The PSDM group of the Biometrics Section (BMS) of the Netherlands Society for Statistics and Operations Research (VVS/OR) cordially invited you to participate in

Open Source Software in Clinical Research:
cost-saving opportunity or high-risk solution?

Tuesday June 19th, 2012
hosted by Julius Clinical Research B.V., Zeist


Final Program
(final abstracts and presentations available)

12:30 Registration, coffee & tea
13:00 The use of Open Source Software in the Pharmaceutical Industry and the Innovative Medicines Initiative Projects
Ann Marie Martin & Philippe Lamote,Innovative Medicines Initiative, Brussels, Belgiumpresentation “IMI”
presentation “Innovation and OpenSource”

Ann Marie Martin & Philippe Lamote,
Innovative Medicines Initiative, Brussels, Belgium

Title: The use of Open Source Software in the Pharmaceutical Industry and the Innovative Medicines Initiative Projects.


The definition of open source. Where is it used? What is open source development? Open source software licenses and dual licensing. Where in the pharmaceutical industry is open source software used? When does it work well and when does it not? Examples of famous open source software development projects, successful use and adoption as well as less successful examples. The concept of open is gaining popularity: we now speak about open data, open publication, open collaboration.
The Innovative Medicines Initiative Joint Undertaking is a public-private partnership between the European Union and the European Federation of Pharmaceutical Industries and Associations (EFPIA). Through its innovative funding scheme, IMI supports more efficient drug discovery and the development of safer and better medicines for patients. The total IMI budget for the period 2008-2017 is €2 billion, including €1 billion contributed by the European Commission’s Seventh Framework Programme and €1 billion provided, mainly as in-kind contributions, by the industry.
Open source software is used in several IMI projects or developed through IMI projects. The projects are partnerships between academic, small medium enterprises, non-profit organizations, patient organizations, regulatory authorities. Examples will be given and we’ll expand on the pros and cons of open source software use. Finally an IMI project is the ideal platform and provides funding to kick-start such a open source project: whether it be by developing software or whether it be for testing and adopting open-source software.


Ann Marie Martin


Ann Marie Martin
Principal Scientific Manager
Knowledge Management
Ann is responsible for the Knowledge Management aspects of the IMI collaborations. She develops and implements the Knowledge Management Strategy addressing the topics of collaboration, document management, data pooling and data processing infrastructure across the IMI Projects and provides input on specific Knowledge Management projects. 

Between 1997 and 2009, Ann Martin held various management positions in the pharmaceutical industry as Global Head of Biostatistics for UCB Pharma (1997-2001), Global Section Head of Statistical Programming for Novartis (2001-2005) and Global Head Statistical Programming Operations, Standards and CDISC Implementation at UCB Pharma (2005-2009), giving her a broad knowledge on drug development and extensive international experience with Europe, the US and India.Between 1987 and 1997, Ann worked for Bristol-Myers-Squibb both as a Junior and Project Biostatistician in multiple therapeutic areas, following a short period as research assistant at the University of Lancaster (1985-1987).

Ann Martin is a Chartered Statistician and holds a Masters degree in Sociology and Statistics from the London School of Economics and Political Science, UK. 

In recent years, Ann Martin has been researching the potential of open source collaborations in both statistical programming and patient initiatives. In this context, she is helping a patient organization dedicated to research in generalized or DYT1 Dystonia, a rare and debilitating disease.

13:45 Implementing OpenCDISC for Compliance Checking
Dirk Van Krunckelsven,
Merck NV/SA, Overijse, Belgium

Implementing OpenCDISC for Compliance Checking

Dirk Van Krunckelsven, Senior Specialist – GPSRS: Global Processes, Standards, Research and Systems for GBS, Merck N.V./S.A, Overijse, Belgium 

Verifying the compliance of your data to the CDISC models is a must! OpenCDISC is a great help in accomplishing this. A minor caveat is that the GUI (Graphical User Interface) does not allow you to select a location for the report, but this can be overcome easily through the command line. Crucial is the interpretation of the report: one still needs to understand the CDISC models and the data in order to make sense of the report and to define the actions to be taken based on it: will one correct the data or the data structure, ignore an issue and explain in for example the Reviewer’s Guide, or does one further investigate. Implementing OpenCDISC is very much worth the effort, it comes with a good basis of checks and you can even extend the checks yourself. On top of that the OpenCDISC website with full descriptions of all checks and an active forum provides a valuable source of information. The most important reason for relying on OpenCDISC for compliance checks is that both CBER and CDER use the tool when you submit data to the FDA.

presentation canceled

14:30 Coffee break
14:45 An Introduction to the Use of R for Clinical Research
Dimitris Rizopoulos,
Erasmus Medical Center, Rotterdam, The Netherlands    presentation “R”

An Introduction to the Use of R for Clinical Research

Dimitris Rizopoulos, Assistant Professor at Department of Biostatistics, Erasmus Medical Center, Rotterdam, The Netherlands

R ( has become the ‘lingua franca’ of data analysis and statistical computing. Its great success is attributed to its free availability and the capability for a wide range of analyses and graphics.

In this talk we will discuss the main features of the R system and its application to clinical research. Particular attention will be given on advantages and disadvantages of the language, obtaining help and support, and reporting results.

15:30 CDISC next steps: reporting. An update from the PhUSE/FDA collaborative meeting.
Kevin Kane,
Phastar Pharmaceutical Services, London, United Kingdom
presentation “FDA CSS PhUSE Initiative
16:15 Plenary discussion: using open source software in clinical trials
17:00 Closure & Drinks

Hosted by Julius Clinical Research B.V., Zeist, the Netherlands.
Price: €50