INNOVATIONSPOTLIGHT SESSION0pen Source Technologies for Precision Medicine

WEDNESDAY 3RD JUNE 2015The Marriott Heathrow, London

PROVENTAI N T E R N A T I O N A L

INNOVATION

INNOVATION SPOTLIGHT

The focus of this Innovation Spotlight Session is the challenge of building a comprehensive and sus-

tainable open source platform and community for Precision Medicine Informatics. The attendees are

pharma R&D IT executives, academic PI’s and MD’s who share a common vision that today’s biomedical

informatics challenges should be and in certain regards can only be met by pre-competitive collabora-

tion. The sponsor of this meeting, The Hyve, is a global open source software service company with a

mission to make open source the de facto standard for R&D IT in the life sciences.

The case study for this meeting is an intersection of a suite of open source software applications for

translational research, including tranSMART, cBioPortal, ADAM and Galaxy, with a few public datasets

such as TCGA, ADNI and CCLE. Speakers will highlight various viewpoints from their own experience

(pharma IT, academic research and clinical application). In a number of focused roundtable sessions

specifi c challenges will be addressed, such as the the business model for collaborative annotation of

public data, the prerequisites for integrating open source software in an enterprise pharma IT land-

scape, and the relevant visualization techniques for navigating clinical and biomarker data.

Online CommunityOur online community enables roundtable discussions to be prolonged and shared globally in a

pre-competetive environment. We keep leaders constantly informed with the latest updates in a user

friendly platform.

Telephone: +44 207 096 1222

SPOTLIGHT SESSION 2015

Telephone: +44 207 096 1222 www.proventainternational.com

Prof. Gerrit MeijerProfessor of PathologyNetherlands Cancer Institute

Kees van BochoveCEOThe Hyve

Paul AvillachAssistant Professor Harvard Medical School

Nikolaus SchultzAssociate Attending Computational Oncologist Memorial Sloan Kettering Cancer Center

Jay BergeronDirector, Translational and BioinformaticsPfizer

Sjoerd van HagenSoftware EngineerThe Hyve

John WiseExecutive DirectorPistoia Alliance

Jan-Willem BoitenProject Manager Translation Research ITCTMM

Jean-Baptiste CazierDirector of Centre for Computational Biology, Prof of BioinformaticsUniversity of Birmingham

Keith O. EllistonPresident and CEO tranSMART Foundation

KEY OPINION LEADERS

www.proventainternational.com

Executive DirectorPistoia Alliance

University of Birmingham

Keith O. EllistonPresident and CEO tranSMART Foundation

IN PARTNERSHIP WITH

TIME AGENDA ROOM

9:00-9:30 REGISTRATION HALL

9:30-9:45 Welcome Address: Kees van Bochove, CEO, The Hyve Goodwood Park Suite

09:45 - 10:15

Opening Presentation: Towards a comprehensive application suite for translational research: integrating clinical, imaging, biobanking and biomarker data

Abstract: Translational research aims to bring our increasing knowledge of biology as new diagnostic and therapeutic solutions to patients, thus changing clinical practice. This requires solid evidence, coming from high quality studies that integrate disease phenotype and readouts of biology. For this purpose, originally siloed domains like clinical registries, imaging, biobanking and omics need to converge. Within the European Strategy for Research Infrastructure (ESFRI) multiple biomedical science infrastructures like BBMRI, EATRIS, and ELIXIR have taken up this challenge, e.g. in the context of the BioMedBridges program.Speaker: Prof. Gerrit Meijer, Professor of Pathology, Netherlands Cancer Institute

Goodwood Park Suite

10:15 - 10:45

Case Study: Toward Precision Medicine: Building a patient centric information commons on common and rare diseases with tranSMART

Abstract: TranSMART is used today at Harvard Medical School as a comprehensive clinical and genomic database for enabling a multidimensional perspective of autism spectrum disorder and Phelan-McDermid Syndrome (n=1100 patients worldwide). Paul will show a live demo to illustrate how his group integrates various sources such as Registry data, Patient reported outcome, longitudinal EHR, Patient consent, Biobank, Exome sequencing data and knowledge from Clinical notes for discovery and analysis.Moderator: Paul Avillach, Assistant Professor , Harvard Medical School

Goodwood Park Suite

10:45 - 11:15 Morning BreakHALL

11:15 - 11:45

Presentation: Imitation and Disruption: The impact of Open Source Software in the Life Sciences

Abstract: There are many successful examples of open source software (OSS) both within and outside of the life sciences community. However, investigators sponsoring software-based efforts need to consider many factors, including resourcing, architecture fragmentation, maintenance and their customer community when selecting between commercial and open license alternatives. This presentation will review the factors involved in successful open source collaborations including business models and socio-psychological factors, and will focus on the IMI eTRIKS translational infrastructure project as an example.Speaker: Jay Bergeron, Director, Translational and Bioinformatics , Pfizer

Goodwood Park Suite

11:45- 12:45

Roundtable Discussion: What are the prerequisites for integrating open source software in an enterprise pharma IT landscape?

Abstract: What are the unique advantages of open source software in the pharma IT context? Using open-source software has many attractions; but it is not without its disadvantages. The attractions need to be clearly identified and articulated, just as the disadvantages – whether real or perceived - need to be clearly understood and addressed in order to integrate open-source software in pharma IT.This round table discussion will set out to identify advantages such as:-Encouraging pre-competitive collaboration, especially with academic organisations - Lowering system implementation costs - Allowing quicker and richer functional development by exposure to wider, more varied communitiesBut disadvantages that need to be addressed will be considered too, such as:- Perceptions of quality compared to commercial product - Difficulties in understanding the licensing terms of open-source software use and development - Change control of open-source software supporting processes in the regulated domain of the industryModerator: John Wise, Executive Director, Pistoia Alliance

Goodwood Park Suite

13:00 - 14:00 Networking LunchHALL

TIME AGENDA ROOM

14:00 - 14:45

Case Study:The cBioPortal for genomics data visualization in a clinical setting

Abstract: As sequencing of tumor samples is entering clinical practice, there is an urgent need for new tools that facilitate the interpretation of sequence data so that they can effectively inform treatment decisions. The cBioPortal for Cancer Genomics is a web-based visualization and analysis engine that makes complex cancer genomics data accessible to a wide range of cancer researchers and clinicians.Moderator: Nikolaus Schultz, Associate Attending Computational Oncologist , Memorial Sloan Kettering Cancer Center

Goodwood Park Suite

15:00 - 16:00

Roundtable Discussion: Is there a business model for collaborative annotation of public data?

Abstract: Annotation of ever larger data sets requires a tremendous effort, leading to increasing difficulty to achieve both Quality and Quantity simultaneously. Automation can go a long way, but the lack of a perfect solution implies competing approaches which in turn require manual curating. These can be just as competitive, and even sometimes contradicting. Traditionally, curation is done in parallel by academic groups as well as by vendors, paid by pharma companies. Is there an interest and a business model for a truly precompetitive effort around data curation of large public datasets such as TCGA, CCLE, GEO studies, dbGaP studies etc? How would this curation work together with the Data Use Agreements of such studies? Moderator: Jean-Baptiste Cazier, Director of Centre for Computational Biology, Prof of Bioinformatics, University of Birmingham

Goodwood Park Suite

16:00-16:15 Afternoon Break HALL

16:00-16:15

Technical Exposition: ADAM: using Apache Spark to build the next-generation infrastructure for genomics data storage and compute.

Abstract: The cost of sequencing whole genomes has dropped significantly during the past decade, leading to a steep increase in the amount of available genomics data. On the phenotype side both smartphones and sensors are getting cheaper and wearables are being introduced, a development that will lead to large amounts of phenotypic data. Similar trends can be observed in other types of data.To extract knowledge from these data we need an approach that is both flexible and scalable, flexible because of the variety in the data and scalable because of the sheer size. These requirements are exactly what sparked the rise of Big Data, which was initially geared towards textual data generated by people on the internet, unstructured and big with small nuggets of knowledge hidden inside. Challenges in biology can be similar: looking for small patterns or correlations in large, semi-structured data.We will do a short introduction into Big Data technologies, how they work on a high level and how they can be applied to biology. The focus will be on Apache Spark, using ADAM as an example of how you could implement ‘Big Data genomics’.Presented by: Sjoerd van Hagen, Software Engineer , The Hyve

Goodwood Park Suite

16:45- 17:45

Roundtable Discussion: How can open source software enable public-private collaboration on real scientific research questions and datasets?

Abstract: Public-private collaborations are a crucial instrument for the translation of academic innovation into practical applications benefiting patients. One of the challenges to deal with in these consortia is the data processing and data sharing infrastructure: proprietary solutions of individual institutes can often not used by other partners in a cost-effective manner. Open-source solutions may offer an attractive alternative for these collaborations, certainly in the context of complex public-private partnerships with many partners as typically seen in the EU-funded IMI program. This round table will focus on the prerequisites for successful usage of open-source software in these collaborations in terms of licensing, maturity of the software, organization of the community, and hosting.Moderator: Jan-Willem Boiten, Project manager Translation Research IT, CTMM

Goodwood Park Suite

17:45- 18:15

Panel Discussion: What value does open source development bring to precision medicine?Panellist: Prof. Gerrit Meijer, Netherlands Cancer Institute Paul Avillach, Harvard Medical School Jay Bergeron, Pfizer John Wise, Pistoia Alliance Kees van Bochove, The HyveKeith O. Elliston, tranSMART Foundation

Goodwood Park Suite

18:30 Gala Dinner

Jay Bergeron, Director, Translational and Bioinformatics - Pfi zer Jay Bergeron is the Director, Translational and Bioinformatics at Pfi zer with his team being responsible for informatics support for Clinical Research and Precision Medicine. Jay is also the Scientifi c Coordinator of eTRIKS (European Translational Research and Information Knowledge Management Services), a 23M EU program to support translational data management for the IMI that uses Open Source Software (tranSMART) as the core system, and co-lead of the code committee of the tranSMART Foundation, a non profi t community organizer for the Open Source tranSMART application. The work to be presented was conducted as part of a MBA thesis associ-ated with faculty at the Rensselaer Polytechnic Institute.

Nikolaus Schultz, Associate Attending Computational Oncologist - Memorial Sloan Kettering Cancer Center Nikolaus Schultz leads the development of the cBioPortal for Cancer Genomics, a popular re-source for the visualization and analysis of large-scale cancer genomics data sets. His research focuses on identifying the genomic alterations that underlie different types of cancer. He is in-volved in several projects of The Cancer Genome Atlas (TCGA) and is an investigator in the Stand Up To Cancer (SU2C) Prostate Cancer Dream Team.Dr. Schultz is an Associate Attending Computational Oncologist in the Department of Epidemiolo-gy and Biostatistics and an affi liate member of the Human Oncology and Pathogenesis Program. He is the Head of Knowledge Systems in the Marie-Josée and Henry R. Kravis Center for Molecu-lar Oncology.

Paul Avillach, Assistant Professor - Harvard Medical School Paul Avillach is a MD in Public Health, Epidemiology and PhD in Biomedical Informatics. Assis-tant Professor of Pediatrics at Harvard Medical School and is on the faculty of Boston Children’s Hospital in the Children’s Hospital Informatics Program http://chip.org . His research focuses on the development of novel methods and techniques for the integration of multiple heterogeneous clinic cohorts, Electronic Health Records data and multiple types of genomics data to encompass biological observations.

John Wise, Executive Director - Pistoia Alliance John Wise is an Executive Director of the Pistoia Alliance and the Programme Co-ordinator for the PRISME Forum. The Pistoia Alliance is a not-for-profi t, cross-company organisation com-mitted to lowering the barriers to innovation in Life science R&D. The PRISME Forum is a not-for-profi t Pharma R&D IT leadership group focussed on the identifi cation and palliation of “hot topics”, and the sharing of industry best practices.John has worked in life science R&D informatics in a variety of organizations including academia, the pharmaceutical Industry, a cancer research charity as well as in the technology supply side of the industry. This has provided him with direct, hands-on experience of delivering comput-er-based services across the life science R&D value chain.John graduated in physiology before obtaining a post-graduate certifi cate in education.

Prof. Gerrit Meijer, Professor of Pathology - Netherlands Cancer InstituteGerrit Meijer is professor of pathology with a special interest in translational cancer research, focusing on the gastrointestinal tract. The work of his research group involves DNA-, RNA-, and protein-based tumor profi ling using -omics techniques, in order to stratify patient groups and ar-rive at individually tailored therapies, as well as for biomarker development to improve colorec-tal cancer screening. In addition, he is involved in several national and international research infrastructure programs like CTMM TraIT, EATRIS, BBMRI and the tranSMART foundation.Gerrit Meijer obtained his medical degree in 1993 and his PhD in 1997, both from VU University in Amsterdam, and he was registered as a pathologist in 2000. He was appointed professor of gastrointestinal pathology in 2004, and he became Chair of the Department of Pathology in 2009. Meijer will join the Netherlands Cancer Institute early in 2015 as head of Pathology. He has pub-lished over 250 papers in peer reviewed journals. Meijer chairs the scientifi c council of the Dutch Cancer Society. Since 2013 he has been national co-director of the European Infrastructure for Translational Medicine (EATRIS).

Sjoerd van Hagen, Software Engineer - The HyveSjoerd van Hagen is a highly adaptive and versatile individual who has a strong theoretical back-ground in algorithms and takes pride in producing quality work. His love for startups and adven-ture has brought him in contact with a wide variety of technologies, especially in the area of Big Data. Here he also developed a keen interest in any skill useful in setting up businesses. He likes teaching and sharing knowledge and will not shy away from a good discussion.Before The Hyve, Sjoerd has obtained a master’s degree in computer science at the University of Utrecht and worked at Cloudscale, a Silicon Valley startup by Bill McColl, after which he and Bill have been researching the possibility of creating a new company.At The Hyve, Sjoerd has been driving Big Data projects for a.o. a large pharmaceutical company, using ADAM, Apache Spark and Cassandra

KEY OPINION LEADERS

Kees van Bochove, CEO - The HyveKees van Bochove is founder and CEO of The Hyve, a company dedicated to the support and facilitation of open source, open standards and open data in bioinformatics and translational re-search. He studied Computer Science at University of Utrecht and Bioinformatics at VU Univer-sity Amsterdam, for which he did his research project on lipoprotein metabolism at TNO Quality of Life in Zeist and the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University Boston.He has been lead architect and project manager in several international open source projects, including the dbNP initiative initated by the European consortia NuGO, EURECCA, Bioclaims and the Dutch consortia Netherlands Bioinformatics Centre (NBIC), Netherlands Metabolom-ics Centre (NMC) and Netherlands Toxicogenomics Centre (NTC). Currently, he is active in the tranSMART initiative, as member of the Board of Directors of tranSMART Foundation and lead-ing the Foundations’ Architecture Working Group. TranSMART is an open source project forming a comprehensive infrastructure for translational research, governed by the tranSMART Founda-tion, with a large international community that includes the CTMM TraIT project with a.o. VUmc, ErasmusMC, UMCG and Philips Research, academic members such as Imperial College, Univer-sity of Michigan, Harvard Medical School, and Johns Hopkins University, patient organizations such as Michael J Fox Foundation, major pharmaceutical companies including Janssen, Sanofi, Pfizer, Takeda and Roche, IT vendors such as Deloitte, Thomson Reuters, Oracle and IBM, and many IMI consortia including eTRIKS, supported by the Pistoia Alliance. All these projects re-volve around introducing open standards and open source software for translational research.Through his many years of experience in open source software and standards development in bioinformatics, Kees has gained a deep understanding of all aspects of collaborative open source development and open data science, including open source community building and gov-ernance, software quality and sustainability requirements, data workflows, enterprise plugin architectures, legal ramifications and practical aspects such as working in virtual teams and code merging and governance.

Jean-Baptiste Cazier, Director of Centre for Computational Biology, Prof of Bioinformatics - University of BirminghamTrained in Mathematical modelling, Jean-Baptiste Cazier is a Professor of Bioinformatics with interest across the broad spectrum of Computational Biology: from Cancer Genetics, Population Genetics and Metabonomics to Swarming. After 5 years working on Population Genetics for deCode Genetics in Iceland, he joined the Cancer Research UK’s London Research Institute, where he worked alongside experts in most aspects of bioinformatics and biostatistics in the context of cancer. While in Oxford from 2008, he supervised the development of analytical approaches and tools for the analysis of whole genome sequencing projects (WGS500) at the Wellcome Trust Centre for Human Genetics with a special focus on immune disorders and cancers; successfully bringing afore new variants functionally associated with the development of diseases. Jean-Baptiste then joined the Depart-ment of Oncology to create a new Bioinformatics infrastructure to both provide support to the department and lead independently funded research. In 2014, Jean-Baptiste moved to the University of Birmingham taking up the new chair of Bioin-formatics to create the Centre for Computational Biology (CCB). The CCB is a university-wide ef-fort aims to promote excellence in Computational Biology, Systems Biology, and Bioinformatics across the range of fundamental and applied sciences, in both the University and allied Health Care arenas.

Keith O. Elliston, President and CEO - tranSMART FoundationKeith O. Elliston, PhD, is a co-founder and the President and CEO of the tranSMART Foundation. Keith is an experienced scientist and entrepreneur with expertise in systems biology and data science, and in the development and growth of new life science and technology ventures. Keith also currently serves as the Managing Director for Seneca Creek Research, where serves and a founder, investor and advisor to various biotechnology startup and early stage companies. Previously, Keith built and managed the systems biology program for CHDI, the Huntington’s disease foundation, as a fully integrated and systems-driven discovery biology program for a genetic disease of neurodegeneration. Keith has authored more than 40 peer-reviewed scien-tific publications, and been a contributor to more than 280,000 sequence entries in Genbank. Entrepreneurially, Keith has played a key role in the founding of more than a dozen biotech ventures; he is a co-founder and CEO for Virtual-Rx, a virtual pharma platform company; was co- founder, president, and CEO of Selventa (originally Genstruct), a venture-backed systems biology platform company; was CEO and co-founder of Viaken Systems, a venture-backed informatics service provider, and was SVP R&D and CSO for Gene Logic (Nasdaq:GLGC), among others. Keith began his career at Merck, where he built and led the bioinformatics and genomics programs, and ran the Merck Gene Index, a privately funded public genome effort that published the first sequence for 3/4 of expressed human genes. Keith has successfully built biotechnology ventures from startup through IPO, and established profitable and capital-efficient companies working both with venture capital and as a founder or advisor. Keith combines extensive ex-perience in pharmaceutical R&D, biotechnology, information technology and data science with successful executive and team leadership into a unique set of skills that drives innovation and value.

Jan-Willem Boiten, Project Manager Translation Research IT - CTMMJan-Willem Boiten leads the Dutch national TraIT (Translational Research IT) program to orga-nize, deploy, and manage a multi-partner IT infrastructure for data and workflow management targeted specifically at translational research. TraIT is organised as a public-private partnership with over 30 partners, and has a clear preference for the application of open-source software. Prior to joining CTMM Dr. Boiten has had several position in research IT management within Pharma (Organon/Schering Plough/ Merck).

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