SME Forum 2016
SME Forum 2016
EMBL-EBI’s freely available biological data and services make it easier for small companies to stay focused on innovation. Our annual SME Forum features talks, workshops and opportunities to network with other biomedical and biotechnology R&D professionals. This year, with the support of One Nucleus, we have the great pleasure of conducting our SME Forum in our South Building on the Wellcome Genome Campus. Join us to learn more about how your company can make the most of public molecular data and services.
Subject matter experts from EMBL-EBI will present high-level overviews of our many freely available bioinformatics tools and data resources, and users from the commercial sector will talk about their experiences integrating these public data resources to derive business benefit. Workshops on the second day of the event cover topics put forward by our industry partners working in biopharmaceutical and biotechnology R&D.
Monday, 7 March 2016
09.15: Registration and refreshments
10.00 Welcome from EMBL-EBI and One Nucleus
- Dominic Clark, Industry Programme Manager, EMBL-EBI
- Harriet Fear, Chief Executive, One Nucleus
10.30: ELIXIR: the European infrastructure for life-science data – Latest news from ELIXIR
- Andrew Smith, Senior External Relations Officer, ELIXIR
10.50: The BioInnovation Centre at the Wellcome Trust Genome Campus
- Adrian Ibrahim, Head of Business Development and Technology Transfer, Wellcome Trust Sanger Institute
11.00: Large Molecular Drug Discovery Bioinformatics
- John Prime, Oncology Research Data Scientist and Strategist, MedImmune
11.30: EMBL-EBI data resources and services: what’s new
- Mary Todd Bergman, Senior Communications Officer, EMBL-EBI
11.55: Drug Discovery Resources: ChEMBL and more
- Anne Hersey, Interim Team Leader, Chemogenomics, EMBL-EBI
12.25: Lunch, networking and demonstrations by subject-matter experts
- Andrew Cowley, Bioinformatics Trainer, EMBL-EBI
- Abhik Mukhopadhyay and David Armstrong, PDBePISA, EMBL-EBI
- Steven Jupe, Reactome
- Margaret Duesbury, IntAct
- Birgit Meldal, Complex Portal
13:20: Introduction to EMBL-EBI Search
- Cath Brooksbank, Head of Training Programme, EMBL-EBI
13.30: CTTV: a new platform for target-validation data
- Jessica Vamathevan (GSK), Operations Director, Centre for Therapeutic Target Validation, CTTV
14.00: The AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge
- Dr Jonathan Dry, Principal Scientist, Bioinformatics, Oncology IMED, AstraZeneca, Waltham MA, US
14.30: Breakout sessions (Dominic Clark to introduce)
- Pre-competitive collaboration: Ian Harrow, representing the Pistoia Alliance, Inc.
- Data Coordination: Guy Cochrane, Team Leader, European Nucleotide Archive, EMBL-EBI.
- Global Alliance for Genomics and Health (GA4GH): Stephen Keenan, Global Alliance working Group Manager, EMBL-EBI.
15.00: Break-out session
15.45: Pause for refreshment
16.15: Breakout session: feedback
17.00: The GENE Consortium
- Paul Jones, CEO at Genomics Enterprises, Genomics England
17.30: Panel discussion: future needs (Chair: Dominic Clark)
- Mary Barlow, LFCF Programme Manager, EMBL-EBI
- Jonathan Dry, Principal Scientist, AstraZeneca
- Tony Jones, Director of Business Development, One Nucleus
- Guy Cochrane, Team Leader, European Nucleotide Archive, EMBL-EBI.
- Adrian Ibrahim, Head of Business Development and Technology Transfer, Wellcome Trust Sanger Institute
- Alexander Henzig, Knowledge Transfer Manager, Biosciences & Biotechnology, Knowledge Transfer Network
18.00-19.30 Networking reception in the EMBL-EBI South Building
Tuesday, 8 March 2016
The second day of the Forum comprises a hands-on training course in Room V1-24, EMBL-EBI South Building. Topics include genomics resources and drug-discovery resources. Participation will be on a first-come, first-served basis, with a maximum number of 30 participants on the course.
09.00: Welcome remarks (Dominic Clark)
09.15: Train online
- Tom Hancocks, Training Programme, EMBL-EBI
09.30: Helen Sparrow, Ensembl Outreach Officer, EMBL-EBI
11.00: Break for refreshment
11.30: The ChEMBL and SureChEMBL databases: Compound-Target Interactions from medicinal chemistry and patents
- Anne Hersey, Interim Team Leader, Chemogenomics, EMBL-EBI and George Papadatos, Senior Technical Officer, EMBL-EBI
Mary Barlow is head of the Strategic Project Management Office at the European Bioinformatics Institute (EMBL-EBI), and has oversight of impact reporting and the development of infrastructure business cases. Prior to taking on this role, Barlow served as a Programme Manager for the multi-million pound investment in EMBL-EBI by the UK government's Large Facilities Capital Fund. This programme included the construction of new office space and the on-going public procurement of ICT infrastructure to support EMBL-EBI's growing public databases. Barlow's work prior to EMBL-EBI focused on ICT integration and intelligent buildings. She began her career working on broadcast projects in BBC Technology, after obtaining her degree in Maths and Engineering at Nottingham University.
Mary Todd Bergman
Before joining EMBL-EBI in 2002, Cath spent a decade as an editor of scientific review journals, cutting her teeth with the Elsevier Trends Journals before launching Nature Reviews Cancer. A brief dalliance with medicine at the University of Oxford led her to seek solace in molecules in Cambridge, where she completed her PhD in biochemistry under the guidance of Robin Irvine. Cath joined EMBL-EBI to develop the outreach programme, and extended her responsibilities to include user training in 2006. Her team now coordinates a wide-ranging portfolio of training and scientific outreach activities reaching tens of thousands of individuals each year. She contributes to a number of pan-European projects including RItrain, CORBEL, BioExcel and ENLIGHT_TEN, and is co-chair of the curriculum and competencies taskforce of the International Society of Computational Biology.
PhD in Medical Informatics, University of Wales, 1988. Imperial Cancer Research Fund, 1987–1995. UK Bioinformatics Manager, GlaxoWellcome R&D Ltd., 1995–1999. Vice President, Informatics, Pharmagene, 1999–2001. Managing Consultant, Sagentia Ltd., 2001-2009. At EMBL-EBI since 2006 (secondment 2006-2009).
Dr Guy Cochrane is the head of the European Nucleotide Archive (ENA). The ENA provides a comprehensive repository for public nucleotide sequence data, attracting users from a multitude of research disciplines and serving as underlying data infrastructure for numerous bioinformatics services. Under Dr Cochrane, the team has launched important new services, including the Sequence Read Archive for raw data from next generation sequencing platforms and the CRAMtools sequence data compression platform. In addition to the leadership of a team of biological curators, bioinformaticians and software engineers, he contributes editorial work to a number of journals and meetings and has been involved in standardisation activities in many areas of bioinformatics. He received his PhD in cancer cell and molecular biology from the University of East Anglia in 1999 and carried out post-doctoral work in the molecular biology of photoreception at Cambridge University prior to joining EMBL-EBI.
Jonathan Dry is a Principal Scientist leading Bioinformatics for the Oncology IMED at AstraZeneca in Waltham, MA, USA. After completing his BSc (hons) Biomedical Sciences at the University of Manchester exploring the genetics of diabetes, Jonathan went on to study Bioinformatics at the University of Exeter where he was sponsored by GlaxoSmithKline to develop machine-learning algorithms predicting protease cleavage from protein sequence. He joined AstraZeneca in 2003, and went on to develop a number of analytical approaches to exploit transcriptomic data for target credentialing and patient selection, pioneering approaches for in vitro biomarker discovery. Jonathan's work for the MEK inhibitor Selumetinib led to the first clinical testing of a transcription based patient selection approach at AstraZeneca. He now leads a global group of 10 bioinformaticians and 3 postdocs supporting target and biomarker discovery and biomarker translation for AstraZeneca’s Oncology portfolio.
Harriet joined One Nucleus as CEO in February 2009. She previously worked as a Diplomat with the British Foreign Office for 21 years serving in over 17 countries around the globe. Half her career was spent in the commercial field, latterly heading UK Trade & Investments national life sciences trade team for over 5 years. During her varied Foreign Office career she was Deputy Ambassador three times, Private Secretary to the Minister for Europe, led an evacuation of Brits out of the Congo and worked in Khymer Rouge territory with Scotland Yard on a hostage crisis. In her role at One Nucleus, she helps companies maximise their competitiveness, responding to an increasingly diverse membership and forming strategic partnerships similar organisations. One Nucleus is the largest membership organisation in Europe. A not-for-profit private company, it has over 450 members including pharmaceutical, biotech, medical device and diagnostic companies and associated technical and commercial service providers.
Tom studied human genetics at the University of Leeds and McMaster University in Hamilton, Ontario, before completing an MSc in Analytical Genomics at the University of Birmingham. He has worked for the NHS in diagnostic genetics and in bioinformatics training for healthcare scientists and clinicians. Tom joined the EBI in 2012 and is responsible for the scientific development and delivery of training for the BioMedBridges project.
Alexander is the Knowledge Transfer Manager in Industrial and Medical Biotechnology at the Knowledge Transfer Network. He brings together businesses, entrepreneurs, academics and funders to develop new products, processes and services. He assists with the development of ideas, expertise and technologies, focussing on bioinformatics and non-animal technologies. Prior to this role, Alexander was Product Manager for Research Analytics at Aridhia Informatics. He was Research Manager at the Cancer Research UK Experimental Cancer Medicine Centre for eight years, coordinating translational research to develop new anti-cancer drugs, support discovery and validation of new diagnostic, prognostic and predictive markers and drug-target discovery. Alexander holds a degree in Chemistry from Leiden, and obtained his MSc (Biological Chemistry), PhD (Cell Biology) and MBA from Edinburgh University.
Tony Jones is Director of Business Development at One Nucleus, developing the organisation's membership offering to reflect the current external environment and the changing needs of business. He leads the delivery of BioWednesdays, the Life Science Leadership Series and the annual Genesis Conference. Tony was Director of Biotechnology and Healthcare at London First, managing the London Biotechnology Network and promotion of London’s excellence in healthcare research and delivery. In 2010 he took London Biotechnology Network into a merger with the nonprofit membership organisation ERBI, consolidating efforts to assist member companies in developing their businesses. Tony obtained his PhD in Biochemistry from the University of Southampton, and conducted several years of post-doctoral research in the oncology field, primarily with the Imperial Cancer Research Fund (now CRUK). He moved into Technology Transfer in 1997 with the Medical Research Council and later at University College London's Wolfson Institute for Biomedical Research.
Dr Stephen Keenan manages the Data and Security Working Groups of the Global Alliance for Genomics and Health. Before joining EMBL-EBI, he worked to build the high-throughput analysis pipelines for the DNA sequence output from the Human Genome Project at the Wellcome Trust Sanger Institute.
Paul Jones leads and manages the commercial interface with industry at the 100,000 Genomes Project. Prior to his current role, Paul led the Life Sciences Practice at Cisco Consulting Services. He spent 7 years advising pharma, biotech and medical device companies on the use of technology to drive commercial innovation. He has worked in and around pharma and healthcare since 1989. Immediately prior to Cisco, Paul led the European Commercial Effectiveness consulting practice at IMS Health. Before that he was Head of Global eMarketing & eSales at Novartis Pharma in Switzerland. Earlier in his career, Paul worked as a management consultant in the Pharma Practice at PricewaterhouseCoopers and held a variety of sales, marketing and general management roles at Astra, Marion Merrell Dow and Sandoz. Paul has a first degree in physiology, an MBA and holds a Postgraduate Diploma in Marketing
Sarah has a BSc and MSc in Biomedical Sciences, followed by a PhD from Cranfield University. Over a 10 year academic career her research has focused on tumour biomarker characterisation and cell-surface interaction. Beyond research she took an active role in the provision of postgraduate taught courses for the University as Lecturer in Molecular Medicine, leading the development and direction of a number of MSc Courses including the MSc in Translational Medicine, the MSc in Molecular Medicine, and more recently acting as director for the MSc Programmes in Advanced Biosciences. She has lectured on a variety of biomedical techniques and topics, including ethics and governance of research.
John Prime is lead bioinformatician in Oncology Research at MedImmune, the biologics arm of AstraZeneca. He provides applied bioinformatics support to 80+ oncology scientists at the Cambridge, UK and Gaithersburg, USA sites. His research activities centre on supporting early-stage to preclinical antibody drug conjugate (ADC) and immuno-oncology drug-development projects; the ‘omic characterisation of tumour model systems, including syngeneic mice; and the analysis of patient data to deliver predictive signatures, markers and disease 'line of sight'. John also chairs a cross-functional OncoBiomics working group, which is tasked with developing and implementing the bioinformatics strategy for Oncology Research. Prior to joining Medimmune in 2010, John was head of Biomics at KuDOS pharmaceuticals (which became the AZ Oncology DNA damage repair (DDR) inhibitor group). He provided support on target selection and network analysis of the DDR pathways, and led a small team in delivering key biomarker results through proteomics approaches that support DNA repair inhibitor drug projects, including Lynparza (olaparib, approved for use in patients with germline BRCA mutated advanced ovarian cancer). John's PhD in Liver Cancer Genetics was carried out in the laboratory of Prof. J. O’D. McGee at the Nuffield Department of Pathology and Bacteriology, University of Oxford.
Julio studied Chemical Engineering at the University of Oviedo in Spain and the University of Stuttgart in Germany (1996-2001), and obtained his PhD from the Max-Planck-Institute for Dynamics of Complex Technical Systems in Magdeburg (2002-2007), under the supervision of E.D. Gilles. After that I was a postdoctoral fellow at Harvard Medical School and MIT, with Peter Sorger and Doug Lauffenburger. Julio was a group leader at EMBL-EBI from 2010-2015, with a joint appointment in the EMBL Genome Biology Unit in Heidelberg, and is a senior fellow at Wolfson College (Cambridge). Julio is generally interested in computational methods and tools to study information transfer within signalling networks, and application to disease-related questions. He is currently faculty at RWTH Aachen Univeristy.
Andrew Smith joined ELIXIR in 2011 to manage ELIXIR’s engagement with member states, funders and policy-makers. He also leads on ELIXIR’s engagement with the EU institutions. Andy is responsible for developing ELIXIR’s industry strategy and runs the ELIXIR Innovation SME programme, a series of events aimed ensuring companies are aware of and can access the resources run by ELIXIR partners. Andy also supports ELIXIR’s Industry Advisory Committee. Andy’s background is in EU research programmes. Previously he worked in Brussels for the UK Research Office (UKRO), covering various research programme and policy fields, including FP7 National Contact Point helpdesks and supporting UK delegations to FP7 Programme Committees. Andy has previously held roles in regional government, focussing on EU Structural Funds, and on education programmes in Slovenia and the Czech Republic.
As Operations Director, Jessica oversees the management of a number of informatics and experimental target validation projects as well as ensuring the strategic deployment and operational translation of Open Targets. Prior to this, Jessica was a Manager in Computational Biology, GlaxoSmithKline, Stevenage UK, working with discovery scientists in many therapeutic areas including Infectious Diseases, Respiratory, Immuno-Inflammation and Rare Diseases to deliver impactful bioinformatics projects. Before GSK, Jessica spent over six years at The Institute for Genomic Research (TIGR) in Maryland, USA working on many pathogen genome sequencing projects plus a year at the Wellcome Trust Sanger Institute in the human genome annotation team. She also taught as a Lecturer in Molecular Evolution at University College London. She holds a PhD in Bioinformatics from University College London, an MSc in Computer Science from Johns Hopkins University and a Bachelor of Medical Science from the University of Sydney.