open sourcedays2013 claus stie kallesoe
TRANSCRIPT
Does the Pharma Industry use Open Source Software?
Why? When? Where?
Claus Stie Kallesøe10 March 2013
@ OpenSourceDays Copenhagen 2013
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Disclaimer
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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.
Agenda
• Who is talking?• The Pharma world Intro
• Use of Open Source in Research InformaticsOS @ Hlu
• Pre-competitive initiativesPistoia/IMI
• Conclusion• Next stepsConclusion
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Two words about myself
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Introducing myself
Current roles:Board of Directors, Pistoia AllianceHead of Global Research Informatics
Background:MSc. Pharm, Uni of Pharma Sciences, Copenhagen, 1997Diploma Software Development, School of Engineering, Copenhagen, 2002E-MBA, INSEAD, France, 2007
Linkedin: http://www.linkedin.com/in/clausstiekallesoe
Blog
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clausstiekallesoe.org
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Pharma 101
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Targetdiscovery
Informatics& functionalgenomics
Hit/Leaddiscovery
Medicinalchemistry
Cellular &Molecular
pharmacology
Leadoptimisation
Drugcandidate
Targetidentification
Targetvalidation
Assaydevelopment
Bioinformatics
Genomics
ProteomicsAssaydevelopment
HighThroughputscreening
Biochemistry& enzymology
Medicinalchemistry
Librarydevelopment
Structure based
Drug design
Drug Mode of action
In vitroDrug activity
Cellular disease models
The drug discovery process
Tox/safety pharmacology
Pharmaco- kinetics
In vivo pharmacology
The new Pharma world
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Rapidly Evolving Pharmaceutical EcosystemThe Pistoia view of the future
ProprietarycontentproviderPublic
contentprovider
Academicgroup
Software vendor
CRO
Service provider
Regulatoryauthorities
Pharma
Patient organization
Big Life Science
Company
General Pharma Research (Informatics) Trends
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Externalisation
Collaboration
Pre-Competitive
Virtualisation
Understand the biology
Translational
Next Gen Sequencing
CRO - Outsourcing
Partnerships
Big Data
Downsizing
Interoperability
Mobile platforms
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
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Open Source @ Lundbeck – The LSP platform
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OptionalToolsLayer
GNU Scientific Lib (GSL)
GNU Plot
Indigo/Bingo
As is: Alternatives:
LSP Development on GitHub
LSP4Lundbeck general look – Extjs and RoR
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MedChem Designer – ext.js + MOE + Google
Curvefit – ext.js + GNU SL + d3.js
Ca flux – Spike detection. Ruby, GNU SL + GNU plot
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LSP4Externals
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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
Insuring InteroperabilityLSP – the integrating platform!
LSPTools/ Technologies
Visualisation
Translational Medicine
Big Data / Cloud CRO’s
Math/Stats support
ELN/BioRails
External Information
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Book chapter about LSP and our way of doing things
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Building research data handling systems with open source toolsClaus Stie Kallesøe
Alternative to use LSP
• No one has a system that covers all areas and data types
Several different vendor packages
• All packages will have a license as well as a maintenance fee
Higher licens and maintenance costs
• Implementing these tools takes time• Integrations between vendor tools are complicated
Long implementation & integration projects
• When one piece gets upgraded the rest has to follow
• You tend to stay with what you have
Constant integration and upgrade
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Cross Pharma (and beyond) projects
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Pre-competitive; Collaboration and Interoperability. It’s happening....
• Central open storage of pharmacological dataIMI OpenPhacts
• Cloud based NGS analysis and collaboration
Pistoia Sequence services
• Open Source Translation Medicine data handling
• Build by J&J from open source tools
IMI eTriks/tranSMART
IMI OpenPhacts
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What does Open PHACTS do? Currently integrated databases
Database Number of triples (million)
ACD Labs / ChemSpider 161.34ChEBI 0.91ChEMBL_v13 146.08ConceptWiki 3.74DrugBank 0.52Enzyme 0.07Gene Ontology 0.85SwissProt 156.57WikiPathways 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?
The Open PHACTS Explorer
The Open PHACTS Explorer allows the user to query and interact with the data present in the Open PHACTS platform. The interface:
• Is intuitive and easy to use• Allows data provenance to
be assessed
Application Programming Interface (API)
The Open PHACTS platform features an API which allows development of applications to query and visualise the data within the platform in novel ways.
Public version released last week!
IMI eTRIKS
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Consortium of 16 PartnersAcademic/Pharma/Coordination/St
andards
Academic LeadDevelopment
EFPIA Lead
Coordination
Hosting
Analytics
Standards
Imperial College London
AstraZeneca
Universite Du
Luxembourg
Sanofi
Roche PfizerMerck Serono
Lundbeck
Janssen idbsGlaxo
SmithKline
Lilly
CNRS CDISCBiosci
Consulting
Bayer
eTRIKS PLATFORM
Founded on tranSMARTGPL v3 Open Source Translational Data
Warehouse
Building upon Janssen’s Award Winning Translational Informatics System
Demonstrated Success with the U-BIOPRED IMI Project
Pistoia Alliance
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The Pistoia Mission
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Lowering the barriers to innovation
by improving inter-operability of R&D business processes
through pre-competitive collaboration
Conclusion and/or Next steps
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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
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Where do we go from here?
HTML5 + javascript
More Semantic linking of diverse data sources
Data Science - Hadoop, NoSql etc
Cloud – AWS, OpenStack
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W3C Health Care & Life Sciences (HCLS) IG
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One solution – Linking data with Semantic technologies – Hlu/DERI/Sindicetech
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LSP- Lundbeck Research SystemSindiceTech HCLS Cloud – linking external public data
Research
Database
Link internal and external data
1)
2)3)
Because you need Semantic SandBoxes
More open data – Open database with health records
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We are hiring….http://www.lundbeck.com/global/career/become-a-brainmate/job-opportunities?Id=E927314en
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These slides are here:
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