Open Source in Healthcare Research Informatics

pielibraryInternet and Web Development

Dec 4, 2013 (3 years and 11 months ago)

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Copyright © 2010 Recombinant Data Corp. All rights reserved.

December 4, 2013

Dan “The Dude” Housman

Managing Director, Analytical
Applications/Open Source Evangelist

Open Source in Healthcare Research Informatics

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Takeaways


Medical science needs open source to progress



Open source is “secretly” driven by competition



Community building is more critical than features



Change is resisted by established systems/vendors


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Health Science Today

Medicine today is built on hundreds of years of
individual observations



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What we have today with translational medicine data

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AMC
-

Personalized Medicine Vision

6,900,000,000 PPL

3,000,000,000 BP

50,000 PPL/GWAS

The use of
Gefitinib

is only
indicated in a very narrow
population of patients.
Fewer than 10% of NSCLC
(Non small cell lung cancer)
patients have the relevant
mutation. And the therapy is
only applicable in patients
with NSCLC.

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To Err is Human

At least 44,000 people, and
perhaps as many as 98,000
people, die in hospitals each year
as a result of medical errors that
could have been prevented,
according to estimates from two
major studies.


Institute Of Medicine 1999

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To Err is Human

Despite finding small improvements
at the margins

fewer patients dying
from accidental injection of potassium
chloride, reduced infections in
hospitals due to tightened infection
control procedures

it is harder to
see the overall, national impact,
Leape

and Berwick say. "[T]he
groundwork for improving safety has
been laid in these past five years but
progress is frustratingly slow,"


Institute of Medicine Oct. 2005


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To Err is Human



A disturbing report released recently
by (AHRQ), found measurable
improvement in fewer than half of the
38 patient safety measures
examined. Research shows it takes
17 years before evidence
-
based
practices are incorporated into
widespread clinical use.




Institute of Medicine May 2009

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Challenges in healthcare IT and research


How can we run ad
-
hoc comparative effectiveness experiments in
growing EHR systems?



Evidence must be an open process. Inquiry must be a central part
of practice in translational and personalized medicine concepts.



Rapid healthcare system changes will harm patients. How will we
know?



Current expenditures for research are ~$20
-
30Billion and it results
in a pipeline of 30 new drugs per year… many that are similar.



Translation of evidence to practice is lacking.


Something needs to change!

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Openness is needed

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Applications

Indivo PCHR

SMArt (Substitutable Medical Applications)

caBIG®/caTissue (Tissue Bank)

I2b2 Cohorts ++

Profiles Research Networking


Data Management Infrastructure


Pentaho Data Integration


Mirth HL7


Shibboleth

Core Infrastructure


SVN/Hudson/Eclipse Development Tools


Java J2EE


MySQL Postgres


Open Source projects supporting our mission

Core Infrastructure

Data Management Infrastructure

Applications

Indivo

PCHR

caBIG
/
caTissue

Tissue Bank

i2b2

Cohorts ++

SMArt

Substitutable Medical Applications

Profiles Research
Networking

Pentaho

Data Integration

Mirth

HL7

Shibboleth

Single sign
-
on

SVN/Hudson/Eclipse

Development tools

Java

J2EE

MySQL

Postgres

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Precompetitive strategy big picture

Product A, B, and C active, Product D is a closed system

Shared capabilities: Standards, Grid/network, Supplier,
Copyright, Data, Knowledge, Patent,
Software

Product C

Product B

Product A

Shared capabilities: Standards, Grid/network,
Supplier, Copyright, Data, Knowledge,
Patent,
Software

Product D

Closed

System

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Pre
-
competitive systems (outside examples)

Traditional industries


Transportation: Train gauge, rail grid, air traffic control


Manufacturing: Automotive parts, Microprocessor design


High Tech


Networking: TCP/IP, 802.11, plugs (phone, network, USB)


Core software: Linux, Apache, Eclipse


Wireless OS: Android OS vs. iPhone/iPad


Science:


Astronomy: Satellite telescopes, web image archives


Physics: Supercolliders


Biology: NCBI
-

Entrez, EBI, Pubmed

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What is open source software?


Software code

Copyright

Asset ownership (logo, brand, etc.)
Licenses

Organizers/Foundations

Free agents, Companies

Culture
Community

Shared development

Control through involvement

Quality management
Methodology

Warning:





Disruptive


Licenses



Software code


Copyright


Asset ownership (logo, brand, etc.)


Community



Organizers/Foundations


Free agents, Companies


Culture


Methodology



Shared development


Control through involvement


Quality management



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Principles



Free means “Freedom” not “free stuff”


Principle of openness


Principle of transparency


Principle of 'Early and Often’


Expectation of community


Hacktivation energy


Forking (Sugar CRM vs. Tiger CRM)


Free riders


Downloaders

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560,699

people in
228

countries* speaking
182

languages power Drupal

External Open Source Yardstick? Drupal

560,699

people in
228

countries
*

speaking
182

languages power
Drupal

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Six Open Source Secrets from Dries (Summary)


Develop with Drupal


8632 modules


1023 themes


5817 developers


This week


5078 Code commits


7084 Issue comments


There is no quick rich formula:
Build a user conference from in 40 people 2005 to 3,000 in 2010. Have many meet
-
ups. Be patient.



Hurray for growing pains:
Funding comes if you are serving the community and they will support you as you grow out of your current capability.



Build an architecture for evolution:
Allow external groups to be able to submit.



Provide the right tools:
Processes and tools. Replace planning with co
-
ordination.



Make money but pay with trust:
The open source currency is trust.



Leadership trumps management:
Make everyone a respected leader and follower


WWDBD
-

What would Dries Butaert do?

There is no quick rich formula:
Build a user conference from in 40 people 2005 to 3,000 in
2010. Have many meet
-
ups. Be patient.


Hurray for growing pains:
Funding comes if you are serving the community and they will
support you as you grow out of your current capability.


Build an architecture for evolution:
Allow external groups to be able to submit.


Provide the right tools:
Processes and tools. Replace planning with co
-
ordination.


Make money but pay with trust:
The open source currency is trust.


Leadership trumps management:
Make everyone a respected leader and follower

Six Open Source Secrets

from Dries…..(summary)

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World view shift: Vendor vs. Community centric

Vendor

Community

Community

Community

Vendor

Vendor

Community

Vendor

Open Source

trust, $, contributions

Community control

Proprietary

$, patents

Vendor control

Community

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Be conservative in what you do.


Be liberal in what you accept
from others.

Jon Postel (original TCP protocol document)

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Principle of transparency

Transparency is the ability of the community to see whats
going on.



A published road map so they know where the
administrators plan to take the project.



A public defect tracking system so they can report and
review defects.



Published design documentation.



Communication about schedules and hurdles.


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Core Infrastructure open source success


Apache: “A patchy server”. Aggregated patches.

(Growth from a meritocracy)



Eclipse: IBM spin
-
out. pre
-
competitive philosophy.

(IBM vs. Microsoft/Oracle/Sun)



Linux: Resurrect Unix without the balkanization.

(Inspired developer & disciples)



Mozilla: Spin
-
off from former Netscape

(Bubble vs. Microsoft)

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Inspired by pure open source: VA VistA request

Community

Development

Manager

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Custodial Agent
-
Initiated


Sponsored ideas


Sponsored ideas + Code


Unsponsored Ideas


Unsponsored Ideas + Code



Custodial Agent


Projects

Custodial Agent Role

Projects



Custodial Agent
-
Initiated



Sponsored Ideas



Sponsored Ideas + Code



Unsponsored Ideas



Unsponsored Ideas + Code


Custodial

Agent

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Open source consortia: Require governance

Executive
committee

committee

Policies, by laws,
and operating
principles

Shared
consortium
resources and
tools

m1

m2

m3

m4

M n

committee

committee

project

committee

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Bylaw contents

Definition of oversight through a hierarchy of a principle board and committees


Roles, responsibilities, rights of general membership and leadership in organized groups


Intellectual Property guidelines and policies


Long term ownership, control, and stewardship of assets (software, copyright, logo, brand)


Development processes and guidelines for contribution of code


Qualification process for developers to become “committers” to the code base.


Management and ownership of the product roadmap


Approval process to execute chartered projects


Assignment/co
-
ordination of resources for major extension projects.

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Code contribution/release process

Community driven but not chaos

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Incentives to contribute


Developer


Employer/user pays salary


Increase employment value/personal brand


Community acceptance/credit


Obtain support for capability or idea


Project success



Business/Corporation


Reduce upgrade risk/support


PR Credit & branding


Recruit and acquire external talent


Block competitor or alternatives


Transition code to free developers to innovate


Define favorable standards


Science


Protocol compatibility/interoperability


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Data Mgmt. Tools: Kettle

Kettle: Allows for deployable/sharable “free” ETL (Extract
Transform and Load) without dependency on specific
data warehouse implementation (Oracle, MSSQL,
Informatica
,
DataStage
, etc.). With support options from
Pentaho
.


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Beekeeper model from Pentaho

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Pentaho: Beekeeper

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Westinghouse vs. Edison


FUD

1903 Topsy “bad” elephant

electrocuted High voltage AC

1893 Niagra falls contract
rising dominance of AC

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Common FUD by vendors and custom build



No quality or quality control


Testing model 5:1 vs. 1000:1 testers (early and often)




It can’t be made secure/reliable


Linux vs. Windows security holes and fixes (Linux virus)

Websphere severe patches (See quality control)



Without a vendor there is no product roadmap


Eclipse foundation annual release on time w/roadmap.

Release train concept

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More FUD


Prevents or slows development


Source code and roadmap allows for “intelligent design”



Have to "give competitive capabilities away for free“


Only with certain license models



No innovation/just copying


Firefox generates tabbed browsing. Microsoft follows



IT organizations can’t commit without “support”


Easily resolved through professional/commercial support