http://pistoiaalliance.org

September 2011

The Pistoia AllianceAnnual General Meeting - 2011

2

Welcome

3

Please mute your line unless you want to ask a question

http://pistoiaalliance.org

September 2011

The Pistoia AllianceMinutes of 2010 AGM

Microsoft Word Document

6

Actions from 2010 Minutes

Action Items:• The board will work with the Operational Team to flesh out other

ideas, and will talk reach out to the wider network to further explore these ideas.

• Ashley to work with the people who proposed these projects to develop PowerPoint presentations that can be used to solicit input from board members to gauge interest.

http://pistoiaalliance.org

September 2011

The Pistoia AllianceBoard and Membership Update

Core Board Member Change

• 10 Core companies• Bi-Annual rotation process• AstraZeneca, BMS, GSK, Lundbeck, Pfizer, Roche agreed to continue• 1 Seat Vacant as Novartis kindly agreed to step down and• 1 Candidate – Merck & Co            

– Decision:– Merck & Co are duly elected to Pistoia Alliance board until

2013 AGM.

8

Participating Board Member Vote

• Annual Rotation Process• 14 Participating companies• 6 Seats vacant (Infosys stepped down and normal rotation process)• 7 candidates – we thank them all for standing• Candidates:

1. Frank Brown VP and CSO Accelrys2. Joe Donahue  Senior Vice President, Global Sales at Thomson

Reuters Life Sciences 3. Alex Drijver, CEO, ChemAxon4. Sean Eakins, Collaborations Director, Collaborative Drug Discovery5. Nicholas Lakin, Cognizant6. Alex Scheer, Director, Informatics & Knowledge Management, Merck

Serono 7. Michael Stapleton , General Manager, Informatics at

PerkinElmer                – Decision: Frank, Joe, Alex D, Sean, Alex S, and Michael are

duly elected to Pistoia Alliance board until 2012 AGM.9

Pistoia Governance

• BoD

• Operational Team

• Technical Committee Chair

Tom FloresGlaxoSmithKlineChristoph Brockel PfizerJason SwiftAstraZenecaIngrid Akerblom Merck & CoSean Eakins CDDMichael Stapleton PerkinElmer

Michael Braxenthaler Roche External LiaisonAshley George GlaxoSmithKline TreasurerJohn Wise Executive DirectorNick Lynch AstraZeneca PresidentDeborah Ausman CommunicationsMartyn Wilkins Company Secretary

VacantSupported by Working Group Chairs and Operational Team

Ramesh Durvasula BMSAlex Drijver ChemAxonFrank Brown AccelrysClaus Stie Kallesøe LundbeckBryn Roberts F. Hoffmann-La RocheAlexander Scheer Merck SeronoJoe Donahue Thomson Reuters

Thanks to Pierre Menard for all his contributions to Pistoia as Technical Committee Chair

10

Pistoia Alliance MembershipSept 2011

Member Summary

Targets for 2011/2012:

• Biotechs & Life Science companies

• Academics/NGOs• CROs• Wider Geographic coverage

(Asia etc)

55 members

Can you help with member recruitment?

10

1431

Members

Core

Participating

Contributing

12

http://pistoiaalliance.org

September 2011

The Pistoia AllianceProject Portfolio Review

Sequence Services Phase 1

• Define standards for the provision of secure access to pre-competitive, shared, hosted, gene sequence databases and software tools.

Objective

• £200,000• end April 2011

Timeline & Funding

• Working prototype implementations demonstrated at the Pistoia Alliance User Conference April 2011

Deliverables

• Phase 2 launched. • RFP published with enhanced user requirements

including addressing NGS data.• RFP responses expected 23-Sep-11• Phase 2 PoC demonstrations at PA User Conference

– April 2012

Next steps

Status: • Phase 1 achieved• Phase 2

commencedProject lead: Simon Thornber GSK

Sequence Squeeze

• Find a new algorithm/technique for compressing next-generation

• sequencing data for use in the Sequenced Services project

Objective

• £12,000 + VAT @ 20% to manage the prize• $15,000 prize money• April 2011 (ready for announcement at the Pistoia

Alliance Users Conference)

Timeline & Funding

• Establish competition website: http://www.sequencesqueeze.org/

• Establish a judging panel• State-of-the-art gene sequence data compression tool

Deliverables

• Project launch – start Q4 2011• Entries close end Q1 2012• Winners to be announced at the Pistoia Alliance Annual

Conference on April 2012.

Next steps

Status: • On trackProject lead: Simon Thornber GSK

SESL Phase 1

• Provide a ‘push model’ for end-user access to biomedical knowledge stored in both published literature and biological database content.

Objective

• £200,000• end June 2011

Timeline & Funding

• A publicly accessible demonstrator http://www.pistoia-sesl.org

• Two publications submitted end Q3 2011

Deliverables

• Terminate project. • Complete demonstrator implementation• Submit publications• Transfer learnings to IMI Open PHACTS project

Next steps

Status: • Phase 1

completion delayed

• Phase 2 terminated

Project Lead: Ian Harrow, (Pfizer), Wendy Filsell, Unilever

ELN

• Provide a query standard to enable chemists to share information between – and to conduct searches across – different brands of ELNs without learning a plethora of search languages.

Objective

• Phase 2 costs: $12,500• Phase 2 completed

Timeline & Funding

• Identified and documented use cases• Elaborated an XML-based query standard – ready for

testing

Deliverables

• Find resource to write and publish a paper highlighting the opportunities and challenges of ELN Query standards.

Next steps

Status: • Project

terminated after Phase 2

Project Lead: Richard Bolton

VSI

• Provide a focus for vocabulary creators /consumers including publishers / Academia /Pharma and SMEs

• Identify gaps in life sciences vocabulary standards space

• Stimulate co-ordinated generation of new vocabularies in precompetitive space

Objective

• December 2009 to June 2011Timeline & Funding

• Paper submitted to and accepted by Drug Discovery Today – June 2011

Deliverables

• Identify and seek funding from interested parties to recruit a qualified consultancy to review vocabulary activities in the Life Sciences R&D domain.

• Identify leaders across companies to maintain momentum• Identify areas for further vocabulary development, either

specific initiatives, or as elements of other Pistoia activities• Assign priority to those areas

Next steps

Status: • Phase 1 complete• Phase 2 waiting

for resourcesProject Lead: Lee Harland (Pfizer), Ian Dix

(AZ)

1. Sequence Services Phase II• Project Analyst support is required going forward

2. Sequence Squeeze• Awaiting kick-off meeting

3. SESL• Develop relationship with IMI OpenPHACTS project?

4. ELN – Project close• Resource for writing up ELN project

5. VSI MDT Phase II• Resource required - Phase II consultant

6. Project Portfolio Questionnaire• 21 responses received – much follow-up required

7. Information Ecosystem Workshop• 18 delegate places already signed up

(1) Recent Accomplishments

(4) Planned Activities

1. Sequence Services Phase II• RFP signed-off - available on PA public-domain web-site• RFP launch meeting completed: 22-Jul-11• Project Analyst – new contract agreed and signed : 29-Jul-11

2. Sequence Squeeze• Gene Sequence Compression Prize – project named!• Appropriately qualified company appointed to run the prize• Contract signed

3. SESL• Main papers in production – outlines concluded mid-July 2011

4. VSI MDT Phase I• Paper accepted for publication (subject to changes) in “Drug

Discovery Today” 28-Jun-11• Reviewer comments addressed 21-Jul-11

5. Project Portfolio Questionnaire• Circulated end June 2011• Used at the 3rd Annual Lab Data Mgmt. Conf. London – June-11• 22 Responses collated and available in basecamp

6. Information Ecosystem Workshop• Kick-off planning meeting Thursday 7-Jul-11• Draft agenda created• Delegates workshop planning meeting arranged 23-Aug-11

1. Sequence Services Phase II (NGS)• RFP response deadline: 23-Sep-11

2. Sequence Squeeze• Compression Algorithm prize to be launched 1-Oct-11

3. SESL• Main papers to be submitted by end Q3 2011• Demonstrator to be available by end Aug 2011• Article for autumn edition of the newsletter

4. VSI MDT Phase II• Funding for consultant to provide background for business case• Generate and distribute RFP to qualified consultancies

5. ELN• Publish the ELN project as a living document e.g. Source Forge

6. Information Ecosystem Workshop• Monday 10-Oct-11 in Hanover, Germany

(2) FY 11 - Projects in Development

(3) Issues / Discussion Points

Project Status LegendSequence Services Phase II On ScheduleSequence Squeeze Caution / IssueELN Wrap-up Not going to meet scheduleSESL Wrap-up Completed

SESL Phase IIVSI Phase IVSI Target Description Phase IIInformation ecosystem workshop

Reflections on Progress

Pistoia Alliance Project Teams - Reflections

Slide 21

STRENGTHS OPPORTUNITIES

• Cross-domain team work (viz: Life Sciences R&D, technology vendors, academia, commercial information suppliers)

• Enthusiastic teams - well respected in the wider industry (e.g. links to IMI)

• Definition of commonly-shared, pre-competitive use cases.

• Definition of functional and non-functional requirements including Security

• Shared funding models allow pilots to be built that would otherwise not be built

• Proofs-of-concept allow insights into optimal technical implementations.

• Establish a base platform for SaaS in Life Sciences discovery

• Publish use cases to a wider audience• Encourage use of standardised

vocabularies• Provide state-of-the-art information

services – even to bench scientists• Align with IMI initiatives

WEAKNESSES THREATS• Projects’ values not always well

understood by senior stakeholders• Fewer user companies represented in

the project teams than desirable• Identifying viable, future, sustainable,

business models for all stakeholders

• Need to identify sustainable business model(s) for the on-going provision and up-grade of services

• Identification of clear roles and responsibilities within volunteer-based project teams

• Need to identify new project leads & co-leads

Pistoia Alliance Publications

1. “The Pistoia Alliance - The Sequence Services Project” - Simon Thornber et al. - G.I.T. Laboratory Journal 1-2/2011

2. “Need for Collaborative Technologies in Drug Discovery” - Chris L. Waller et al. Book Chapter in “Collaborative Computational Technologies for Biomedical Research” – Edited by Sean Ekins et al. Wiley May 2011

3. “What are the obstacles to innovation in the Pharmaceutical Industry? The Pistoia Alliance responds” – The Pistoia Alliance – Drug Discovery World

4. “Empowering Industrial Research With Shared Biomedical Vocabularies” – Lee Harland et al - Drug Discovery Today in press

5. “ELNs - An Essential Productivity Tool – But Which One to Use” – John Wise - European Pharmaceutical Review - Issue 4, 2011 22

http://pistoiaalliance.org

September 2011

The Pistoia AllianceProject Portfolio Questionnaire Analysis

Project Portfolio Questionnaire – Summary

Analysis out of 22 Question # Interested?Contribute Users

to define Requirements?

Contribute a Project

Manager?

Contribute Funding?

Chemistry - Collaboration Backbone

2 15 8 1 1

Chemistry - (Hosted) Ordering / Requesting Services

3 9 4 3 1

Chemistry - Hosted ELN and Services

4 12 6 1 1

Chemistry - Collaboration Brokering

5 9 5 0 1

Chemistry - Analytical Data Standards

6 11 7 1 2

Chemistry - Hosted Registration Services

7 12 4 1 0

Life Sciences - Information Ecosystem Workshop

8 19 13 8 2

Projects which are important to you /your company.

9 7 1 1 1

1

At GQ we believe that both sequencing and sequencing analysis/data management are pre-competitive. To date, Pistoia has focused only on basic sequence analysis. I know that phase II of the sequence piece will include NGS. However, I like the way you outlined the chemistry piece above, much more life-cycle centric. I’d argue you should do the same with NGS Sequencing and NGS Informatics.

2 Interested in the Semantic Web

3It’s important that Pistoia picks a few key projects and nails them now, so a general steer would be not to dilute efforts or become over ambitious now. Put maximum energy and resource into a small number of projects and ensure success to ‘prove’ Pistoia works.

4Multi-party collaboration, project management, reporting tools including hosted, cloud-based or internal platforms. Multi-vendor integration approaches. Multi-discipline data integration.

5 Pharma is moving towards externalization and the key to success is a standardized, scalable collaboration backbone.

6 Platform for sharing in-house code externally

7 SEND (the CDISC standard for non-clinical data) Tox/DMPK area - Archiving

8 Standardisation of clinical data format (by this comment was meant the exchange of information with CROs)

9 Standards are important to us, as are projects involving making data more accessible to end users.

10

We are very interested in external collaborative systems. However our current focus is to 'find' a vendor already in this space and ensure that the Vendor is driven by open standards (where they exist). I hope that Pistoia will eventually lead to a standards body for data sharing formats. Perhaps our goal should be to have Vendors proud to bear the mark 'Verified by Pistoia'. I wonder where this fits into the various standards coming from W3C? The list above does not yet seem to ask questions regarding data formats for Assay/Protocol transfer. I think this is a critical issue when collaborating with multiple organisations. Is there a project looking into this?

11 We focus on services around workflows for data integration/analysis, moving towards self-service workflows.

Open Question - 9

http://pistoiaalliance.org

September 2011

The Pistoia AllianceInformation Ecosystem Workshop (IES)Overview

IES Workshop: Logistics

• All day Monday, October 10, 2011When?• Radisson Blu Hotel Hannover• EXPO Plaza 5• 30539 Hannover, Germany

Where?

• More information on the Pistoia website

• http://www.pistoiaalliance.org/2011-Events/infoecoworkshop.html/

How?

Agenda and Deliverables Outline

1• IES straw man presentation

2• Work in breakout groups on IES

concepts

3• Breakout group reports on

concepts

4

• Consolidated feedback from morning session and proposals for breakout groups

5• Work in breakout groups on IES

roadmap

6• Breakout group reports on

roadmap

Morning session:What is the IES? Develop common understanding on what the IES should deliver (use cases)

Afternoon session:How do we get there? Develop a roadmap of projects and activities

White Paper:The Key Concepts

of the Information Ecosystem

IES Roadmap:Projects and

Follow-up activities

More info at http://pistoiaalliance.org/2011-Events/infoecoworkshop.html

http://pistoiaalliance.org

September 2011

The Pistoia AllianceViews of a new member

“Thoughts of a new member of the Pistoia Alliance”

Presentation to the Pistoia Alliance AGMNick Trigg, CEO

Constellation Technologies13th Sept 2011

30

Constellation Technologies• Involvement with Pistoia

– contributing supplier since 2010– paid up “Participating” member since 2011

• “Technology provider”– Technology provider with technology from CERN and UK particle

physics programme specialising in providing “big data and bioinformatics” expertise to industrial customers.

– Looking for partners with which to develop next generation products for bioinformatics

• Delivered solution to Pistoia “Sequence Services Phase 1”– Partnership with Microsoft and STFC– Demonstrated solution at the Pistoia Users Conference, Boston, April

2011

31

Pistoia -An alliance of interested parties • Pharmas

– Large/medium/small• Biotechs• Academic institutions• Technology providers• Information providers• Infrastructure providers

32

Demand side

Supply side

Objectives of Pistoia• Fundamentally

– Make more money!– Solve complicated problems better/faster

• How does it do that?– Access to customers/suppliers– Access to partners/collaborators– Latest thinking/trends– Opportunity to influence/direct

33

How to increase value for members

• More in = more out• Keep it relevant• Maintain momentum with innovative projects• Work efficiently

– Same time as other events/Teleconferencing• Raise additional funding for projects from

other sources– Government etc

34

How to attract new members

• It is unique• Added value of a special interest “club”

– More customers or suppliers than normally possible

• Leverage of everything– Money, ideas, technologies, etc

35

Summary• Recognise that Pistoia is probably unique in

the world• Keep it going!• Realise “failures” are not all bad• Manage back into your organisations• Don’t let it die slowly through expectation that

it will die slowly

36

http://pistoiaalliance.org

September 2011

The Pistoia AllianceSummary

39

Thanks for your engagement in the coming year!