Open sourcedays2013 claus stie kallesoe

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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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ResearchInformatics

Ruby on RailsPhusion PassengerActs_as_authenticated…..…

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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