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ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure
Harry Freitas da Cruz, Milena Kraus, Dr. Matt...
Heart
Failure
Sleeping
disorder
Fibrosis
Blood
pressure
Blood
volume
Gene ex-
pression
Hyper-
trophyCalcium
meta-
bolism
E...
■  Process definition through
user interviews
■  Identification of time-consuming and
manual process steps
■  Requirements f...
■  In-Memory Database (IMDB) as
data integration platform
■  Automatic synchronization of
partner data
■  Event-driven not...
Combined column
and row store
Map/Reduce Single and
multi-tenancy
Lightweight
compression
Insert only
for time travel
Real...
■  IMDB provides
□  Data integration platform, and
□  Real-time analysis
■  Data is automatically integrated in IMDB throu...
■  User can subscribe for specific events to receive instant e-mail notifications
■  Amongst others events are
□  New or upd...
3. Reproducible Data Processing:
Transfer of Processing Logic to Cloud Platform
Freitas da Cruz, Kraus,
Schapranow, Oct 5,...
■  Analysis applications for proteome and
modeling data
■  Statistical and machine learning
methods to derive new insights...
■  Streamlined research process for systems
medicine (indication heart failure)
■  Systematic integration of partner data ...
Let us stay in contact!
Freitas da Cruz, Kraus,
Schapranow, Oct 5,
2016
ICT Platform to Enable
Consortium Work for
Systems...
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ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure

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The slide deck "ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure" was presented on Oct 5, 2016 at the 2016 e:Med Meeting on Systems Medicine in Kiel, Germany.

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

  1. 1. 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 A R T + T RAM S + S M
  2. 2. 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 2
  3. 3. ■  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 3
  4. 4. ■  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
  5. 5. 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 + ++ + + P v +++ t SQL x x T disk 5 Freitas da Cruz, Kraus, Schapranow, Oct 5, 2016 ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure
  6. 6. ■  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
  7. 7. ■  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
  8. 8. 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 8 ■  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
  9. 9. ■  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
  10. 10. ■  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 10
  11. 11. 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 11 Harry Freitas da Cruz PhD cand. Harry.FreitasDaCruz@hpi.de Dr. Matthieu-P. Schapranow Program Manager E-Health & Life Sciences schapranow@hpi.de

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