tranSMART Foundation

tranSMART Foundation

The live webinar was held September 16, 2013, 11:00 am – 12:30 pm US Eastern Time (this is the “follow-up” tranSMART Webinar designed to enhance the discussion we had on the topic at the spring meeting in Paris – review Michael Braxenthaler’s presentation here).


This tranSMART webinar recording will:

showcase the tranSMART Platform in use to support:

  • TRANSLATIONAL SCIENCE – Paul Avillach, MD, PhD, Assistant Professor, Paris Descartes Université; PostDoc, Harvard Medical School, Center for Biomedical Informatics.
  • PATIENT ORGANIZATIONS – Magali Haas, MD, PhD, Chief Science & Technology Officer,One Mind for Research;  Sirimon O’Charoen

and will address:

  • THE ROLE OF THE tranSMART FOUNDATION in providing the sustainability model for the tranSMART standard – Michael Braxenthaler, PhD, Co-CEO, tranSMART Foundation



avillachPaul Avillach holds an MD in Public Heath, Epidemiology, Biomedical Informatics and PhD in Biomedical Informatics. He is Assistant Professor at Paris Descartes University and has started a Postdoctoral training at the Center for Biomedical Informatics, Harvard Medical School, under the supervision of Professor Isaac Kohane.

Contact: Paul_Avillach@hms.harvard.edu 



Michael Braxenthaler, PhD, is  Global Head Strategic Alliances, Pharma Research and Early Development Informatics, Roche, President, Pistoia Alliance; and Co-CEO, tranSMART Foundation.

After brief university appointments at the University of Salzburg and the University of Maryland, Michael joined Roche in 1996 as a bioinformatics scientist. He has spent his career there in positions of increasing responsibility, culminating in his current role as global head of strategic alliances in pharma research and early development informatics.

Michael joined the Pistoia Alliance in 2009 as external liaison and stepped into the role of president in 2011. In this position, he intends to foster the creative potential of the Alliance’s uniquely diverse membership to find new, impactful ways to address R&D challenges while maintaining an emphasis on delivering value.

Michael received his PhD from Tübingen University.

Contact: michael.braxenthaler@pistoiaalliance.org

Magali Haas, MD, PhD, is Founder and CEO of Orion Bionetworks. She also serves as Chief Science and Technology Officer for One Mind for Research, a nonprofit organization launched in May 2012, which seeks to advance the development of preventions and cures for brain disorders in this decade.

Magali has over 15 years of pharmaceutical executive and clinical research experience, predominantly at Johnson & Johnson, where she assumed broad end-to-end development leadership roles in medical marketing, full clinical development, early development, and translational and biomarker sciences in psychiatry and neurology. As an “intrapreneur” at J&J she established the first NS Integrative Solutions department, and co-founded the first Companion Diagnostics Center of Excellence as well as the first Healthcare Innovation team. She serves on several advisory boards including the Irish Health Review Board, International Neuroinformatics Coordinating Facility, IMEC for nanoelectronics, and Guardian Angels for biosensors.

Magali earned her bachelor of science degree in bioengineering from the University of Pennsylvania, a master of science degree in biomedical engineering from Rutgers University, New Jersey, and a medical degree and doctorate in neuroscience from Albert Einstein College of Medicine, New York.

Contact: magali.haas@1mind4research.org

sirimonDr. Sirimon O’Charoen is Manager, Translational Medicine, atLife Science Professional Services, Thomson Reuters, and has over than 5 years of experience in data curation and annotation. Past projects include leading curation and workflow development for gene expression studies, clinical studies, and literature. Before joining Thomson Reuters, she was a Senior Research Scientist and reported directly to the company’s CEO at Torrey Path, Inc, a provider of omics data repositories and annotation software for gene expression data. During 3 years at Torrey Path, she directed the team to develop curation platform for public gene expression data. The platform was integrated with tissue, disease, MeSH, and SNOMED ontologies for annotation and BioConductor packages for data pre-processing. She defined the commercial content products as well as user-interface features for accessing the company’s content. At Thomson Reuters, she started as a Research Scientist working with tranSMART and developed an annotation template with control terminology for Janssen’s facet search interface. The ontologies and standards used are MedDRA, MeSH, and CDISC. She delivered several custom curation projects such as annotation of historical experiments for a new searchable database at a customer’s site. One noteworthy project also included an alignment of common data elements from multiple sources. Sirimon is now leading tranSMART and  curation projects at Thomson Reuters.

Contact: sirimon.ocharoen@thomsonreuters.com



John-Wise (1)John Wise is PRISME Forum’s Program Coordinator.  He also serves as the Executive Director for the Pistoia Alliance where he is responsible for the Alliance’s working groups while serving as the primary liaison between the project teams and the operational team and board. He is committed to encouraging pharma to use expert, third-party, cost-effective, regulatory-compliant, hosted information services.

Previously, John has held Informatics leadership roles in a variety of organizations including the University of London, Sandoz, ICRF, Roche, Ipsen, and Daiichi Sankyo. In these roles, John has gained direct hands-on experience writing analytical software, teaching computation, delivering IT services, and providing computer-based services to the discovery, non-clinical development, clinical development, and regulatory affairs domains of the life-science industry.

Contact: programme@prismeforum.org



Quick jump to:

Magali Haas: 0:3:16
Sirimon O’Charoen: 0:10:38
Paul Avillach: 0:21:10
Questions for the first three presenters: 0:37:13
Michael Braxenthaler: 1:02:55
Questions for the entire panel: 1:16:13


To download Magali/Sirimon’s slides, click here.

To download Paul’s slides, click here.



eCollaboration and Microsoft 2013 Platform

e-Collaboration – held April 10, 2014, 10 am US Eastern Time

eCollaboration and Microsoft 2013 Platform


The purpose of this webinar was to bring recommendations about e-Collaboration to the PRISME Forum meeting scheduled for May 2014. (Session was not recorded.)



Last Name First Name Organization
Binnie Alastair Bristol-Myers Squibb
Budin-Jones Slava GSK
Danilovich Yann Takeda Pharmaceuticals
Desmarquet Christelle Sanofi
Francis Joe GSK
Holst Paige Amgen
Jost Juergen Merck KG aA
Olszewski John B-I
Romig Timothy Amgen
Sedlock David Takeda Pharmaceuticals
Skorupa Greg GSK
Stanculescu Nico PRISME Forum
Wise John PRISME Forum



Building on the discussions we had about eCollaboration at the Fall 2013 PRISME Forum Meeting, we are planning our first PF webinar of 2014 to be about eCollaboration and to be scheduled for Thursday, April 10, 2014.

This webinar continued our knowledge sharing around eCollaboration and the Microsoft 2013 Platform.  A number of individual “company-to-company” discussions have occurred around the broader topics of eCollaboration over the last few months.  Mark Yuzuk from BMS kindly agreed to chair and facilitate the webinar.



This first PRISME Forum eCollaboration webinar will be focused on sharing learnings about Microsoft’s 2013 platform.  The purpose of the webinar is to share current status, plans, and implementation learnings of the product.  Recognizing that many companies are just underway with these types of initiatives, the webinar will be sharing in-flight/draft plans and/or the findings from due diligence efforts in which companies have been engaged. Topics that will be covered include:

  • New features that will impact how people work
  • Deprecated functionality not available in 2013
  • Integration with the rest of the Microsoft stack
  • Cloud vs. On-Premise Implementation considerations
  • The webinar will be focused around the product only.  Discussions around pricing, implementation partner performance, or other topics that pertain to individual companies are off limits
  • If individuals in your organization have interest in further shaping the agenda and/or facilitating the webinar please reach out to Mark directly at Mark.Yuzuk@bms.com.



  • People involved in any Microsoft 2013 upgrade project or strategy in your organization
  • People who are focused at Team effectiveness and/or collaboration (aka how people are working and sharing information internally and with partners) leveraging the Microsoft platform of collaboration technologies
  • People who are looking not just at the technical functionality of what SharePoint can do for a particular Division or department, but focused on how to deliver common enterprise wide services to clients to improve how they work leveraging collaboration technologies.




Mark Yuzuk, leads Bristol-Myers Squibb’s group responsible for enabling collaboration technologies within R&D while driving adoption and value realization of these capabilities. Mark and his team are tasked with the identification, prioritization and execution of high-impact opportunities that demonstrate the value of collaborative cultures, work practices, and behaviors for team, individuals and the enterprise. Mark led the rollout and support of SharePoint for R&D, as well as other platforms like Ideation, OCS, LiveMeeting, and evaluation of other collaborative solutions.

Previously at BMS Mark led the Solution Delivery and Support organization for R&D Operations. He has also been the capability management lead for the M&A organization – Strategic Transactions, and has lead work streams integrating acquired companies into BMS.

Prior to joining BMS, Mark was an executive in the R&D practice of Accenture. Mark specialized on strategy and implementation of large scale technology and process capabilities working with various clients in the Life Sciences.







by Matteo di Tommaso

I recently spoke at a FDA-PhUSE conference and there are additional people with whom we could engage, including individuals from the  FDA, who expressed interest in the topic at the meeting.

I recommend that the PRISME Forum formally charter a team and define practical and tangible outcomes of value to the individual’s on this e-mail and other members contributing (ET-project-Template).

Tangible outcomes could include:

– A published summary of analysis of our survey results

– A checklist for cloud validation (link “Purpose” -> “regulatory requirement”  -> “best practice technical solution”)

IMO the survey results will  stimulate good discussion at our PRISME Forum Meeting in Paris, and provide excellent substrate for a document / publication that PRISME Forum members and other communities committed to life sciences R&D would be eager to read.

The PRISME Forum Steering Committee circulated a brief questionnaire to the PRISME Forum membership. So far, we have received 14 responses from 14 different pharmaceutical companies. The questions were:

1)      What do you see as the top opportunity for “Cloud” for your company?

2)      What do you see as the best example in the pharma industry of value delivered by the “Cloud”?

3)      What specific technical issues have kept you from putting validated applications in the “Cloud”?

4)      What specific non-technical issues (both real and perceived) have inhibited your company’s use of the “Cloud”?

5)      What key issue would you recommend that the industry tackle together?

6)      What or who is driving your company’s interest in the “Cloud” today?

7)      Any other comments?

We took a quick look at Question 1 “What do you see as the top opportunity for Cloud for your company?”  to try to surface some key themes and we found that themes of Flexibility, Reduced Cost, and Sharing of Data rank high in the 14 responses on the value of the cloud:

Theme Count
Flexible, OnDemand


Reduce Cost


Shared Data








Hosted solutions for Clinical Trials






Speed to Solution


Shared Solutions


In the responses to the 5th question : What key issue would you recommend that the industry tackle together?  We have some good material to inform discussion about deliverables: Sharing of Examples, Business Cases, Technical Solutions, Approaches to Addressing Regulatory Requirements, and Standards all show up in members recommendation for  areas on which to collaborate.

Three specific requests –

  • Follow-up Telecon: The PRISME Forum would value your recommendations on whether we should advance a PRISME Forum effort in this area, designed to get tangible outcomes that would be valuable to you and your teams.  I have asked John to set up a teleconference with you all to discuss.
  • Volunteer/Leader for PRISME Discussion: we would appreciate a volunteer to lead discussion on this topic at the PRISME Meeting, summarizing and presenting the survey data to open discussion.
  • Draft Charter: To draft a  charter with specific deliverables, participants, roles that can be reviewed and if necessary refined at the PRISME Forum Meeting in Paris.



“Big Data” Working Session

The 2013 Spring Meeting of the PRISME Technology Group focused on the topic of “Big Data & Pharmaceutical IT”.   Analysis and visualisation of internally generated and external  Big Data is critical to the on-going success of the Pharma R&D organisation as it searches for patterns, trends and sequences in the drug discovery and clinical trials process.

The ‘Big Data’ challenge is rapidly becoming a key strategic theme for the pharmaceutical sector as the industry is faced with an explosion of biomedical data being generated and made available for R&D use. Across the pharmaceutical indus-try, five key data domains have been identified:

  • externally-sourced molecular life science data
  • internally-generated clinical trial data with patient-centric genetic and molecular profile data
  • Real World Evidence data, including EHR and insurance claim data
  • Business intelligence data (to support R&D portfolio and in-licensing decisions)
  • Telemedicine and the potential future impact of data from remote monitoring of patients on pharmaceutical de-livery and R&D.

Given much of the data in question is external to any individual pharma company, new business models will need to be established involving collaboration between a multiplicity of entities including academia, CROs, government agencies, health providers, technology companies and even between the Pharmaceutical companies themselves. Only through innovative, cross-organizational cooperation will the sector be able to derive the necessary insights

In this paper we summarize the output of the members working session on “Big Data”.


Across member companies a diverse set of technologies, organizational constructs, and infrastructure are being put in place to support “Big Data”.   While varied, there is strong consensus that applications of “Big Data” in R&D are still in their infancy and rapidly evolving.

The Art of the Possible

As the hype around the term “Big Data” has grown, R&D leads must focus on the substance behind the hype.   Communication at this time is critical for setting realistic expectations with stakeholders as to what Big Data can realistically accomplish in the short, medium, and long term. Meaningful dialog can help ensure impactful investments in  available technologies and support business processes changes that result in improvements in cycle time, R&D costs, and success rates in  bringing new medicines to market.

“The Question is King”

Members of the PRISME Forum, highlight the importance of Big Data services and solutions being centered on the business problem rather than on data integration projects that don’t have use cases.   Resources can be easily wasted building infrastructure and integrating data that will never be used.  Key areas for opportunity in leveraging diverse data sources include:

  • Competitive Intelligence & Business Development: understanding industry trends, competitor products, and licensing opportunities to increase the success of portfolio investments and quality of decisions
  • Drug Repositioning & Life Cycle Management: identifying  alternative indications for drugs within the company and identifying drugs from across the industry that represent an indication opportunity for a proven mechanism, providing an accelerated path to new therapeutics
  • Translational Medicine: identifying dysregulated mechanisms in disease, selecting targets, and discovering biomarkers for patient segmentation from diverse molecular and clinical data toincrease the success rate in clinical trials.

Change Required

To achieve the benefits of these new approaches requires much more than the adoption of new technologies such as MongoDB & Hadoop.  There will be significant changes required in skill set, business process, organizational structure, and technology to be successful.

  1. Skill Sets

There is a growing role for data experts who understand what data is available, and the limitations and uses of the data sets; as well as the technologies for analyzing the data and visualizing the results.   Data analysts, data diplomats, data angels, data valet, data stewards, data modelers there are many emerging terms for these data experts which represent a growing and essential core competency required for successful drug discovery. The individuals will need to have strong business acumen to be able to understand the questions that need addressing, and strong communication skills to enable communication of the results to scientists and business leaders.

  1. Organization

There is a changing role for IT in the industry.   With most companies having embraced a model that is much more tightly integrated with R&D through business partners and services, the role of IT in Big Data is shifting from a “Product” or “Project” view of the world to a much more “Service” oriented role with rapid turn-around of agile and iterative experiments, assembling data and tools quickly to address the needs of R&D project teams.   Through this work data pipelines and structured data collections will accumulate at a rapid pace. The data pipelines and collections will vary in the level of permanence and robustness needed as some are used once and discarded and others become heavily used utilities distributed broadly in the organization.

  1. Business Process

Drug project teams will need to change their thinking to consider the new types of experiments and include members with the cross functional expertise to recognize opportunities in use of Big Data to accelerate project teams and increase confidence in drug programs.

New interfaces and governance will need to be defined within groups to create the necessary cross functional teams, and organizational responsibilities redefined.

  1. Technologies

IT will have to create the “Data Sandbox” where pipelines can be developed rapidly, reused, and modified and where a rapidly changing collection of large data sets can be used or accessed.  This will require new technologies from NoSQL databases as well as new roles for well proven technologies like relational databases and text mining tools.

Traditional approaches to data leverage multi-year capital projects to structure and integrate data sets into a fixed form for transactional data capture and reporting solutions.   To take advantage of Big Data and the rapid changes in data and usage will require a more flexible infrastructure.   Instead of pre-integrating data, services are needed to dynamically curate and structure data to answer specific business questions.

  1. Collaboration

It is the people that work on the challenges that will make the difference between success and failure.  Big Data efforts are inherently cross-functional and require expertise from multiple disciples:

  • Scientific expertise to define the business problem
  • Technology expertise to acquire data, automate data processing and structure data
  •  Knowledge of data to enable selection of data sets and taxonomies, understand the strengths and limitations of data sources, and define the approach to integrating and querying data to address the specified business need
  • Computational modeling and statistical expertise to determine the approaches to understanding the data and evaluate relevance and applicability of findings
  1. Data Preparation

Preparing data for use requires significant investment

  • Data quality must be fit for purpose – this will often mean working with imperfect data sources and requires understanding of the defects and limitations of data sets as well as their utility for the purpose at hand
  • Identification of data sources, and aggregation of data should center around the business problem and attempts to pre-integrate may result in wasted effort
  • Data standards, format, taxonomy can help with integration but can also be overused
  • Unstructured data sources are as important as structured data sources
  • Sharing of data across pharma will sometimes be required to achieve data sets that are large enough to support critical experiments

Where to Start?

  • Given the current period of change and exploration, companies must invest in the low cost and parallel experimentation that will be required to change culture, business process and determine the highest value new approaches
  • Communicate & demystify Big Data and most importantly the business needs that your organization sees it addressing.  Share success stories and experiences both internal and external.
  • Sponsor open innovation initiatives (internal to a company or external) that identify and share the best examples of Big Data analysis and visualization approaches
  • Establish cross-functional teams to recommend strategy
  • Create cross-functional Big Data teams organized around specific business needs or challenges
  • Sponsor the organizational changes that establish Data Scientist roles and responsibilities
  • Invest in the required skill sets & allocate the individuals to developing the new services that are required
  • Create the Sandbox and provide teams with access to data and tools, investing as value is demonstrated
  • Evaluate and pilot technologies to understand the capabilities of both technology and data sources





At the Spring 2013 Meeting of the PRISME Forum, it was agreed that e-collaboration in general and SharePoint in particular was a “hot topic”. Some companies were experiencing good success with e-collaboration platform technologies while others were finding some obstacles to its implementation and successful uptake. The PRISME Forum Steering Committee was asked to consider how best to pursue the topic of e-collaboration such that best practise might be shared amongst the PRISME Forum members.

The Steering Committee initiated discussions with Alastair Binnie (PF Steering Committee member) and Mark Yuzuk (Director, Collaboration & Personal Productivity, Enterprise Services, BMS) about how best to proceed.

The proposal was:

a) to circulate a brief questionnaire to all PRISME Forum members addressing the strategy, planning, implementation and support of e-collaboration, and

b) to organize a webinar based on responses to this questionnaire – towards the end of September 2013 – to review e-collaboration in the context of the pharmaceutical company enterprise but with a special focus on R&D.

With the increasing externalisation / virtualisation of R&D activities this topic is of strategic importance. The webinar will be led by Mark Yuzuk but is anticipated to involve other PRISME Forum interested parties too.

Ideally, webinar participants should be those who are accountable for driving the successful use of e-collaboration in the context of R&D personal productivity, internal project team communications and information exchange and external collaboration best practices. Please note, participants will not necessarily be the e-collaboration tool technical specialists.

We would very much like to attract participants from companies who feel they are getting good value out of their e-collaboration environment but also – and very importantly – from companies who feel they are encountering some obstacles with the deployment of such platform technologies.

Time will be set aside at the Fall 2013 Meeting of the PRISME Forum in Boston in October to review the questionnaire and the webinar and to see what lessons can be learned and what steps might be taken to optimize the use of e-collaboration technologies within pharma R&D.



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  • Wise-J-C-M. ELNs An essential productivity tool – but which one to use? European Pharmaceutical Review 3 Volume 16, Issue 4, 2011
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