Free/Libre Open Source Software in Medical Informatics ...Open source Software Development cycle....

Free/Libre Open Source Software in Medical Informatics Research and Education

Joint Workshop of

EFMI EDU WG & EFMI LIFOSS WG

Thomas Karopka, John Mantas, Arie Hasman, Ricardo Cruz-Correia , Christian Lovis, Holger Schmuhl and Björn Bergh

EFMI LIFOSS WG

EFMI EDU WG

IMIA OS WG http://www.imia-medinfo.org/new2/node/147

Evaluate

Engage

Extend

Explain

Explore

Learing cycle

Kolb

Test

Share

Modify/Improve

Analyze

Inspect

Open sourceSoftware

Developmentcycle

Examples - Community

MedFLOSS.org

266projects

85 serviceproviders

142publications

11events

FLOSS-HC

Swarm intelligenceSwarm intelligence

Conclusions

There are excellent tools and projects in the domain of Free/Libre Open Source Software for Health Care

However, the potential impact is quite limited so far Ecosystem building is of paramount importance

This includes responding to end user needs, modular development, financing/funding, regional capacity building and education, dissemination

Use the power of networking

Thank you for your attention!

Mille grazie!

Swarm up!

1© Hôpitaux universitaires de Genève, service des science de l’information médicale

Christian LovisService des sciences de l’information médicales

Open source @ University Hospitals of Geneva


OS@HUG

Using open source Electronic Patient Record Numerous Apps

Building open source several large «experiences»


Using Open Source

Large EHR Java based Components, services, messages Cloud ready

numerous OS sources such as hybernate jBoss Process Manager etc …


Building Open Source

Some «emblematic» developments Success

http://www.osirix-viewer.com/


Building Open Source

Less success .. … ….

http://www.bolinos.ch

BolinOS, Medical Content Management System, ~50’000 downloads in 2004, +/- sleeping since 5 years because of lack of resources.


Challenges

Using OS in production/critic systems liability sustainability (example: Sun – Oracle) backwards compatibility etc

Producing OS increasing users -> increasing costs need for resources to provide sustainable system


Using OS – a delicate necessity

Health Informatics for Development:

Challenges and Opportunities for Free Software in

Health Care Delivery

Thomas Karopka,

Chair of IMIA Open Source working group (IMIA OS WG)

Chair of EFMI Libre/Free Open Source working group (EFMI LIFOSS WG)

Germany

IMIA OS WG http://www.imia-medinfo.org/new2/node/147

EFMI LIFOSS WG

MedFLOSS.org

Free/Libre Open Source Softwarein

Health Care (FLOSS-HC)

Objective:

Provide good quality health care to everyone in needin the most efficient way

11.01.2012 6 International Workshop on E-Health in Emerging Economies – IWEEE 2012 | Granada, Spain, January 11

Challenges:

Fragmentation – How to gather a critical mass ?Community – How to create a community ?Usability – Do we really address end user needs ?

„Technology focus“ or „user focus“ ?Governance – How to implement the vision ?Education – How to train endusers ?Finance – How to get funding ?Outreach – How to reach the end user ?Dissemination – How to spread the word ?Impact – How to set up a sustainable ecosystem ?


Fragmentation

Examples - Community

Examples – Community: Humanitarian FOSS


Source: http://www.ipath.network.org

Example – Education: iPath – Telemedicine Platform

Collaborative platform for exchange of medical knowledge, distance consultations, group discussions and distance teaching in medicine

Active Users: 3591Groups: 150

Originally developed at the University of Basel, now offered by basysdata

Example – Education: Big Blue Button

Examples – User Needs: Ushahidi

Examples – Outreach: IntraHealth

Examples – Funding: IntraHealth

Examples – Governance: Sahana

Example – Dissemination: MobileActive.org

Education – Capacity Building

Example – Impact: GNU Health & IWEEE

ProprietoryHealth IT

FLOSS-HC

Swarm intelligenceSwarm intelligence

MedFLOSS.org

266projects

85 serviceproviders

142publications

11events

Conclusions

FLOSS-HC is doing well! – But we can even do better!!

The potential impact is quite limited so far

Ecosystem building is of paramount importance This includes responding to end user needs,

modular development, financing/funding, regional capacity building and education, dissemination


A big

Muchas GraciasTo all projects and the people behind

To all people engaging in providing health care

To YOU

Conclusions

There are excellent tools and projects in the domain of Free/Libre Open Source Software for Health Care

However, the potential impact is quite limited so far Ecosystem building is of paramount importance

This includes responding to end user needs, modular development, financing/funding, regional capacity building and education, dissemination



Muchas gracias!

Swarm up!

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Medfloss.org

Discussion

References

Successfully applying FLOSS principles inmedical informatics research projects

EFMI LIFOSS/EDU Workshop: Free/Libre Open SourceSoftware in Medical Informatics Research and Education

H. Schmuhl1,2,3, H. Demski1,3, B. Bergh2,4, C. Hildebrand1

1Laboratory for Medical Information Systems, Institute of Biological and Medical Imaging, HelmholtzZentrum Munchen (GmbH); 2Dept. for Information Technology and Medical Engineering, University

Hospital Heidelberg; 3EFMI Libre/Free and Open Source Software in Health Informatics WG; 4OpeneHealth Foundation

EFMI MIE 2012; 29th of August 2012; Pisa, Italy

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Medfloss.org

Discussion

References

Outline

1 Introduction

2 FLOSS in Research

3 Medfloss.org

4 Discussion

5 References

FLOSS inResearch

H. Schmuhl

Outline

Introduction

References inliterature

Free and OpenSource software

Typical set up ofa researchproject

FLOSS inResearch

Medfloss.org

Discussion

References

Any relevance in medical informatics?References in literature

Number of publications containing the keyword “Open Source”at PubMed (MEDLINE)1

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011

200

400

600

Year

#o

far

ticl

es

1http://www.ncbi.nlm.nih.gov/pubmed/, last visited 03/2012

http://www.ncbi.nlm.nih.gov/pubmed/

FLOSS inResearch

H. Schmuhl

Outline

Introduction




FLOSS inResearch

Medfloss.org

Discussion

References

Free and Open Source softwareUlilization in research projects

Why FLOSS?

Continuously growing relevance in research

High potential also in the field of medical informaticsresearch

Intention of this talk

Starting point for utilizing FLOSS in your own researchprojects

Basis for todays discussion (round table)

FLOSS inResearch

H. Schmuhl

Outline

Introduction




FLOSS inResearch

Medfloss.org

Discussion

References

Typical set up of a research project

Financed by public funds (EU, National)

Partners from private and public sector

Complex information systems (modular architecture)

Common requirements for core functionality

Standardized interfaces and data structures

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Opportunities

Threats

Licensing

How to creategood opensource software

Projects inHeidelberg

Projects inMunich

Medfloss.org

Discussion

References

OpportunitiesFLOSS in Research

Iterative and collaborative software development; Effectiveuse of public funds

Utilization of FLOSS components in areas of exploration,prototyping, testing and piloting; Faster project evolutionand research progress

Fallback solution in case of delays in development or lossof partner

Guaranteed re-use authorization/permit for future work

Development and testing support by community; Crowdsourcing

Attract and motivate skilled software developers

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Opportunities

Threats

Licensing



Projects inMunich

Medfloss.org

Discussion

References

ThreatsFLOSS in Research

Dozens of repositories with millions of projects; Spoilt forchoice

External projects may develop in wrong direction, beabandoned or forked; Dependency on community

Responsible colleague(s) may leave; Dependency onpeople/skills

Partners may want to commercially exploit results;Intellectual property concerns

Industry partners may not ��like support FLOSScomponents; Conservative nature of vendors

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Opportunities

Threats

Licensing



Projects inMunich

Medfloss.org

Discussion

References

LicensingFLOSS in Research

Common FLOSS licenses vary in allowance of

Linking with code using a different licenseReleasing changes under a different license

Types and examples

Permissive free software licenses: developments can bereleased under different licenses, also proprietary (BSD,MIT, Apache)Copyleft licenses: developments must be released undersame terms (GPL, LGPL, MPL)

More information

Wikipedia “Comparison of free and open-source softwarelicenses”2

St. Laurent “Understanding open source and free softwarelicensing”3 [1]

2http://en.wikipedia.org/wiki/Comparison of free software licences, last visited 08/20123http://oreilly.com/openbook/osfreesoft/book/index.html, last visited 08/2012

http://en.wikipedia.org/wiki/Comparison_of_free_software_licences

http://oreilly.com/openbook/osfreesoft/book/index.html

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Opportunities

Threats

Licensing



Projects inMunich

Medfloss.org

Discussion

References

How to create good open source software“The Cathedral and the Bazaar” by Eric S. Raymond [2]

Excerpt of described guidelines4:

Every good work of software starts by scratching adeveloper’s personal itch.

Good programmers know what to write. Great ones knowwhat to rewrite (and reuse).

When you lose interest in a program, your last duty to it isto hand it off to a competent successor.

Treating your users as co-developers is your least-hassleroute to rapid code improvement and effective debugging.

Release early. Release often. And listen to your customers.

Smart data structures and dumb code works a lot betterthan the other way around.

4http://www.catb.org/esr/writings/homesteading/, last visited 08/2012

http://www.catb.org/esr/writings/homesteading/

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Opportunities

Threats

Licensing



Projects inMunich

Medfloss.org

Discussion

References

COMS and PORSProjects in Heidelberg

Consent Management Suite (COMS)5

for the management of patients’ consent

Provider and Organization Registry Service (PORS)6

for the identification of healthcare providers

Central components of the standards-based PEHRinfrastructure for the Rhein-Neckar region [3, 4]

Developed by the Dept. for Information Technology andMedical Engineering, University Hospital Heidelberg

Released via Open eHealth Foundation

5http://www.openehealth.org/display/COMS/, last visited 08/20126http://www.openehealth.org/display/PORS/, last visited 08/2012

http://www.openehealth.org/display/COMS/

http://www.openehealth.org/display/PORS/

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Opportunities

Threats

Licensing



Projects inMunich

Medfloss.org

Discussion

References

EHRflex and Medfloss.orgProjects in Munich

EHRflexArchetype-based clinical registry system (EHR) independent ofa particular reference model, uses archetypes as guidelines forthe automatic generation of web interfaces7

Medfloss.org

Comprehensive and structured overview of FLOSS projects inthe domains of medical informatics and health care

Developed by the Laboratory for Medical InformationSystems, Helmholtz Zentrum Munchen

7http://ehrflex.sourceforge.net/, last visited 08/2012

http://ehrflex.sourceforge.net/

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Medfloss.org

Discussion

References

Medfloss.orgThe Medfloss.org Web site [5, 6]

Online since Feb. 20108, based on Drupal

Users can add and modify any content, free registrationrequired to prevent Spam

Language: English

Provided in cooperation with the IMIA OS WG, EFMILIFOSS WG, Helmholtz Zentrum Munchen and theUniversity Hospital Heidelberg.

8http://www.medfloss.org/, last visited 08/2012

http://www.medfloss.org/

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Medfloss.org

Discussion

References

Medfloss.orgStructured and interlinked information

Tags in numerous categories, like Application Type e.g.“PACS”, Enterprise Function [7] e.g. “MedicationManagement”, supported Standard e.g.“HL7”/“DICOM”, . . .

275 projects

89 professional service providers

171 scientific publications

27 events (conferences, trade shows)

43 organizations and other resources (Web sites, etc.)

Linux distributions

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Medfloss.org

Discussion

References

DiscussionQs & As and discussion


Helmholtz Zentrum MunchenGerman Research Center for Environmental HealthInstitute of Biological and Medical ImagingLaboratory for Medical Information SystemsIngolstadter Landstr. 185764 NeuherbergGermany

Holger SchmuhlMail: [email protected]

mailto:[email protected]

FLOSS inResearch

H. Schmuhl

Outline

Introduction

FLOSS inResearch

Medfloss.org

Discussion

References

References

[1] St Laurent AM.Understanding open source and free software licensing.1st ed. Beijing: O’Reilly; 2004.

[2] Raymond ES.The cathedral and the bazaar: musings on Linux and Open Source by an accidental revolutionary.Rev. ed ed. Beijing: O’Reilly; 2001.

[3] Heinze O, Brandner A, Bergh B.Establishing a personal electronic health record in the Rhine-Neckar region.Stud Health Technol Inform. 2009;150:119.

[4] Heinze O, Birkle M, Koster L, Bergh B.Architecture of a consent management suite and integration into IHE-based Regional Health InformationNetworks.BMC Med Inform Decis Mak. 2011;11:58.

[5] Schmuhl H. Medfloss.org – A comprehensive platform for medical free/libre and open source software[Presentation at Med-e-Tel 2010];.Available from: http://goo.gl/opyFo.

[6] Demski H, Hildebrand C, Jossif A, R E.Information on Open Source Solutions in Healthcare - the OSSHealth Repository.In: Med-e-Tel; 2010. .

[7] Haux R, Ammenwerth E, Winter A, Brigl B.Strategic information management in hospitals: an introduction to hospital information systems.Health informatics series. New York: Springer; 2003.

http://goo.gl/opyFo

http://cintesis.med.up.ptPorto, Portugal

Free/Libre Open Source Software in Medical Informatics Research and

Education Workshop

the UPorto experience on Education

Ricardo João Cruz Correia

MIE 2012 @ Pisa, Italy

29th August 2012


Educational Setting @ UPorto

● Health professionals● Medicine Degree

– Medical Informatics (1st year medical students)

● PhD program on Clinical and Health Services Research– Clinical Research Informatics

● Engenieers & Health Professionals

● MSc Medical Informatics – Health Information Systems

– Programming for Health

● Summer Courses– Interoperability

– Medical Informatics


Medicine Degree

● E-learning● Moodle● Linux+Moodle for Exams

● Productivity tools● LibreOffice

– Base for the creation of relational databases

● OpenProj– For students to manage their

projects

● Have adapted moodle to our authentication mechanism

● Linked it the student management system

● Programmed reports that help us discovery how much copying btw students

● Great control over the tool

● Work on Linux, Mac and Windows

● Easy to use

● Easy to distribute


Clinical Research Informatics @ PhD

● Use of ● Libre Base

● Tools to test the creation of OpenEHR Archetypes and Templates


Programming for Health @ Msc MI

● Use to teach HL7● Mirth – Open source HL7 Interface Engine● HAPI – The free, open HL7 parser and library

for Java

● Program modules for● CMS (e.g. Joomla)● Wikis


Projects @ Msc MI

● GEODÁDIVAS – OpenSource system for the management of blood donations● http://sourceforge.net/projects/geodadivas

● SimECG – ECG Simulator for educational

purposes

● http://sourceforge.net/projects/simecg/● > 11.000 downloads

http://sourceforge.net/projects/simecg/


Near Future

Medical course

● Learn how to use EPR by using OpenEMR / VistA

PhD

● Learn how to use OpenClinica

MSc in Medical Informatics

● Programming for health

– Develop modules for open source patient records


Discussion

● On the use of open source

+ Most tools used, exist in many platforms

● Programming

+ Helps to teach programming because developers:

+ must follow the predefined structure (e.g. MVC)+ must read “good” code and hopefully learn

● Everything is easier when standards exist

● Having access to what software does is somehow related to evidence based medicine

Free/Libre Open Source Software in Medical Informatics ...Open source Software Development cycle....

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