transmart roadmap presentation amsterdam 2015
TRANSCRIPT
TranSMART Roadmap TRANSMART ANNUAL MEETING 2015
AMSTERDAM, OCTOBER 19, 2015
Kees van Bochove, Chair Architecture Working Group @ tranSMART Foundation | CEO @ The Hyve
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!
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
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.