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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-
trophyCalcium
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
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
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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
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
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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
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
4

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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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disk
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Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure

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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
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
6

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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
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
7

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3. Reproducible Data Processing:
Transfer of Processing Logic to Cloud Platform
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
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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

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■ 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
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
9

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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:
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
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Let us stay in contact!
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems Medicine of
Heart Failure
Hasso Plattner Institute
Enterprise Platform and
Integration Concepts Chair
August-Bebel-Str. 88
14482 Potsdam
Milena Kraus
PhD cand.
Milena.Kraus@hpi.de
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Harry Freitas da Cruz
PhD cand.
Harry.FreitasDaCruz@hpi.de
Dr. Matthieu-P. Schapranow
Program Manager
E-Health & Life Sciences
schapranow@hpi.de