Open sourcedays2013 claus stie kallesoe


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Open sourcedays2013 claus stie kallesoe

  1. 1. Does the Pharma Industry use Open SourceSoftware? Why? When? Where? Claus Stie Kallesøe 10 March 2013 @ OpenSourceDays Copenhagen 2013 This work is licensed under a Creative Commons Attribution-NonCommercial- ShareAlike 3.0 Unported License.
  2. 2. Disclaimer The views and opinions expressed in this presentation are those of the authors/presenter and do not necessarily reflect the official policy or position of H.Lundbeck A/S. 2
  3. 3. Agenda • Who is talking? Intro • The Pharma world • Use of Open Source in Research OS @ Hlu Informatics Pistoia/IMI • Pre-competitive initiatives • Conclusion Conclusion • Next steps 3
  4. 4. Two words about myself 4
  5. 5. Introducing myself Current roles: Board of Directors, Pistoia Alliance Head of Global Research Informatics Background: MSc. Pharm, Uni of Pharma Sciences, Copenhagen, 1997 Diploma Software Development, School of Engineering, Copenhagen, 2002 E-MBA, INSEAD, France, 2007Linkedin: 5
  6. 6. Blog 6
  7. 7. 7
  8. 8. Pharma 101 8
  9. 9. The drug discovery process Informatics Cellular & Target Hit/Lead Medicinal Lead & functional Molecular discovery discovery chemistry optimisation genomics pharmacology Drug candidate Target Bio Assay Library In vitro Pharmaco-identification informatics development development Drug activity kinetics Target Genomics High Structure Cellular In vivo validation Throughput based disease pharmacology screening Drug design models Assay Proteomics Biochemistry Medicinal Drug Mode Tox/safetydevelopment & enzymology chemistry of action pharmacology
  10. 10. The new Pharma world 10
  11. 11. Rapidly Evolving Pharmaceutical EcosystemThe Pistoia view of the future Proprietary content Public provider content provider Big Life CRO Patient Science organization Company Pharma Regulatory authorities Academic group Service provider Software vendor
  12. 12. General Pharma Research (Informatics) Trends Partnerships Externalisation TranslationalBig Data Pre-Competitive Interoperability Collaboration Mobile platforms VirtualisationDownsizing CRO - Outsourcing Understand the biology Next Gen Sequencing 12
  13. 13. Why use Open Source – why now? We have actually done so for a long time – at least Linux/Apache/Perl The ”new way of walking” and the more complex data flow Less people and less money in internal informatics departments HIGH NEED FOR : More for less INTEROPERABILITY Flexibility 13
  14. 14. Open Source @ Lundbeck – The LSPplatform 15
  15. 15. Ruby on Rails Phusion Passenger Research Acts_as_authenticatedInformatics ….. …
  16. 16. Optional GNU Scientific Lib (GSL) Tools GNU Plot Layer As is: Alternatives: Indigo/Bingo
  17. 17. LSP Development on GitHub
  18. 18. LSP4Lundbeck general look – Extjs and RoR 19
  19. 19. MedChem Designer – ext.js + MOE + Google
  20. 20. Curvefit – ext.js + GNU SL + d3.js
  21. 21. Ca flux – Spike detection. Ruby, GNUSL + GNU plot 22
  22. 22. LSP4Externals 23
  23. 23. Why open source software? Everything is open => everything is possible We have the people to handle it Our problems are not unique Someone else might have a (free) solution Other advantages:  Download, adapt and implement  No maintenance of specific tools – only the combination  Spend time on value adding solutions Perspectives on Free and Open Source Software, 2005, MIT Press E. von Hippel, Democratizing Innovation, 2005, MIT Press 24
  24. 24. Insuring InteroperabilityLSP – the integrating platform! Big Data / CRO’s Cloud Translational Math/Stats Medicine support Visualisation ELN/BioRails Tools/ Technologies LSP External Information 25
  25. 25. Book chapter about LSP and our way ofdoing things Building research data handling systems with open source tools Claus Stie Kallesøe 26
  26. 26. Alternative to use LSP Several different • No one has a system that covers all areas and data vendor packages types Higher licens and • All packages will have a license as well as a maintenance costs maintenance fee Long implementation • Implementing these tools takes time & integration projects • Integrations between vendor tools are complicated • When one piece gets upgraded the rest has to Constant integration follow and upgrade • You tend to stay with what you have 27
  27. 27. Cross Pharma (and beyond) projects 28
  28. 28. Pre-competitive; Collaboration and Interoperability.It’s happening.... • Central open storage of IMI OpenPhacts pharmacological data Pistoia Sequence • Cloud based NGS analysis and services collaboration • Open Source Translation Medicine IMI data handling eTriks/tranSMART • Build by J&J from open source tools
  29. 29. IMI OpenPhacts 30
  30. 30. What does Open PHACTS do? Currently integrated databases Number of Database triples (million) ACD Labs / ChemSpider 161.34 ChEBI 0.91 ChEMBL_v13 146.08 ConceptWiki 3.74 DrugBank 0.52 Enzyme 0.07 Gene Ontology 0.85 SwissProt 156.57 WikiPathways 0.14 TOTAL 470.21 Open PHACTS draws together multiple sources of publicly- available pharmacological and chemical data, allowing public access to the information via the Open PHACTS Explorer, an intuitive interface.
  31. 31. How does Open PHACTS work?
  32. 32. Public version released last week!The Open PHACTS ExplorerThe Open PHACTS Explorerallows the user to query andinteract with the data presentin the Open PHACTS platform.The interface:• Is intuitive and easy to use• Allows data provenance to be assessedApplication Programming Interface (API)The Open PHACTS platform features an API whichallows development of applications to query andvisualise the data within the platform in novel ways.
  33. 33. IMI eTRIKS 34
  34. 34. Consortium of 16 Partners Academic/Pharma/Coordination/Standards EFPIA Lead Analytics ImperialAcademic Lead Universite Du Development College AstraZeneca Luxembourg Sanofi London Merck Roche Pfizer Lundbeck Serono Glaxo Janssen idbs Lilly SmithKline Hosting Biosci CNRS CDISC Bayer Consulting Standards Coordination
  35. 35. eTRIKS PLATFORM Founded on tranSMART GPL v3 Open Source Translational Data WarehouseBuilding upon Janssen’s Award Winning Translational Informatics System Demonstrated Success with the U-BIOPRED IMI Project
  36. 36. Pistoia Alliance 39
  37. 37. The Pistoia Mission Lowering the barriers to innovation by improving inter-operability of R&D business processes through pre-competitive collaboration 40
  38. 38. Conclusion and/or Next steps 44
  39. 39. Do Pharma use Open Source Software? Yes! A lot in some areas. And we promote open source and open standards in our pre- competitive collaborations like IMI Pistoia Why? We need interoperability in order to make the new complex data world fit together 45
  40. 40. Where do we go from here? HTML5 + javascript More Semantic linking of diverse data sources Data Science - Hadoop, NoSql etc Cloud – AWS, OpenStack 46
  41. 41. W3CHealth Care & Life Sciences (HCLS) IG 47
  42. 42. One solution – Linking data with Semantic technologies – Hlu/DERI/Sindicetech SindiceTech HCLS Cloud –LSP- Lundbeck Research System linking external public data 1) 3) 2) Link internal and external data Research Database 48
  43. 43. Because you need Semantic SandBoxes
  44. 44. More open data –Open database with health records 50
  45. 45. We are hiring…. 51
  46. 46. These slides are here: 52