ict platform to enable consortium work for systems medicine of heart failure
TRANSCRIPT
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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T R A M
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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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Freitas da Cruz, Kraus, Schapranow, Oct 5, 2016
ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure
■ 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:
Freitas da Cruz, Kraus, Schapranow, Oct 5, 2016
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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. [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]