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Open sourcedays2013   claus stie kallesoe

Open sourcedays2013 claus stie kallesoe






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  • ha, the date on the first slide is wrong! I did the talk today March 9th and not the 10th! Apparently the audience were too polite to tell me...as I only just noticed
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    Open sourcedays2013   claus stie kallesoe Open sourcedays2013 claus stie kallesoe Presentation Transcript

    • 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.
    • 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
    • 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
    • Two words about myself 4
    • 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: http://www.linkedin.com/in/clausstiekallesoe 5
    • Blog clausstiekallesoe.org 6
    • 7
    • Pharma 101 8
    • 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
    • The new Pharma world 10
    • 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
    • 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
    • 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
    • Open Source @ Lundbeck – The LSPplatform 15
    • Ruby on Rails Phusion Passenger Research Acts_as_authenticatedInformatics ….. …
    • Optional GNU Scientific Lib (GSL) Tools GNU Plot Layer As is: Alternatives: Indigo/Bingo
    • LSP Development on GitHub
    • LSP4Lundbeck general look – Extjs and RoR 19
    • MedChem Designer – ext.js + MOE + Google
    • Curvefit – ext.js + GNU SL + d3.js
    • Ca flux – Spike detection. Ruby, GNUSL + GNU plot 22
    • LSP4Externals 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
    • Insuring InteroperabilityLSP – the integrating platform! Big Data / CRO’s Cloud Translational Math/Stats Medicine support Visualisation ELN/BioRails Tools/ Technologies LSP External Information 25
    • Book chapter about LSP and our way ofdoing things Building research data handling systems with open source tools Claus Stie Kallesøe 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
    • Cross Pharma (and beyond) projects 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
    • IMI OpenPhacts 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.
    • How does Open PHACTS work?
    • 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.
    • IMI eTRIKS 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
    • 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
    • Pistoia Alliance 39
    • The Pistoia Mission Lowering the barriers to innovation by improving inter-operability of R&D business processes through pre-competitive collaboration 40
    • Conclusion and/or Next steps 44
    • 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
    • Where do we go from here? HTML5 + javascript More Semantic linking of diverse data sources Data Science - Hadoop, NoSql etc Cloud – AWS, OpenStack 46
    • W3CHealth Care & Life Sciences (HCLS) IG 47
    • 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
    • Because you need Semantic SandBoxes
    • More open data –Open database with health records 50
    • We are hiring….http://www.lundbeck.com/global/career/become-a-brainmate/job-opportunities?Id=E927314en 51
    • These slides are here: 52