ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure

ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure

Harry Freitas da Cruz, Milena Kraus, Dr. Matthieu-P. Schapranow Hasso Plattner Institute

e:Med Meeting on Systems Medicine 2016

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Heart Failure

Sleeping disorder

Fibrosis

Blood pressure

Blood volume

Gene ex-pression

Hyper-trophy Calcium

meta-bolism

Energy meta-bolism

Iron deficiency

Vitamin-D deficiency

Gender

Epi-genetics

■  Integrated systems medicine based on real-time analysis of healthcare data

■  Initial funding period: Mar ‘15 – Feb ‘18

■  Funded consortium partners:

Systems Medicine Approach for Heart Failure (SMART) Project Overview

Freitas da Cruz, Kraus, Schapranow, Oct 5, 2016


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■  Process definition through user interviews

■  Identification of time-consuming and manual process steps

■  Requirements for a computer-aided research process:

1.  Sharing of data

2.  Improved communication

3.  Reproducible data processing

Requirements Engineering for System Medicine Computer-aided Systems Medicine Process



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■  In-Memory Database (IMDB) as data integration platform

■  Automatic synchronization of partner data

■  Event-driven notifications

■  Specific real-time analysis workflows, e.g. for RNAseq

SMART Platform



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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 Foundation: In-Memory Database Technology

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SQL

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■  IMDB provides

□  Data integration platform, and

□  Real-time analysis

■  Data is automatically integrated in IMDB through sync client

■  Automatic harmonization of partner data

■  SMART platform provides central data access for all partners

1. Sharing Data: IMDB as Foundation for our SMART platform



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■  User can subscribe for specific events to receive instant e-mail notifications

■  Amongst others events are

□  New or updated patient data is available,

□  Analysis results from consortium partners are provided, or

□  Completion of processing tasks.

2. Improved Communication: Event-driven User Notification



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3. Reproducible Data Processing: Transfer of Processing Logic to Cloud Platform



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■  Example: Tuxedo protocol for processing of RNASeq data

■  Standardized model using Business Process Modeling and Notation (BPMN)

■  Use of standardized pipeline models enable reproducible research

■  Specific analysis extensions to enable real-time data analysis

■  Further analysis applications:

□  Proteome data,

□  Modeling of results, and

□  Graphical data exploration of data

■  Analysis applications for proteome and modeling data

■  Statistical and machine learning methods to derive new insights

■  Graphical exploration of data and analysis results

Future Work Real-time Analysis Applications



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■  Streamlined research process for systems medicine (indication heart failure)

■  Systematic integration of partner data from heterogeneous sources into central software infrastructure

■  Event-driven notifications to guarantee flow of process steps

■  Reproducible research through standardized processing and analysis pipelines

What to take home Re-usable SMART artifacts:



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Let us stay in contact!



Hasso Plattner Institute Enterprise Platform and Integration Concepts Chair August-Bebel-Str. 88 14482 Potsdam

Milena Kraus PhD cand. [email protected]

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Harry Freitas da Cruz PhD cand. [email protected]

Dr. Matthieu-P. Schapranow Program Manager E-Health & Life Sciences [email protected]

Health & Medicine

ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure