Date post: | 19-Jan-2015 |
Category: |
Health & Medicine |
Upload: | kees-van-bochove |
View: | 317 times |
Download: | 0 times |
TranSMART: how open source so3ware
revolu6onizes drug discovery through cross-‐pharma collabora6on
Kees van Bochove, CEO The Hyve October 23, 2013, Princeton
The Open Source Defini6on 1. Free Redistribu6on 2. Availability of Source Code
3. Allow Derived Works
4. Integrity of The Author's Source Code
5. No Discrimina6on Against Persons or Groups
6. No Discrimina6on Against Fields of Endeavor
7. Redistribu6on of License
8. License Must Not Be Specific to a Product
9. License Must Not Restrict Other So3ware
10. License Must Be Technology-‐Neutral
Open Source
• Source code for so3ware is openly accessible and reusable for everyone
• Contrasts with tradi6onal IT business model: selling so3ware ‘in a shrink-‐wrapped box’
• For IT vendors, revenue is earned with services rather than with products
• Example of well-‐known open source products: Linux (e.g. RedHat, Ubuntu, Android), Firefox, WordPress, OpenOffice, VLC, OpenStack
OpenStack Contribu6ons
Source: Bitergia, hfp://blog.bitergia.com/2013/10/17/the-‐openstack-‐havana-‐release
How does open source work with scien6sts in academia?
Let’s zoom in on a well-‐known bioinforma6cs problem
In 2003… (Ancient history; before Facebook)
Yet Another ‘New’ Web-‐based Solu6on for the Management of Microarray Data ?!
Not Invented Here Syndrome
Image from Rob Hoo3, CTO Netherlands Bioinforma6cs Centre hfp://nothinkingbeyondthispoint.blogspot.nl/2011/11/decision-‐tree-‐for-‐scien6fic.html
Different Non-‐Func6onal Requirements
• Bioinforma6cian in academics: solve a novel problem or at least create a novel solu6on that has publica6on value – So3ware should demonstrate working principle
• Bioinforma6cian / IT Services in pharma/clinic: – So3ware should allow tes6ng of hypotheses, and should be well tested, maintainable, extensible, scalable etc.
share
reuse
specialize
Sharing?! Pharma IT as the proverbial fortress.
• Browse clinical trials • Import / load clinical trial data • Define virtual cohorts • Perform exploratory analy6cs • Search / view published analysis results • Support for 'omics' data • Load public data -‐ TCGA, 1000 Genomes
$$ $$ $$ $$ $$ $$
• Browse clinical trials • Import / load clinical trial data • Define virtual cohorts • Perform exploratory analy6cs • Search / view published analysis results • Support for 'omics' data • Load public data -‐ TCGA, 1000 Genomes
$$ $$ $$ $$ $$ $$ $$$$$$$$$$$ $$$$$$$$$$$
There has to be a befer way.
is now Open Source!
No-‐brainer, zero cost!
Ehm.. wait a minute…
February 2012
Janssen makes a bold move.
TranSMART Open Source History
• February 2012: J&J releases tranSMART as open source on GitHub under GPL v3
• December 2012: CTMM TraIT project decides to use tranSMART as core infrastructure component
• January 2013: IMI eTRIKS starts, uses tranSMART as core infrastructure component
• February 2013: kickoff of tranSMART Founda6on, U. Michigan publishes PostgreSQL port
• March 2013: IMI EMIF kickoff, tranSMART is used as data integra6on component
VUmc
Sanofi
Recombinant / Deloitte
University of Michigan
Thomson Reuters Pfizer Astra
Zeneca
CDISC
University of Luxembourgh
Philips Johnson & Johnson
The Hyve
Amsterdam, June 2013: tranSMART Workshop
Afendees from 10 Pharma companies, 11 University Medical Centers and 12 IT companies
hfp://lanyrd.com/2013/transmart
TranSMART in a nutshell
• Datawarehouse bringing together scien6sts from clinical sciences, preclinical research and discovery – around the data
• Combina6on of internal datasets and documents with public datasets and knowledge
• Tailored to both biologists/clinicians and bioinforma6cians
• Dual nature: in use for transla6onal research in both pharma and hospitals/clinic
eTRIKS Consor6um
tranSMART Founda6on Board
Brian Athey, PhD, University of Michigan
Michael Braxenthaler, PhD, Roche, Pistoia Alliance
Kevin Smith, MSIS, University of Michigan
Ashley George, PhD, GlaxoSmithKline, Pistoia Alliance
Keith Elliston, PhD, Seneca Creek Research
Yike Guo, PhD, Imperial College London
Center for Translational Molecular Medicine (CTMM)
• Public-private consortium • Dedicated to the development of Molecular Diagnostics and
Molecular Imaging technologies
• Focusing on the transla6onal aspects of molecular medicine.
• 120 partners – universi6es, academic medical centers,
medical technology enterprises and chemical and pharmaceu6cal companies.
• Budget 300 M€
• 22 projects / research consor6a
• TraIT is the Translational Research IT project supporting these projects with a joint IT infrastructure
TraIT February 2013: 26 partners
Growing TraIT project team
EUR 16 million / 4 years
CTMM TraIT Goal
• To build an IT infrastructure for transla6onal research for all 20 CTMM disease projects and other major Dutch ini6a6ves and ins6tu6ons, such as all UMC’s, NKI, De Maastricht Studie etc.
• Data integra6on and viewing is done with a.o. tranSMART.
• Approach: Think big, start small, act now
TraIT ‘Founda6on Team’
2 FTE
4 FTE
2 FTE
• Core infrastructure development: adopt & adapt tranSMART, Galaxy, OpenClinica, BMIA, etc.
• Distributed Scrum Team
TraIT tools & applica6ons: the landscape
Hospital (IT) Transla6onal Research (IT) data domains
clinical data
imaging data
experimental data
biobanking
integrated data
transla<onal analy<cs workbench
HIS
PACS
LIS
Galaxy
tranSMART/ cohort explorer
R tranSMART/i2b2 datware house CBM-‐NL
OpenClinica
NBIA + AIM
e.g. PhenotypeDB, Annai Systems
e.g. Galaxy, Chipster
Samples (IT)
Pseudonymization
Public Data
BIMS
Day to day virtual collabora6on
Day to day virtual collabora6on
TranSMART seems to do well and certainly has a lot of momentum at
this point. It s6ll needs a lot of work though, to
ensure long term success…
So… is open source a silver bullet to make so3ware collabora6ons work?
Let’s look at a couple other projects.
What about all these great FP6, FP7, IMI, … projects?
Source code of major projects is readily available on GitHub
That’s great! But… I’m afraid it’s s6ll up to you and me to put the pieces together.
Phenotype Database Wrifen in Grails, supports several types of omics data, provides data integra6on and visualiza6on, has R, Groovy and PHP API’s. Very similar to tranSMART
hfp://phenotypefounda6on.org
R and Bioconductor
Who doesn’t love R?
Website looks as if dates from Stone Age. Must be those LaTeX-‐loving physicists.
Very ac6ve community, and… lots of packages.
Governance of R community
Brian Ripley: “The R Project is governed by a self-‐perpetua6ng oligarchy, a group with a lot of power. R was principally developed for the benefit of the core team.”
As cited on hfp://blog.revolu6onanaly6cs.com/2011/08/brian-‐ripley-‐on-‐the-‐r-‐development-‐process.html
Galaxy
Galaxy is the most widely used open source bioinforma6cs web interface AFAIK.
Probably in no small amount thanks to their con6nuous dedica6on to
improving the UI. But there’s something else.
Galaxy Toolshed
I2B2 (from Harvard) is deployed in ~100 medical centers across U.S.
I2B2 is clinical and genomics data repository and an important cornerstone of tranSMART.
Apps in a hospital: SMART
• SMART = Subs6tutable Medical Apps Reusable Technologies
• Write app once, and run it on any SMART-‐supported EHR system!
• Interfaces with major EHR vendors to get a common Applica6on Programming Interface (API)
h?p://smartplaAorms.org hfps://www.|ordnet.com/ workdetail/harvard-‐medical-‐school
Pa6ent Level View
App inside hospital firewall: Cardiac Risk
• An open source CMS (Content Management System) wrifen in Python, nowadays backing thousands of produc6on grade websites
• Started by 2 developers in 2000, now an ac6ve open source project with hundreds of ac6ve developers
• In 2004, the Plone Founda6on was formed to formalize IP and secure the future of Plone
• Plone Collec6ve has hundreds of plugins
What do all these success stories have in common? Bioconductor Packages
Galaxy Toolshed
Plone Collec6ve
Drupal Modules
SMART Apps
Success factors Lessons learned about open source projects
• Solve an unmet business need • Strong, ac6ve community
• Engage mul6ple vendors
• Enable real 6me collabora6on
• Modular architecture: ‘app store’, data marketplace etc.
• Sustainable funding / business model
• And some good luck!