1. Retrospective The Cross Pharma HPC Forum (almost) four years on…
Rob Stansfield
October 13, 2011

2. Quantitative & Qualitative
(almost) 4 years
Since December 12, 2007
6 companies + Intel at the start
BMS, GSK, J&J, Merck, Pfizer, Wyeth + Intel
16 face to face meetings
Quarterly
Up to ~16 companies represented
Abbott Labs, Astra Zeneca, Biogen Idec, BMS, Boehringer-Ingelheim, Congenomics, Eli Lilly, GSK, J&J, Merck, Novartis, Pfizer, Roche, Sanofi-aventis, Schering-Plough, Wyeth + Intel
Up to ~30 attendees at a meeting
Dave Torgersen (Pfizer)
2008
Gene Fluder (Merck)
2009
John Morris (Wyeth >> Pfizer)
2010
Zheng Yang (GSK  BI)
2011
Rob Stansfield (Sanofi)
2012

3. SPECTRE SPEcific Computing for Tomorrow’s Research Environment
Zheng Yang (Dr. No) Dr. No
Gene Fluder (Blofeld) Diamonds Are Forever
Jeff Mathers (Goldfinger) Goldfinger
Tim Wagner (Scaramanga) Man With the Golden Gun
John Morris (Le Chiffre) Casino Royale
Dave Torgersen (Max Zorin) A View To A Kill
Mike Shevlin (Nick Nack) Man With the Golden Gun

4. F2F Meetings Attendance
Propose 1.5 days meeting
Oct ’09 : Merck  Schering Plough
Nov ’09 : Pfizer  Wyeth

5. Themes Early proposals Member companies Early 2008 Late 2008
Standardization
Software license models
API standards
Non-proprietary code exchanges
Member companies
Presentations
HPC Overview
Early 2008
Forum charter and mission, Voting rights, Visibility, Publish an article?
Governance, Role of Central IT
Growth of Linux, Grid computing (Univa/UD), Computing on demand
Storage, Collaborative (Open Source) software development
Vendor management, License management  ROI analyses
Late 2008
Clear and attainable goals for Forum
Invite ISV’s vs. do not invite ISV’s
New technologies, Cloud Computing
Doing science better  Doing better science

6. Themes (continued) Early 2009 Late 2009 Early 2010 Late 2010
Best practices, Conference reports
NONMEM rewrite?, GPU
Storage / Specialized storage
Late 2009
Introspection – User Group? Special Interest? Task Force?
Emerging technologies (and ICAP companies), HPC benchmarking
File systems (e.g. pNFS vs. PVFS)
Emerging Science (enabled by HPC)
Sub groups / Tech committee on advanced topics, working via teleconference
GUI for Molecular Dynamics, CCG (MOE)
Early 2010
Big data (Broad Institute)
HPC at Intel
Cray Computer
Workflow tools (Pipeline Pilot, Knime, et al)
Late 2010
Next-gen sequencing
NVIDIA (GPU, CUDA, NONMEM)

7. Six Illustrative Themes
2007 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
2008
2009
2010
2011
MISSION / CHARTER
VENDOR MANAGEMENT
SOFTWARE LICENSING
CLOUD COMPUTING
BEST PRACTICES
MARKETING

8. Mission / Charter 2007 2008 2009 2010 2011 MISSION / CHARTER 1 2 3 4 51 2 3 4 5 6 7 8 9 10 11 12 13 14 15
2008
2009
2010
2011
MISSION / CHARTER
To (accelerate) improve pharmaceutical research and scientific outcomes by collaborating to optimize HPC capabilities, promote standards, and develop best practices
“Get my stuff done and make sure my manager can get to it and if there are mistakes re-run the job and also make sure it integrates with the tools I am using today” Jeff Mathers, J&J, Meeting #1, 30-Jan-08
Group goals and purpose redux
Action to draft charter
Final version agreed
“To improve the level of support and responsiveness to the scientific community” Executive Summary, Meeting #0
Ref: Pistoia Alliance presentation

9. Charter
Mission
The mission of the Cross-Pharma HPC Forum is to improve the outcomes of scientific research, in time, quality, and cost, by maximizing the value of HPC in pharmaceutical R&D through collaboration to optimize capabilities, to promote standards, and to develop best practices
The major goals of the Cross-Pharma HPC Forum are to:
Establish and maintain a network among the member companies that fosters open communication of non-commercially sensitive information;
Educate members regarding best practices in the exploitation and management of HPC in the pharmaceutical and other industries;
Promote the development and use of open standards for specialized scientific applications in pharmaceutical R&D;
Identify challenges, scientific and otherwise, where the collective influence and pooled efforts of the members can be leveraged for mutual benefit;
Create opportunities for open and informal dialogue between the members and suppliers of HPC products and services;
Alert members to new and emerging information technologies and products of special relevance to HPC in pharmaceutical R&D and to coordinate efforts accordingly.
Goals

10. Vendor Management / OS Framework
2007 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
2008
2009
2010
2011
Ref: Peter Krey JPMorganChase
Ref: BioConductor “R” presentation Ref: Open Source SB-Grid presentation
Advice from Wall Street “Step on the air hose – when they can’t breathe, then they’ll listen” Peter Krey, JPMorganChase, Meeting #3
VENDOR MANAGEMENT
Proposal for Open Source initiative to develop a frame-
work to optimize (counter / enhance) vendor solutions
Top 10 vendors
Top 5 vendors -Schrodinger -Accelrys -Mathworks -Ariadne -Ingenuity
Intel ISV engagement model
Group agrees to not to pursue further
Working Group - focus on Chemistry
Reference: Collaborative Software Initiative (CSI) for OS development Reference: ACORD strategy (standards-setting for insurance industry)

11. Software Licensing 2007 2008 2009 2010 2011 SOFTWARE LICENSING 1 2 3 41 2 3 4 5 6 7 8 9 10 11 12 13 14 15
2008
2009
2010
2011
HPC SW Licensing Scorecard
Discussion ends naturally
Pfizer’s “S” curve
Revisited
Several companies experiencing challenges in negotiating licenses
SOFTWARE LICENSING
Outline for a licensing position paper
Top 10 vendors
Top 5 vendors -Schrodinger -Accelrys -Mathworks -Ariadne -Ingenuity
Intel ISV engagement model
Working Group

12. Vendor Management & Software Licensing
Valuable documents
Licensing position paper from 2008
HPC SW Licensing scorecard from 2008
Valuable reference models
“S” curve – as a model of desirable software licensing
ACORD – as a model of standards setting
BioConductor, Open-SB, CSI – as models of collaborative and Open Source software development
Wall street – as a model for vendor management
Vendor identification
And identification of alternatives
Intel as facilitator

13. Cloud Computing 2007 2008 2009 2010 2011 CLOUD COMPUTING 1 2 3 4 5 6 71 2 3 4 5 6 7 8 9 10 11 12 13 14 15
2008
2009
2010
2011
BioIT World
BioIT World
EMC on Cloud storage
Moderated discussion  5 “pilots”
GSK (UK) on the economics of Cloud Computing
Co-meeting with Sanofi-aventis & Sanofi Pasteur
CLOUD COMPUTING
Lilly Cloud 1.0 live demo using AWS for IaaS
Lilly update
Pfizer update
Chris Dag (BioTeam)
Everyone is in this game !! (see next slide)

14. Meeting #14, 2Q (Jun 22-23), 2011
Every Pharma company represented is either already using AWS or starting evaluations and pilots
Pfizer use AWS for production scientific HPC with a "DIY" approach to building and automating the service
Merck will copy Pfizer
Eli Lilly have worked with Cycle Computing as an intermediary to AWS for three years
JnJ already use AWS for some other purposes (e.g. TranSMART), and are starting an evaluation with Cycle Computing
Boehringer Ingelheim and Roche expressed their intent to start evaluating public cloud this year
Novartis (NIBR) have been working with CloudSwitch for secure hybrid cloud since one year
Conclusion - good for external application hosting, not good for HPC
and have evaluated several sources for external scientific HPC, including Dell and Cycle Computing

15. Best Practices 2007 2008 2009 2010 2011 BEST PRACTICES 1 2 3 4 5 6 7 81 2 3 4 5 6 7 8 9 10 11 12 13 14 15
2008
2009
2010
2011
Report on PRIME meeting of Apr 30
Proposal from Tabor Research
Survey definition 7 companies commit
BEST PRACTICES
Tabor  InterSect 360
Final report

16. Best Practices Final report Expected Unexpected
Seven participating (paying) companies
Very diverse approaches in each organization
Different users distributions
Different organizations
Different architectures
Expected
Common issues, challenges, to which organizations adapt
Unexpected
No single Best Practice identified
A successful collaboration on a jointly financed exercise
Motivated by self-interest in anonymized benchmarking

17. Marketing
2007 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
2008
2009
2010
2011
Plan for ACS Fall presentations
Yahoo  Website
Four public presentations at the ACS Fall annual meeting
MARKETING

18. Personal (Sanofi) Highlights
Pat Gelsinger (Intel)
April 2008, e.g. future of Infiniband vs. 10Gb Ethernet
Between meetings (2Q 2008)
Clustered storage discussion facilitated by G.Pocina (Pfizer)
Experiences of Michael Parker and John Dey at Merck (Rosetta) with multiple storage solutions, as well as Pfizer
Pointed us to Isilon systems
Evaluation  Benchmarking  Purchase
Peter Krey (JPMorganChase)
July 2008, Tough approach to vendor management
Dave Powers, Andrew Kaczorak (Eli Lilly)
Sep 2008, Cloud Computing live demo

19. -Pharma
HPC
Thank You!

20. Date Location Attendees Companies Agenda & Presentations
Quarterly Meetings
Date
Location
Attendees
Companies
Agenda & Presentations

21. Meeting #0 The Kickoff ! “Pharma IT Forum” Attendees (~10)
December 12, 2007
Mediterra Restaurant, Princeton, NJ
“Pharma IT Forum”
Attendees (~10)
Companies (7)
BMS, GSK, Intel, J&J, Merck, Pfizer, Wyeth
Agenda & Presentations
Discussion around forming the group
Organizational situation
Principles for the “forum”
Ongoing challenges
Branding
SPECTRE = SPEcific Computing for Tomorrow’s Research Environment
HPC in Pfizer
Dave Torgersen
Linux and HPC
John Morris, Wyeth Research

22. Meeting #1 1Q 2008 “Pharma IT Forum” Mission Statement (WIP)
January 30, 2008
J&J R&D, Raritan, NJ
“Pharma IT Forum” Mission Statement (WIP)
“To (accelerate) improve pharmaceutical research and scientific outcomes by collaborating to optimize HPC capabilities, promote standards, and develop best practices.”
Attendees (~11)
Companies (7)
BMS, GSK, Intel, J&J, Merck, Pfizer, +Wyeth
Agenda & Presentations
Pfizer company presentation
Dave Torgersen
Merck company presentation
Gene Fluder
J&J company presentation
Jeff Mathers
Wyeth Research presentation
John Morris
GSK company presentation
Zheng Yang
BMS company presentation
Tim Wagner

23. Meeting #2 2Q 2008 “Cross Pharma HPC Consortium” Attendees (~20)
April 29, 2008
Intel, Cambridge, MA
“Cross Pharma HPC Consortium”
Attendees (~20)
Companies (10)
+Astra Zeneca, BMS, GSK, Intel, J&J, Merck, Novartis, Pfizer, +Sanofi-aventis, Wyeth
Preceding evening
Dinner with Pat Gelsinger, SVP and General Manager of Intel’s Digital Enterprise Group
Agenda & Presentations
Sanofi-aventis presentation
Rob Stansfield
Novartis company presentation
Jason Calvert
Vendor Management & Licensing
Mike Miller, Pfizer
Licensing discussion
Application Deployment best practices in Scientific Computing
Tim Wagner, BMS
Intel CTO

24. Meeting #3 3Q 2008 “Cross Pharma HPC Forum” Attendees (~20)
July 15, 2008
GSK, Collegeville, PA
“Cross Pharma HPC Forum”
Attendees (~20)
Companies (9)
BMS, GSK, Intel, J&J, Merck, Novartis, Pfizer, Sanofi-aventis, Wyeth
Preceding evening
Hosted dinner courtesy IBM
Steven Simon, Director of IBM’s System and Technology Group Industry Solution Centers
Peter Krey, Wall Street Executive
Agenda & Presentations
Licensing Working Group
Draft position paper
Discussion over working lunch
Presentation on Wall Street experience with vendor management
Peter Krey, Krey Associates, Head of Research & Engineering, IB Architecture, JPMorganChase
Open Source Working Group
Status and next steps

25. Meeting #4 4Q 2008 Attendees (~27) Companies (11) Preceding evening
September 23, 2008
Merck, Rahway, NJ
Attendees (~27)
Companies (11)
BMS, +Eli Lilly, GSK, Intel, J&J, Merck, Novartis, Pfizer, Sanofi-aventis, +Schering-Plough, Wyeth
Preceding evening
Dinner courtesy of IBM
Michael Hehenberger, IBM Global Life Science R&D Solutions
Agenda & Presentations
Schering Plough presentation
Corey Strickland
Eli Lilly company presentation
Andrew Kaczorek
Licensing Position Paper
Goran Pocina (Pfizer)
Forum goals and purpose redux
John Morris (Wyeth)
Vendor Management
Top ten ranked in order
Top five ranked by votes
 SW Licensing Scorecard
Cloud Computing
Dave Powers (Eli Lilly)
Open Source project
Mike Miller (Pfizer)

26. Meeting #5 1Q 2009 Attendees (~33) Companies (15) Preceding Evening
January 14, 2009
Novartis (NIBR), Cambridge, MA
Attendees (~33)
Companies (15)
+Abbott Labs, BMS, +Boehringer-Ingelheim, +Congenomics, +Harvard Med School, Eli Lilly, GSK, Intel, J&J, Merck, Novartis, Pfizer, Sanofi-aventis, Schering-Plough, Wyeth
Preceding Evening
Dinner courtesy of EMC
Agenda & Presentations
BI company presentation
Miguel Teodoro
(cont.)
Abbott Labs presentation
Scott Brown, Steve Muchmore
BioConductor project
Vincent Cary, Harvard Medical School
Open Source SB-Grid
Piotr Sliz, Harvard Medical School
SuperComputing 08 recap
J.Morris (Wyeth), A.Kaczorak (Lilly), G.Stiegler (BMS), G.Pocina (Pfizer)
Best Practices proposal w Tabor
John Morris (Wyeth)
Pistoia Alliance
Debbie Igo (Novartis)
ISV Engagement Model
Henry Gabb (Intel)

27. Meeting #6 2Q 2009 Attendees (~20) Dinner Companies (11)
May 5-6, 2009
Sanofi-aventis, Bridgewater, NJ
Attendees (~20)
Companies (11)
BMS, BI, Congenomics, GSK, Intel, J&J, Merck, Pfizer, Sanofi-aventis, Schering-Plough, Wyeth
Day 1 : Agenda & Presentations
Best Practices survey
John Morris (Wyeth)
Invite 13 companies
Review of PRIME meeting on April 30 in Groton (Pfizer)
Vendor interaction
Mike Miller (Pfizer)
Dinner
Day 2 : Agenda & Presentations
Formal charter discussion
Gene Fluder (Merck)
HPC Storage
John Morris (Wyeth), Rich Bach (Merck)
Future Topics
Cloud Computing
M.Teodoro (BI), S.Piotrowski (J&J)
 Five companies pursuing

28. Meeting #7 3Q 2009 Attendees (~21) Companies (14)
August 10-11, 2009
BMS, Pennington, NJ
Attendees (~21)
Companies (14)
Abbott Labs, BMS, BI, Congenomics, Eli Lilly, GSK, Intel, J&J, Merck, Novartis, Pfizer, Sanofi-aventis, Schering-Plough, Wyeth
Day 1 : Agenda & Presentations
Intel Capital’s Investment portfolio, emerging technologies
Six company presentations
Dinner
Hosted by Intel
Day 2 : Agenda & Presentations
Vendor interaction update
Mike Miller (Pfizer)
Best Practices survey update
John Morris (Wyeth)
HPC enablement for Molecular Dynamics
Zheng Yang (GSK)
Forum objective and strategy
Gene Fluder (Merck)
pNFS vs. PVFS
Rich Bach (Merck)

29. Meeting #8 4Q 2009 (RS not present) Attendees (~?) Companies (?)
October 22-23, 2009
Pfizer, Groton, CT
Attendees (~?)
Companies (?)
Day 1 : Agenda & Presentations
Review/Acceptance of Mission Statement
John Morris (Wyeth)
GUI discussion
Miguel Teodoro (BI)
Best Practices survey update
Addison Snell (Tabor), John Morris (Wyeth)
Dinner
Hosted by Isilon
Day 2 : Agenda & Presentations
Marketing and publicity
Gene Fluder (Merck), Zheng Yang (GSK)
Current efforts / update
Gene Fluder (Merck)
Mike Miller (Pfizer)
Technology roundtable
Greg Stiegler (BMS), Corey Strickland (S-P)
Industry Trends
Chris Dwan (BioTeam)

30. Mergers & Acquisitions
Oct : Pfizer  Wyeth
Nov 2009 : Merck  Schering-Plough

31. Meeting #9 1Q 2010 Attendees (~19) Companies (10)
March 1-2, 2010
B-I, Ridgefield, CT
Attendees (~19)
Companies (10)
BMS, BI, Congenomics, Eli Lilly, GSK, Intel, J&J, Merck, Pfizer, Sanofi-aventis, [Wyeth]
Day 1 : Agenda & Presentations
MOE / NAMD GUI dev. Update
Paul Labute (CCG Inc.)
Broad Institute infrastructure
Matt Trunnell
HPC at Intel
Shesha Krishnapura (a talk delivered at SC ’09)
Dinner
Hosted by Intel
Day 2 : Agenda & Presentations
HPC Grid at GSK
Jeremy Martin
Workflow tools update
Steve Litster
HPC at Sanofi-aventis
Rob Stansfield
Marketing/Publicity & ACS
Z.Yang (GSK), G.Fluder (Merck), R.Bruccoleri Congenomics), M.Miller (Pfizer
 Fall ACS National Meeting
Cloud Computing
G.Stiegler (BMS), D.Powers (Lilly), M.Miller (Pfizer)
Best Practices Report
Addison Snell (InterSect 360)

32. Meeting #10 2Q 2010 Attendees (~24) Dinner Companies (10)
May 13-14, 2010
Merck (ex S-P), Kenilworth, NJ
Attendees (~24)
Companies (10)
BMS, BI, Congenomics, GSK, Intel, J&J, Merck, Novartis, Pfizer, Sanofi-aventis
Day 1 : Agenda & Presentations
2010 BioIT World Summary
R.Stansfield (Sanofi-aventis), G.Stiegler (BMS), J.Morris (Pfizer)
ACS Conference preparations
Z.Yang (GSK)
Cross Pharma HPC website
R.Bruccoleri (Congenomics)
Cray Computer
Barry Bolding
Dinner
Hosted by Cray Computer
Day 2 : Agenda & Presentations
Workflow tools
Steve Litster (Novartis)
Funding of projects
Gene Fluder
HPC at Merck
Cloud Technologies
Chris Dagdigian (BioTeam)
Advanced Linux topics
Greg Stiegler (BMS)

33. Meeting #11 3Q 2010 (plus ACS) Attendees (~?) Companies (?) Dinner
½ day, August 24, 2010
Novartis (NIBR), Cambridge, MA
Attendees (~?)
Companies (?)
BMS, BI, Congenomics, GSK, Intel, J&J, Merck, Novartis, Pfizer, Sanofi-aventis
ACS Fall Annual Meeting
August 25, 2010
Boston, MA
ACS Agenda
Intro to X-Pharma HPC Forum
John Morris (Pfizer)
Applications & Use of Cloud…
Mike Miller (Pfizer)
(cont.)
Current Trends of HPC in Pharma
Steve Litster (Novartis)
Challenges & Collaboration...
Rob Stansfield (Sanofi-aventis)
Dinner
Hosted by VMWare
Agenda & Presentations
Website update
R.Bruccoleri (Congenomics)
GSK HPC update
Workflow (Knime) update
Steve Litster (NIBR)
Advanced Linux topics
G.Stiegler (BMS)
VMWare presentation

34. Meeting #12 4Q 2010 (RS not present) Attendees (~16) Companies (8)
November 11-12, 2010
J&J, Spring House, PA
Attendees (~16)
Companies (8)
BMS, BI, Congenomics, GSK, Intel, J&J, Merck, Pfizer
Day 1 : Agenda & Presentations
Advanced Linux Topics
Greg Stiegler (BMS)
Protein Database System
Corey Strickland (Merck) Proasis, Marti Head (GSK) PSILO
Brainstorm on collaboration topics
G.Fluder (Merck), Z.Yang (BI)
 NONMEM optimization
Dinner
Hosted by SGI?
Day 2 : Agenda & Presentations
Website update & LinkedIn
R.Bruccoleri, Z.Yang (BI)
Intel many-core strategy
Mike Shevlin
Cray feedback
Gene Fluder (Merck)
HPC at J&J and Cloud Computing
Zhen Min, Sebastian Piotrowski
New topics

35. Meeting #13 1Q 2011 Attendees (~) Companies ()
March 3-4, 2011
Sanofi-aventis, Bridgewater, NJ
Attendees (~)
Companies ()
Day 1 : Agenda & Presentations
Co-meeting with Sanofi-aventis and Sanofi Pasteur
NVIDIA presentation
Kimberly Powell et al
Dinner
Hosted by NVIDIA
Day 2 : Agenda & Presentations
Eli Lilly company presentation
Jon Klinginsmith
Workflow update
Steve Litster (Novartis)
Intel-Oracle presentation
Discussion over ECLC

36. Meeting #14 2Q 2011 Attendees (~) Companies ()
June 22-23
BMS, Lawrenceville, NJ
Attendees (~)
Companies ()
Day 1 : Agenda & Presentations
Large scale data movement
Mike Miller (Pfizer)
License practice discussion
Stewart Samuel
Next generation sequencing
Bob Bruccoleri (Congenomics)
IBM presentation
Dinner
Hosted by IBM
Day 2 : Agenda & Presentations
Network connection discussion
Steve Litster
Roche company presentation
Michael Braxenthaler
Membership discussion
HP tech briefing
Follow-up discussion of GPGPU with NVIDIA
Gene Fluder (Merck)
Preparation for Q3 meeting