real-time data analysis

□  Maintained software

■  Restrictions

□  Data privacy

□  Data locality

□  Volume of “big medical data”

■  Solution?

□  Federated In-Memory Database System vs. Cloud Computing

Software Requirements in Life Sciences



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Approach I: Multiple Cloud Service Providers



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Approach II: A Single Service Provider



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CloudSynchron ization

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Multiple Sites Forming the Federated In-Memory Database System (FIMDB)



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Federated In-M em ory D atabase System

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FIMDB: Cloud Service Provider



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■  Change of cloud computing paradigm: Transfer (small) algorithms to (big) data

■  In-Memory Database (IMDB)

□  Landscape of IMDB nodes

□  Stored IMDB procedures and algorithms

□  Master data for applications

■  In-Memory File System (IMDBfs)

□  Integration of file-based tools

□  Managed services directory

□  OS binaries compiled and statically linked for individual platforms

1.  Establish site-to-site VPN connection b/w site and cloud service provider

2.  Mount remote services directory

3.  Install and configure local IMDB instance from services directory

4.  Subscribe to and configure selected managed services

FIMDB: Setup of a New Client



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■  Data partitioning protects sensitive data by storing it on local hardware resources only

■  Supports parallel query execution, i.e. reduced processing time

■  Efficient use of existing hardware resources

FIMDB: Incorporating Local Compute Resources



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■  Brings algorithms to data

■  Forms a single database across individual sites and locations

■  Master data managed by service provider whilst sensitive data resides locally

What to Take Home? Test it Yourself: AnalyzeGenomes.com



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Pros Cons

Single database license Complex operation

Easy to consume services Time-consuming infrastructure setup

Query propagation by IMDB

Only a single source of truth

■  Online: Visit we.analyzegenomes.com for latest research results, slides, videos, tools, and publications

■  Offline: High-Performance In-Memory Genome Data Analysis: In-Memory Data Management Research, Springer,

ISBN: 978-3-319-03034-0, 2014

■  In Person: Join us for Intel Tech Talks at SAPPHIRE booth 625 daily!

□  May 17 12.30pm: A Federated In-Memory Database Computing Platform Enabling Real-time Analysis of Big Medical Data

□  May 18 12.30pm: In-Memory Apps for Next Generation Life Sciences Research

□  May 19 11.30am: In-Memory Apps Supporting Precision Medicine

Where to find additional information?



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Keep in contact with us!

Dr. Matthieu-P. Schapranow Program Manager E-Health & Life Sciences

Hasso Plattner Institute

August-Bebel-Str. 88 14482 Potsdam, Germany

[email protected]

http://we.analyzegenomes.com/



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Date post:	09-Jan-2017
Category:	Healthcare
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