transmart roadmap presentation amsterdam 2015

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TranSMART Roadmap TRANSMART ANNUAL MEETING 2015 AMSTERDAM, OCTOBER 19, 2015 Kees van Bochove, Chair Architecture Working Group @ tranSMART Foundation | CEO @ The Hyve

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Page 1: TranSMART Roadmap Presentation Amsterdam 2015

TranSMART Roadmap TRANSMART ANNUAL MEETING 2015

AMSTERDAM, OCTOBER 19, 2015

Kees van Bochove, Chair Architecture Working Group @ tranSMART Foundation | CEO @ The Hyve

Page 2: TranSMART Roadmap Presentation Amsterdam 2015

What is tranSMART? APPLICATION?

PLATFORM?

COMMUNITY?

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TranSMART Platform: Scientific Function

CLINICAL GENETICS SENSORS IMAGING

DATA

UNDER STANDING BIOLOGY MEDICINE

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TranSMART Platform: Business Function u  Share data in consortia & collaborations: academia,

pharma, biotech…

u  Store data for research purposes within an organization

and allow users to explore and download data

u  Computational facility: Explore data, perform analytics,

test hypotheses

u  Commons function: share public data & annotations as

well as proven analytics workflows across the community

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Open Source in Precision Medicine

Study design:

Biobanking:

Scientific compute:

Data visualisation:

Workflow / NGS:

Datawarehousing:

Imaging:

Clinical - eCRF & apps:

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Analytics – what makes it hard? u  Clinical Genomics: how can I accurately find and reliably measure clinically relevant

genomic variations using high-throughput techniques? (genetic testing, population study)

u  Cancer Genomics: how can I reliably sequence the cancer genome and compare with

germline to identify cancer subspecies? (diagnostics / precision medicine)

u  Molecular Biology: what is the relation between the properties of the DNA and

transcription and translation processes in the cell? (gene-centric, epigenetics, multi-omics)

u  Evolutionary Genetics: how can we quantify and explain inter-species and intra-species

genetic variations?

u  Bioinformatics: how can I improve signal to noise ratio in sequencing pipelines and

accurately call genomic variants?

u  Computer Science: which compute architecture fits data analysis & visualization needs?

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TranSMART as an open source translational medicine platform

u  Robust handling of lots of different data types

u  Security, scalability, interoperability and federation built in as

core principles, facilitating good data management

u  Plug-in architecture to provide a consistent user experience

(functionality, layout) and developer experience (APIs)

u  Ontology management: vocabularies, public data & annotations

u  Great documentation & ease of use!

Page 8: TranSMART Roadmap Presentation Amsterdam 2015

Amsterdam, June 2013: tranSMART Workshop Attendees from 10 Pharma companies, 11 University Medical Centers and 12 IT companies

http://lanyrd.com/2013/transmart

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VUmc

Sanofi

Recombinant / Deloitte

University of

Michigan

Thomson Reuters Pfizer Astra

Zeneca CDISC

University of Luxembourg

Philips Johnson &

Johnson

The Hyve ~70

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TranSMART 1.2 Development

Prioritized features in Paris, Nov 2013

Summer 2014 - Organized Hackathons, Testathons

Production v1.2 released (Aug’14)

Implemented Code Governance (Sep 2014) • Regular bug fixes and

patches • Documentation • Tutorials • Training

Regular Scheduled Updates to v1.2 (2015)

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January 2015, Utrecht, The Hyve: TranSMART 2.0 Architecture Workshop

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Architecture Workshop Recommendations u  Make it easier to for new developers and less tedious for our current

developers to add features and contribute to tranSMART

u  Improve the maintainability of the code base

u  Make tranSMART more suitable as a component in larger IT landscapes

u  Standardize the way of working in the open source community

u  Replace the current user interface with a modern web application to

enhance the user experience

u  Improve testability and robustness

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EU Project Informatics Alignment Workshop April 2015, Imperial College London u  18 European projects all using tranSMART to share data!

u  Top requests:

u  Support for large volumes of NGS data (‘scalable genomics backend’)

u  Better handling of longitudinal data

u  Better handling of cross-trial data loading & browsing

u  Improve cohort selection on high dimensional data

u  Improve ETL, logging, auditing, visualizations etc. etc.

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TranSMART 1.3 (expected Q1 2016) u  New Analytics Framework: improved user experience of

Advanced Workflows

u  Improvements to the APIs and functionality for GWAS

u  SmartR: interactive analytics workflows

u  Several visual improvements (e.g. summary statistics)

u  Improvements for Federation

u  Prototype of new cohort selection interface

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New Cohort Selection Interface - alpha

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TranSMART Platform: Scientific Function

CLINICAL GENETICS SENSORS IMAGING

DATA

UNDER STANDING BIOLOGY MEDICINE

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New version of tranSMART Platform

SECURE SCALABLE MODULAR &

INTEROPERABLE

DOCUMENTED

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Text TranSMART Enterprise Platform u  Be the platform where enterprise-wide clinical and high-dimensional biomarker data can be loaded,

curated, harmonized, annotated, and exported.

u  Be the platform where scientists can browse, discover, integrate, and collate translational data across

studies and platforms, for further visualization and analysis.

u  Be a commercial-quality, secure, high-performance, and fully supported platform that scales to

1000’s of studies and 100’s of users, with flexible and scalable deployment.

u  Provide well-documented APIs designed to encourage integration with existing analysis & visualization

tools, and IT infrastructure.

u  Be supported by a professional-quality Tier I-III support infrastructure

u  Have professional developed and maintained documentation

u  Utilize a professional and disciplined approach to development and support.