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52_18695_BIO0305 2/18/05 5:16 PM Page 52

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Together, your possibilities are endless.

Find out about Inform 2005, May 24 - 26, 2005 • Visit www.inform2005.com
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© 2005 Waters Corporation Waters, eLab Notebook, NuGenesis, Empower and MassLynx are trademarks of Waters Corporation.

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01r2_695_BIO0305 2/22/05 4:45 PM Page 1

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www.bio-itworld.com

BioIT WorldTECHNOLOGIES DRIVING DISCOVERY, DEVELOPMENT, AND CLINICAL TRIALS

Trekking Toward
a Medical Tricorder
Philip Schiller, Apple
senior vice president
of worldwide product
MARCH 2005 • VOL. 4, NO. 3

Is That a
SCIENCE + TECHNOLOGY Tiny electrode
marketing
Target on
sensors from Vanderbilt’s Institute for
Integrative Biosys-
Her Back?
tems Research and
Education may
DATA • Q&A with
soon yield diagnos- Deborah Zarin, head
tic devices worthy of ClinicalTrials.gov
of Bones McCoy’s
MPTV.NET

clinic on the U.S.S. By Mark D. Uehling

Enterprise. 24 NOT SINCE THE EARLY years of
GenBank have so many in aca-
demia and industry been so in-
Show Me the Money terested in a mundane federal
database. ClinicalTrials.gov, run
BUSINESS + STRATEGY Harvard by the NIH’s National Library of
Business School panel debates best Medicine, was born as a match-
business models for bioinformatics making Web site for patients
– if that’s not an oxymoron. 13 seeking to participate in federal-
ly sponsored clinical trials. Now,
ANNE HAMERSKY

in the wake of the Vioxx recall

J&J Plans Global Grid and controversy over belatedly
or never-published pediatric
IT + INFORMATICS J&J plans to expand data from psychiatric trials,
its grid computing initiative from 450 to ClinicalTrials.gov is being buf-
more than 3,000 nodes worldwide. 40 feted by new demands from two
directions.

Coming Attractions
FIRST BASE Kevin Davies lays out the
top 10 reasons you
A PERFECT First, the editors of medical
journals are clamoring for Clini-
calTrials.gov to morph into a sci-
entifically useful repository of all
trial data — something that the
should attend this
year’s Bio•IT World
Conference + Expo. 6

PLUS
ABI’s New, More Sensitive Machine 20
REVENGE IS SWEET FOR APPLE,
RANDALL SCOTT

Microsoft Does Europe 42

Shanghai’s Grid Computing Project 44 NOW SAVORING THE RISE OF
Deborah Zarin
MAC OS X AND XSERVE IN THE U.S. Congress permitted, but nev-
er required, in the Food and Drug
LAB, BUT THIS IS STILL THE Administration Modernization
Act (FDAMA) of 1997. Pharma-
PLANTING. A DIFFICULT ceutical companies, meanwhile,
are pressuring Congress to make
GROWING SEASON LIES sure that ClinicalTrials.gov re-
mains a voluntary, partial archive
AHEAD. 26 of clinical trial data.
(CONTINUED ON PAGE 12)

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02_18695_BIO0305 2/16/05 9:11 PM Page 2

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E D C - e n a b l e d : LifeTree's electronic data

capture platform, LifeTree ICTM, enables
you to control and accelerate every
aspect of your study:
■ eCRFs you can build
■ easy-to-add edit checks
■ PDFs with one keystroke
■ data on demand
■ user-friendly technology

C u s t o m e r S a t i s f a c t i o n : LifeTree delivers
exceptional project management – from study
start-up to database lock.

S t a b i l i t y : LifeTree is a member of the FFF Enterprises

family of companies, a healthcare leader since 1988,
assuring you the stability you need in a clinical research partner.

www.lifetree-tech.com
www.fffenterprises.com
© 2004 LifeTree Technology LLC. The LifeTree logo, EDC Results and Accelerating clinical development, from data capture to market are trademarks of LifeTree Technology LLC.
The FFF Enterprises logo is a trademark of FFF Enterprises Inc. 1204

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03_18695_BIO0305 2/17/05 8:50 PM Page 3

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What if moving from one particular

protein to the most relevant journal
and patent literature were as easy
as pushing a button?

It is.
Not only does SciFinder provide access to more proteins and nucleic acids than any
publicly available source, but they’re a single click away from their referencing patents
and original research.

Coverage includes everything from the U.S. National Library of Medicine’s (NLM) MEDLINE® and
much more. In fact, SciFinder is the only single source of patents and journals worldwide.
Once you’ve found relevant literature, you can use SciFinder’s powerful refinement tools to focus on a
specific research area, for example: biological studies such as target organisms or diseases; expression
microarrays; or analytical studies such as immunoassays, fluorescence, or PCR analysis. From each reference,
you can link to the electronic full text of the original paper or patent, plus use citation tools to track how
the research has evolved and been applied.
Visualization tools help you understand results at a glance. You can categorize topics and substances,
identify relationships between areas of study, and see areas that haven’t been explored at all.
Comprehensive, intuitive, seamless—SciFinder directs you. It’s part of the process. To find out more, call
us at 1-800-753-4227 (North America) or 1-614-447-3700 (worldwide) or visit www.cas.org/SCIFINDER.

Part of the process.SM

A division of the American Chemical Society. SciFinder is a registered trademark of the American Chemical
Society. “Part of the process” is a service mark of the American Chemical Society.

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04_18695_BIO0305 2/22/05 1:54 PM Page 4

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Contents 03·05
Business + Strategy IT+ Informatics
^1 Is That a Target on Her? 40 Global Grid Team
DATA Chatting with Deborah Zarin, GRID COMPUTING J&J teams with
PAUL TROMBLEY, UNIVERSITY OF MICHIGAN
CENTER FOR BIOLOGIC NANOTECHNOLOGY

head of ClinicalTrials.gov. United Devices for grid pilot, to

13 Debating Business Models
STRATEGY Panel tackles informatics’
basic question: Where’s the money?
14 What’s New at Big Blue?
18 Nothing Ventured The scale of
computing has improved dramatically
in the life sciences. BY MICHAEL A. GREELEY
16 Trends in Biomarkers
Insights | Outlook Companies are
centralizing biomarker research to help
reduce spending. BY PATRICIA L. REILLY
12 News Blast
Science + Technology
expand to 3,000 nodes by year-end.
42 Microsoft Invests in Europe
SYSTEMS BIOLOGY Gates unveils
EuroScience research center initiative.
42 Birney Wins Franklin
INFORMATICS LEADER Ensembl project
leader to be honored at Bio•IT World
Conference + Expo in May.
44 Data-Sharing Approach
WORKFLOW InforSense CEO Yike Guo
discusses Shanghai’s giant grid
computing project to link scientists.
46 Relief for File Servers
Inside the Box Montilio’s RapidFile
PCI-X card relieves network file server
congestion. BY CHRIS DAGDIGIAN

18 Nano Poised for Liftoff 47 New Genes Studied

DATA MINING Primate-specific family
NANOBIOTECH First ‘nano’ technologies illustrates how genes have evolved.
yield fruit, with more to come.
ANNE HAMERSKY

40 News Blast
19 In Darwin’s Wake
26 DISCOVERY J. Craig Venter talks about 48 New Products
his voyage and its impact.

26 A Perfect X 20 Reaching New Peaks In Every Issue

Revenge is sweet for Apple, now
savoring the rise of Mac OS X
and Xserve in the lab, but this is
still the planting. A difficult
growing season lies ahead.
BY JOHN RUSSELL
EQUIPMENT ABI’s MS machine billed
as most sensitive for small molecules.
22 Chips Reveal Gene Activity
LAB TECHNIQUES Broad-Affymetrix
collaboration studies chromatin role.
24 Toward a Tricorder
Fully Equipped Portable devices are
more reality than science fiction.
BY ROBERT M. FREDERICKSON
6 Coming Attractions
First Base Ten reasons why you can’t
miss the Bio•IT World Conference +
Expo in May. BY KEVIN DAVIES
50 Entelos’ Lofty Aspirations
The Russell Transcript A survivor of
the systems biology trend, Entelos
wants more. BY JOHN RUSSELL

18 News Blast 8 Advertiser Index

22 New Products 8 Company Index

Bio •IT Bulletin @ www.bio-itworld.com/news

» Genzyme Q4 Drop Relates to Acquisition Costs (DocFinder 7517) Plus: ECLINIQUA — Provocative
commentary by science editor
» Sun's Opteron Chief Readying Galaxy of Servers (DocFinder 7514)
Mark D. Uehling on the latest
» Affymetrix Partners in Atherosclerosis Study (DocFinder 7499) in clinical trials technology.
» Group Pushes Open Source for Biotech Innovation (DocFinder 7485) (www.bio-itworld.com/opinion)

4 · BIO•IT WORLD March 2005 www.bio-itworld.com

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 06r1_695_BIO0305 2/22/05 4:24 PM Page 6

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First Base · K e v i n D av i e s
······························································································································································
······························································································································································

Coming Attractions
THE 2005 BIO•IT WORLD CONFERENCE & EXPO takes
place in Boston from May 17 to 19. You will be shocked
no doubt to discover that it is by some margin the best
line-up we’ve ever assembled. Here are 10 reasons why
you really should be there:
1. Headlines and Legends. Sir Tim Berners-Lee and J.
Craig Venter headline the keynote speakers this year. Ven-
ter will temporarily leave his research vessel, Sorcerer II,
to describe the latest progress in his astonishing round-
the-world voyage, yielding reams of new genome data on
previously undiscovered microbes. Berners-Lee, who cre-
ated the World Wide Web 15 years ago, has served for the
past decade as director of the World Wide Web Consor-
tium (W3C). Last year, he was knighted by the Queen,
and named Greatest Briton 2004, an honor that he said
made him “chuffed to bits.” His talk will focus on the po-
tential life science applications of the semantic Web.
2. Advances in Genomic Medicine is a two-day track
that opens with a featured presentation from Glaxo-
SmithKline vice
president Allen
Roses, one of the
world’s leading au-
thorities on phar-
macogenomics and
personalized medi-
cine. Other talks
will highlight new
technologies for
disease gene identi-
fication, progress in
ROB TRINGALI/SPORTSCHROME
ment of Systems Biology, Entelos, Gene Network Sci-
ences, and Genstruct. The featured presenter is Steve
Walker, CIO of the UK Biobank project.
4. Venture Forum. A highlight of the third and final
day is this special focus on the world of venture capital,
co-organized by Ernst & Young and IDG Ventures. In ad-
dition to expert forecasts and panel discussions, this
year’s forum will spotlight invited presentations from a
significant number of promising startup companies.
5. In its second year, the E-Clinical Trials and Re-
search conference track, generously co-organized by
Ken Getz (Tufts) and Becky Kush (CDISC), brings togeth-
er a superb line-up of speakers to discuss issues of elec-
tronic data capture, safety surveillance, e-clinical
standards, the NIH Roadmap, clinical trial registries, and
more. The featured presenter is Sylva Collins, vice presi-
dent of Advanced Clinical Systems at Novartis.
6. Franklin Fever. We’re delighted to welcome Bioin-
formatics.Org back to the show. The open-source organi-
zation will be presenting its 2005 Benjamin Franklin
Award to Ewan Birney of the European Bioinformatics
Institute at the show on May 19 (see page 42). Bioinfor-
matics.Org will also be organizing a special track of pre-
sentations on open-source programs.
7. Best in Show. This year’s agenda carves out more
time to allow attendees to visit dozens of exhibitors. On
Day 2, the best of the new product launches will be vying
for our prestigious “Best of Show” award, judged by a
band of Bio•IT World senior editors and invited experts.
8. Workshops Galore. Intensive workshops will give
attendees the opportunity to acquire detailed informa-

the HapMap proj- tion on critical aspects of drug discovery, development,

ect, and NitroMed’s
Manuel Worcel on
the first ethnic
drug, BiDil.
3. IT Solutions for Drug Discovery presents a stimu-
lating mix of users and vendors addressing critical issues
such as rational drug design, knowledge management,
and how to build the perfect life sciences IT infrastruc-
ture. Over two days, you’ll hear presentations from IT gi-
ants Hewlett-Packard (track sponsor), Oracle, and
Apple, as well as big names from big pharmas Sanofi-
Aventis, Eli Lilly, and Johnson & Johnson. A two-hour
session is devoted to a discussion of progress in in silico
biology, featuring presentations from Harvard’s Depart-
and clinical trials, including toxicogenomics, text mining,
visualization, predictive modeling, and e-clinical trial im-
plementation. Hosts and organizers include netNumina,
Equbits, Iconix, Linguamatics, and Assero.
9. The Hub. The central location of the Hynes Conven-
tion Center, just one block from Newbury Street, provides
an ideal setting for networking, information exchange,
deal making, and socializing. A selection of high-class
restaurants (including Bio•IT World’s favorite steakhouse)
and other attractions are all within walking distance.
10. Patriot Games. If scientific arguments can’t suf-
fice, why not revel in the aura of Boston, home of the
“world champions” in football and baseball? Oh, and it
doesn’t snow in May.

6 · BIO•IT WORLD March 2005 www.bio-itworld.com

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07_18695_BIO0305 2/16/05 9:17 PM Page 7

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08_18695_BIO0305 2/23/05 11:00 AM Page 8

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Company Index 03·05

®

Technologies Driving Discovery,

Development, and Clinical Trials

Accelrys . . . . . . . . . . . . . . . . . . . . . . . ^18 GPC Biotech . . . . . . . . . . . . . . . . . . . . ^40 Novartis . . . . . . . . . . . . . . . . . . . . . ^6, ^26

EDITOR-IN-CHIEF
AccuSoft . . . . . . . . . . . . . . . . . . . . . . . ^48 Harvard Business School. . . . . . . . . . . ^13 Open Bioinformatics Foundation . . . . . ^42 Kevin Davies (508) 628-4818
American Diabetes Association . . . . . . ^50 Harvard University. . . . . . . . . . . . . . ^6, ^16 Opteron. . . . . . . . . . . . . . . . . . . . . . . . ^30
Apple Computer . . . . ^6, ^28, ^29, ^30, ^31 Hewlett-Packard. . . . . . . . . . . . ^6, ^30, ^48 Oracle . . . . . . . . . . . . . . . . . . . . . . ^6, ^30 EXECUTIVE EDITOR
Applied Biosystems . . . . . . . . . . . ^20, ^40 IBM Thomas J. Watson Organon Pharmaceuticals . . . . . . . . . . ^50 John Russell (508) 628-4827
Assero. . . . . . . . . . . . . . . . . . . . . . . . . . ^6 Research Center . . . . . . . . . . . . . . . ^14 Oxford University . . . . . . . . . . . . . . . . . ^42 ART DIRECTOR
Atlas Venture. . . . . . . . . . . . . . . . . . . . ^13 IBM . . . . . . . . . . . . . . . . . . . . . . . ^30, ^44 Perlegen Sciences . . . . . . . . . . . . . . . . ^18 Mark Gabrenya (508) 628-4825
Bear Stearns . . . . . . . . . . . . . . . . . . . . ^20 Iconix . . . . . . . . . . . . . . . . . . . . . . . . . . ^6 Pfizer Research Technology Center. . . . ^13
Becton Dickinson . . . . . . . . . . . . . . . . ^29 Idaho State University . . . . . . . . . . . . . ^26 Pfizer. . . . . . . . . . . . . . . . . . . . . . . . . . ^50 SENIOR IT EDITOR
Bill and Melinda Gates Foundation . . . ^42 IDG Ventures . . . . . . . . . . . . . . . . . . . . . ^6 Phase Forward . . . . . . . . . . . . . . . . . . ^13 Salvatore Salamone (508) 628-4826
Bioinformatics.Org . . . . . . . . . . . . . ^6, ^42 Illumina. . . . . . . . . . . . . . . . . . . . . . . . ^22 Pria Diagnostics . . . . . . . . . . . . . . . . . ^24 SENIOR SCIENCE EDITOR
BioTeam. . . . . . . . . . . . . . . . . . . . ^26, ^46 Imperial College London . . . . . . . . . . . ^44 Quark Biotech . . . . . . . . . . . . . . . . . . . ^12 Mark D. Uehling (508) 628-4839
Boston College . . . . . . . . . . . . . . . . . . ^26 InforSense. . . . . . . . . . . . . . . . . . . . . . ^44 Quintiles Transnational . . . . . . . . . . . . ^12
WEB EDITOR
Bristol-Meyer . . . . . . . . . . . . . . . . . . . . ^50 Ingenuity Systems . . . . . . . . . . . . ^13, ^50 Roche . . . . . . . . . . . . . . . . . . . . . . . . . ^18
Catherine Varmazis (508) 628-4824
Broad Institute . . . . . . . . . . . . . . . . . . ^22 Intel . . . . . . . . . . . . . . . . . . . . . . . ^30, ^48 Sanofi-Aventis . . . . . . . . . . . . . . . . . . . . ^6
Cambridge Computer . . . . . . . . . . . . . ^46 International HapMap Consortium . . . . ^18 Sanwa Kagaku Kenkyusho. . . . . . . . . . ^12 COPY EDITOR
Carnegie Mellon . . . . . . . . . . . . . . . . . ^26 Isis Pharmaceuticals . . . . . . . . . . . . . . ^26 Shanghai Center for Bioinformation Shabnam Sigman (925) 631-4011
CDISC . . . . . . . . . . . . . . . . . . . . . . . . . . ^6 Johnson & Johnson . . . . . . . . . ^6, ^18, ^40 Technology . . . . . . . . . . . . . . . . . . . ^44 IDG NEWS SERVICE
Celera Genomics . . . . . . . . . . . . . ^13, ^19 Life Science Insights . . . . . . . . . . . ^16, ^26 Spotfire . . . . . . . . . . . . . . . . . . . . . . . . ^13 Nancy Weil (Boston)
Center for Biologic Nanotechnology Linguamatics. . . . . . . . . . . . . . . . . . . . . ^6 Sun Microsystems . . . . . . . . . . . . . . . . ^48
at the University of Michigan . . . . . . ^18 Linux Networx . . . . . . . . . . . . . . . . . . . ^30 Syrrx . . . . . . . . . . . . . . . . . . . . . . . . . . ^12 CONTRIBUTING EDITORS
ChondroGene . . . . . . . . . . . . . . . . . . . ^16 Lucent. . . . . . . . . . . . . . . . . . . . . . . . . ^18 Takeda Pharmaceutical . . . . . . . . . . . . ^12 Michael Goldman, Karen Hopkin,
ClinicalTrials.gov . . . . . . . . . . . . . . . . . . ^1 Massachusetts General Hospital . . . . . ^18 Teranode . . . . . . . . . . . . . . . . . . . . . . . ^22 Deborah Janssen, Pauline Parry,
Cyclone Commerce . . . . . . . . . . . . . . . ^40 MDS/Sciex . . . . . . . . . . . . . . . . . . . . . ^20 Tufts University . . . . . . . . . . . . . . . . . . . ^6 Tracy Smith Schmidt
Dell Computer . . . . . . . . . . . . . . . . . . . ^30 Medical College of Wisconsin . . . . . . . ^26 United Devices . . . . . . . . . . . . . . . . . . ^40
Elan . . . . . . . . . . . . . . . . . . . . . . . . . . ^18 Merck . . . . . . . . . . . . . . . . . . . . . . . . . ^50 University of California at San Diego . . ^16 Bio•IT World Inc.
Eli Lilly . . . . . . . . . . . . . . . . . . . . . . ^6, ^12 Microsoft. . . . . . . . . . . . . . . . ^26, ^29, ^42 University of Florida. . . . . . . . . . . . . . . ^18 PRESIDENT & PUBLISHER
Entelos. . . . . . . . . . . . . . . . . . . . . . ^6, ^50 Millennium Pharmaceuticals . . . . . . . . ^16 University of Idaho . . . . . . . . . . . . . . . ^26 Alan Bergstein (508) 628-4806
Equbits . . . . . . . . . . . . . . . . . . . . . . . . . ^6 MIT. . . . . . . . . . . . . . . . . . . . . . . . ^14, ^22 University of Pittsburgh Graduate FOUNDER & SENIOR ADVISOR
Ernst & Young . . . . . . . . . . . . . . . . . . . . ^6 Molecular Devices . . . . . . . . . . . . . . . . ^24 School of Public Health . . . . . . ^26, ^29 Morris Levitt (508) 628-4800
European Bioinformatics Institute . . ^6, ^42 Montilio. . . . . . . . . . . . . . . . . . . . . . . . ^46 University of Trento . . . . . . . . . . . . . . . ^42
European Molecular Biology National Cancer Institute . . . . . . . . . . . ^18 University of Washington . . . . . . . . . . . ^18 ASSOCIATE PUBLISHER AND VICE PRESIDENT, SALES
Laboratory . . . . . . . . . . . . . . . . . . . . ^47 National Human Genome Research Upstate Group. . . . . . . . . . . . . . . . . . . ^22 Capel States (646) 495-5588
Fujitsu America . . . . . . . . . . . . . . . . . . ^40 Institute. . . . . . . . . . . . . . . . . . . . . . ^18 Vanderbilt University’s Institute for VICE PRESIDENT, WESTERN REGION SALES
GenBank . . . . . . . . . . . . . . . . . . . . . . . . ^1 National Library of Medicine . . . . . . . . . ^1 Integrative Biosystems Research Alan El Faye (213) 300-3886
Gene Logic . . . . . . . . . . . . . . . . . . . . . ^13 NetNumina . . . . . . . . . . . . . . . . . . . . . . ^6 and Education . . . . . . . . . . . . . . . . . ^24
VICE PRESIDENT, ADVERTISING
Gene Network Sciences. . . . . . . . . . . . . ^6 New Jersey Institute of Technology. . . . ^18 Virginia Tech . . . . . . . . . . . . . . . . . . . . ^26 Jeffrey Hyman (508) 628-4816
Genstruct. . . . . . . . . . . . . . . . . ^6, ^13, ^50 New Jersey Nanotechnology VizX Labs. . . . . . . . . . . . . . . . . . . . . . . ^13
Geospiza . . . . . . . . . . . . . . . . . . . . . . . ^40 Consortium . . . . . . . . . . . . . . . . . . . ^18 Wellcome Trust Sanger Institute. . . . . . ^42 DIRECTOR OF AUDIENCES
GlaxoSmithKline . . . . . . . . . . . ^6, ^12, ^44 NeXT Computer . . . . . . . . . . . . . . . . . . ^26 Whitehead Institute . . . . . . . . . . . ^26, ^29 Deborah Walsh (508) 628-4809
GlobalNet Services . . . . . . . . . . . . . . . ^40 NitroMed . . . . . . . . . . . . . . . . . . . . . . . . ^6 World Wide Web Consortium . . . . . . . . . ^6 DIRECTOR OF FINANCE
Kelly Haley (508) 628-4807
Advertiser Index DIRECTOR OF MARKETING COMMUNICATIONS
Gina Bajenaru (508) 628-4821
Agilent Technologies . . . . . . . . . .41 IDBS . . . . . . . . . . . . . . . . . . . . . .33 Penguin Computing . . . . . . . . . . .43
SALES ASSISTANT
www.agilent.com/chem/ www.idbs.com www.penguincomputing.com/bio
Robyn Mellish (508) 628-4817
makeyourlabsmarter InterSystems . . . . . . . . . . . . . . . .23 PharmaDiscovery . . . . . . . . . . . . .47
VICE PRESIDENT, MANUFACTURING
Analtech Inc. . . . . . . . . . . . . . . . .21 www.InterSystems.com/lab www.pharmadiscovery2005.com
www.analtech.com Carolyn Medeiros (508) 620-7733
Labware . . . . . . . . . . . . . . . . . . .49 Redline Networks . . . . . . . . . . . . .31
Applied Biosystems . . . . . . . . . . . .5 www.labware.com www.redlinenetworks.com PRODUCTION MANAGER
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Bio-IT World Conference www.mathworks.com/bio www.shimadzu.com
& Expo . . . . . . . . . . . . . . .36-39 Microsoft . . . . . . . . . . . . . . . . . .15 Silicon Graphics . . . . . . . . . . . . . .7
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www.bio-itworldexpo.com www.microsoft.com/digitalpharma www.sgi.com/altix Beth E. Arnold, Jeffrey Augen,
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CAS SciFinder . . . . . . . . . . . . . . . .3 MiraiBio . . . . . . . . . . . . . . . . . . .29 Storage Networking World . . . . . .48 Steve Dickman, Richard Dweck,
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Fujitsu America . . . . . . . . . . . . . .45 Ontario Ministry of Economic Virginia Economic Development . .17 Caroline Kovac, John Reynders,
www.us.fujitsu.com/computers/R&D Development and Trade . .10-11 www.YesVirginia.org Thomas E. Sullivan, Bernard P. Wess Jr.
www.2ontario.com Waters . . . . . . . . . . . . . . . . .35, 52
www.waters.com IDG Corp.
This index is provided as an additional service. The publisher does not assume any liability for errors or omissions. BOARD CHAIRMAN
Patrick J. McGovern
VOLUME 4, NO.3 PRESIDENT & CEO
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09_18695_BIO0305 2/16/05 9:19 PM Page 9

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NEW
BIOINFORMATICS

MATLAB for ® TOOLBOX

computational Statistics Toolbox

biology. Image Processing Toolbox

Database Toolbox

Excel Builder

MATLAB is a powerful technical computing software environment for data Excel Link

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analysis, visualization, and algorithm development.
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Use the Bioinformatics Toolbox to easily read data from
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online databases, such as GenBank, EMBL, PDB, and PIR,

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visit www.mathworks.com/bio

Pharmaceutical firms and universities

worldwide use MATLAB for sequence analysis,
mass spectrometry, and microarray data analysis.

Visit www.mathworks.com/bio

©2004 The MathWorks, Inc.

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10_18695_BIO0305 2/16/05 9:24 PM Page 10

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11_18695_BIO0305 2/16/05 9:27 PM Page 11

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If you’re expanding in the life sciences,

see how we stack up.

The world’s leading pharmaceutical and life

sciences companies are currently investing the • A critical mass of 35,000 life science professionals
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www.2ontario.com • A quality of life ranked among the best anywhere.

1 800 819-8701

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12_18695_BIO0305 2/18/05 9:25 PM Page 12

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News • Analysis • Policy

Business + Strategy
What’s New at Big Blue? 14 | Biomarkers: Trends and Potential 16
··········································································································································
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Chatting with the New News Blast

Boss at ClinicalTrials.gov QUARK INKS DEAL
Sanwa Kagaku Kenkyusho
(CONTINUED FROM PAGE 1) Co. and Quark Biotech
Who’s in the middle? have entered into an
Federal employees seeking agreement for Quark to
to comply with the law and license the Phase II com-
balance the interests of the pound BT16 to Sanwa for
public and the industry. Af- the treatment of dyslipi-
ter just a few weeks on the demia, a blood lipid disor-
job, Deborah Zarin, the new der that can lead to a
director of ClinicalTrials.gov, significantly increased risk
spoke to Bio•IT World’s Mark of cardiovascular disease.
D. Uehling. Zarin, a physi- The license provides Sanwa
cian with background in out- with exclusive develop-
comes research, supervises a ment, manufacturing, and
staff of 15 to 20 employees marketing rights for the
and contractors at the NIH compound in Japan and
and FDA. other Asian countries.
RANDALL SCOTT

Q: What’s your highest SYRRX SNAPPED UP

priority at the moment?
Zarin: There is growing recognition that we
have more than one user group. Initially, it was
consumers and their healthcare providers. The
research, academia, policy-maker world is an-
other user group that is very important. We have
to work to increase confidence in the registry,
both in terms of which trials are in, and which
data elements are completed.
The data get into ClinicalTrials.gov through
‘trusted intermediaries’ and a little help from
the FDA?
We do closely collaborate with the FDA. We’re
implementing the process, but they have a
strong role to play in terms of being the data
provider for all the investigational new drug
(IND) trials. The FDA certifies the data
providers, as some in the industry might put
their own data in there. There is a protocol regis-
tration system on the Internet that is a separate
site — it’s not a public site. Then you can just reg-
ister your trial online.
Whether a drug works or not — the result of a
trial — was that something that Congress
required to be listed in ClinicalTrials.gov?
There are a number of different kinds of data el-
ements, including the title of the study, the inclu-
sion-exclusion criteria for the subjects, where
Japan’s largest drug maker,
the trial is being conducted, issues of trial de- Takeda Pharmaceutical,
sign, details about where the active research will acquire Syrrx, a pri-
sites are, and whether it’s recruiting or not. vately held San Diego-
FDAMA says you have to register certain types of based biotechnology
trials, and it has to include these data fields. We company working on treat-
can’t make more than those fields mandatory. ments for cancer and dia-
betes, for about US$270
Once a trial is put in your system, a sponsor is million in cash. Takeda has
supposed to update the information to indi- been trying to add new
cate if it is still actively recruiting patients. drugs to its product line to
How would you characterize compliance with stay competitive. Syrrx has
that aspect of the law? diabetes drugs in the early
There has been uneven compliance, both with clinical trial and pre-clini-
initial registration and with keeping things up to cal trial stages.
date. FDAMA specified ‘severe and life-threaten-
ing illnesses.’ But it never fully defined ‘severe SPEED BUMP IN N.C.
and life-threatening.’ Clearly, there is agreement Research Triangle Park,
that it includes cancer and AIDS. But what else it N.C., is staggering from a
includes has never been clearly defined. It’s hard pullback in life science
to answer that. employment. Glaxo-
SmithKline recently cut
In the future, after additional legislation, how approximately 125 jobs at
might a community physician or a member of its drug sales and market-
the public know if all the trials for a particular ing operations in Research
drug or disease were listed at Triangle Park. More than
ClinicalTrials.gov? 300 scientists lost their jobs
That depends on what kind of enforcement after Eli Lilly shut its R&D
mechanism, what kind of system, Congress lab, and Quintiles Transna-
would authorize. But it doesn’t necessarily have tional has also had layoffs.

12 · BIO•IT WORLD March 2005 www.bio-itworld.com

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13_18695_BIO0305 2/18/05 9:29 PM
Å Previous Page Contents
to be that staff-intensive, as long as
there is a clear system of how it’s
supposed to happen. It might be
like filing taxes.
In the future, how might the
results from a clinical trial be
structured and displayed by your
search engine?
The most no-brainer way is linking
to published articles. But that’s a
very complicated question. This
would involve more detail than
would be on a label. How do you
do that? There are enormous vol-
umes to be written on the results
of a clinical trial. When you submit
an article to a peer-reviewed jour-
nal, there is sometimes a lot of
back and forth about what is the
appropriate, dispassionate, fair
way to report those data.
Medical journal editors want
each clinical trial registered prior
to any publication of the trial
results. Would that really help
ordinary physicians?
Unless somebody mandates the
inclusion of results for every clini-
cal trial, there are going to be in-
stances where sponsors choose
not to publish — or maybe they
try to publish and no one is ac-
cepting it. Who knows? But at a
minimum, if things worked, you’d
have the denominator. You could
say, ‘Gee, this drug company did
12 studies of this drug, and I can
only find two published. Isn’t that
interesting?’
Q: Critics of the industry are
skeptical that the industry will
comply with any new or existing
law ...
Some of the issues that played out
with antidepressants in kids —
there were actually 20-odd studies
that were done. Approximately
eight were published. The FDA had
all those studies. They weren’t re-
quired, or even allowed, to publi-
cize them because they are
considered proprietary informa-
tion. That’s how the law is written.
But imagine if, on a public Web site,
all 20 studies were listed. Thought-
ful physicians could say, ‘Gee,
where are the other 12 studies?’ ●
MORE ONLINE
Read the full interview online at
www.bio-itworld.com/news,
DocFinder 7432.
Å Previous Page Contents
Page 13
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Business + Strategy
Debating Business Models for
Bioinformatics Companies
STRATEGY • HBS tackles
informatics’ basic question:
Where’s the money?
By John Russell
TO A HAMMER, almost everything else
looks like a nail. That perspective was appar-
ent during a panel discussion* about busi-
ness models for bioinformatics, held during
Harvard Business School’s 10th annual Cy-
berposium. Most panelists were bruised trav-
eling bioinformatics’ rutted road, and their
prescriptions for success resembled the busi-
nesses they currently run. What a shock.
Nailing down a single formula for success-
fully selling bioinformatics products or serv-
ices has proven elusive.
Failures outnumber suc-
cesses, and many of the
“I feel like I have a
companies still in the
game can’t dump the
big bull’s-eye on my
“bioinformatics label”
fast enough. chest right now.”
“We like to call our-
selves a biotechnology Enoch Huang, Pfizer tions t hat create re-
company,” said Keith
Elliston, CEO of Genstruct, whose predictive
modeling platform is helping fellow panelist
Enoch Huang, director of molecular infor-
matics at Pfizer Research Technology Cen-
ter, identify mechanisms of action for
compounds.
Peter Barrett, senior partner at Atlas Ven-
ture and former chief business officer at Cel-
era Genomics, agreed. He noted a client
company that “some people would look at as
a bioinformatics company. Frankly, we call it
a cancer diagnostics company.”
Not lost on the panel was that pharma
picks up the bioinformatics tab. Huang wryly
noted: “We subscribe to the Ingenuity Path-
ways Analysis platforms. We were sub-
scribers to Celera Discovery systems. We
subscribe to Bio•IT World magazine. We still
have a collaboration with Gene Logic. In
many respects, we are the industry and rep-
resent the way the industry thinks about
bioinformatics. I feel like I have a big bull’s-
eye on my chest right now.”
Ramon Felciano, CTO of Ingenuity Sys-
tems, said the subscription business model is
working well for his six-year-old company,
although it took about four years before the
product was ready. “I’m not sure I’d have sat
on this panel a couple of years ago,” he said.
“We are now starting to see more compa-
nies become interested in enterprise-type so-
www.bio-itworld.com
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lutions because some companies don’t want
their scientists sending their data over the
Web to our servers, so they want to grab a
snapshot of that entire thing and put it inside
their firewall. We just did a deployment at
Merck at the end of last year,” Felciano said.
Two problems often cited with subscrip-
tion models are the low price points com-
manded by software and the small size of the
life science market. “It’s very hard to get good
value for what you’ve created from the com-
pany because it’s only ‘software,’” Barrett said.
A few companies, notably Spotfire (visu-
alization tools), Phase Forward (clinical tri-
als software), and VizX Labs (GeneSifter),
are succeeding, but, Barrett warned, “You
have to pick a big enough niche, and you re-
ally have to understand the customer.”
Elliston took pains
to divide the bioinfor-
matics world in two: IT-
centric systems best
suited for organizing
and presenting science
data versus heavy-duty
computational applica-
sults. There’s a need for
both, he argued, but the market dynamics
are different.
“The market for information technology
tools in the IT side of bioinformatics is going
to be a very tough one for some time. One of
the reasons we believe that is science does
not work well in a browsable environment,”
Elliston said, seemingly at odds with Ingenu-
ity. “Value creation is not in the end product
of providing a tool; it’s in developing the
valuable piece of information or the valuable
end result.”
Barrett pressed Pfizer’s Huang on the
point. “[Attrition] is the thing that costs you
hundreds of millions of dollars, yet when it
comes to the poor companies that are provid-
ing maybe the value there, you don’t want to
give them royalties. You want to give them a
subscription-based model, and that’s where I
think the innovation stops, because unless
it’s a fair balance of innovation to value, no
one’s going to invest in that in the field.”
This is hardly a new complaint. However,
many bioinformatics technologies have not
delivered as promised, and the proliferation
of unproven tools has presented pharma with
a smorgasbord that is difficult to digest. ●
* “Bioinformatics: Is There a Winning Business Model?”
Harvard Business School 10th annual Cyberposium:
Cambridge, Mass., Jan. 28-29, 2005.
March 2005 BIO•IT WORLD
· 13
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14_18695_BIO0305 2/17/05 8:52 PM Page 14
Å Previous Page Contents Zoom In Zoom Out
Business + Strategy
Nothing Ventured · Michael A. Greeley
······························································································································
What’s New at Big Blue?
AS HEAD OF the Computational Biology Center at IBM’s
Thomas J. Watson Research Center, Ajay Royyuru is fo-
cused on Big Blue’s bio-IT initiatives, including exciting
applications of the Blue Gene supercomputer (see Oct.
2004 Bio•IT World, page 44). “There is a tremendous
sense of excitement as we see more evidence that the in-
dustrialized approach to commercializing the biotech
field is taking hold,” Royyuru says.
As I have said before, bio-IT tools must be more
broadly embraced across the greater life sciences
“ecosystem” before we see meaningful revenue traction
in this industry. This wave of industrialization will drive
that adoption.
Royyuru, a molecular biologist by training, points to a
number of recent developments that give cause for opti-
mism: Greater dependence on open-source solutions is
driving a greater sense of interdependence in the life sci-
ences ecosystem, and the scale of computing
has improved so dramatically that problems
previously thought to be unsolvable are now
within reach. “Early adopters will need to
“There is a tremendous
sense of excitement that the
industrialized approach to commercializing
the biotech field is taking hold.” Ajay Royyuru, IBM
embrace complexity,” Royyuru says. Biological systems
are inherently complex, poorly understood, and do not
readily lend themselves to analysis — or so much of the
pharma industry thinks. With proven discovery success-
es, customer adoption will improve.
This complexity is a central frustration for many bio-IT
entrepreneurs, and ultimately explains why so many com-
panies have struggled in recent years. Calculating the ROI
for bio-IT investments is problematic when companies are
unable to single out successful compounds derived by
these tools. Having said that, much industry-academic
collaboration is under way that should provide important
proof of principle for these tools. For instance, IBM is
working with MIT on the BioHaystack initiative in a col-
laborative research effort to drive interoperability.
Ajay Royyuru will speak at the Bio•IT World
Conference + Expo, in Boston, May 17-19.
14 · BIO•IT WORLD March 2005 www.bio-itworld.com
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Three Trends
Royyuru points to three emerging trends over the next
12 months that bio-IT entrepreneurs will find important:
• The broader acceptance of grid computing support-
ed by open-source initiatives
• The improvement of dedicated high-end computing
functionality (as represented by Blue Gene)
• The complexity of metabolic pathways that can be
represented and analyzed “holistically”
The underlying theme is the acknowledgement that
multi-scale simulations that span many levels of com-
plexity can be detailed and their interdependencies bet-
ter understood.
In addition to the industry collaborations that are so
prevalent today, IBM is focusing increasingly on graduate
schools training tomorrow’s technical leaders to use these
bio-IT tools. This new generation of scientists promises
that the bio-IT industry will flourish. The debate is only
about when — not whether — that happens.
So where are near-term opportunities? Royyuru says
meaningful advancement of the bio-IT cause is predicat-
ed on platform technologies that will generate
more relevant, complete data “that will allow for
the interrogation of biological systems.” These
represent exciting entrepreneurial opportunities,
he says. “We are all data-hungry.”
From a software perspective, the most power-
ful opportunities revolve around the area of data
integration. “We need to be able to integrate
across all the layers of complexity in order to understand
metabolic pathways,” Royyuru says. The biologist is now
the customer and an important champion of these tools.
The distribution of computing power to the benchtop has
driven much of the interoperability and open-standards
debate. Point analytics solutions are just not that com-
pelling in this environment.
So what is not to like about this scene? Royyuru wor-
ries most about the “revolution of rising expectations.”
Has the bio-IT industry over-promised, and does it risk un-
der-delivering? Ultimately, customers will want to see a re-
turn on these investments, and that won’t happen in two
to three years.
Michael A. Greeley is managing general partner of IDG Ven-
tures, a global family of funds operating in North America,
Europe, and Asia, with approximately $600 million under
management. E-mail: mgreeley@idgventures.com.
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15_18695_BIO0305 2/22/05 12:24 PM Page 15

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© 2005 Microsoft Corporation. All rights reserved. Microsoft, the Windows logo, Windows Server System, and “Your potential. Our passion.” are either registered trademarks or trademarks of
Microsoft Corporation in the United States and/or other countries. The names of actual companies and products mentioned herein may be the trademarks of their respective owners.
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Business + Strategy
Insights | Outlook · Patricia L. Reilly
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Biomarkers: Trends and Potential
AS THE ELUSIVE AND EXPENSIVE search for validated
molecular biomarkers continues apace, medical and re-
search proponents remain optimistic that the utilization
of these entities will lead to better, safer, and cheaper
therapeutics. With current estimates for successful drug
development hovering in the $800-million to $1.5-billion
range, the implications of finding relevant markers to
predict toxicity, efficacy, and treatment outcomes are
profound. Identifying such markers facilitates earlier
go/no-go decisions in drug development.
So, what does the future hold for biomarker research
and applications? In a recent survey of opinion leaders,
Life Science Insights has determined that the hunt for
specific, sensitive indicators has fueled investments in
new technologies and research. Indeed, investments have
increased more than 200 percent in the past several years
and will double in the next few years, driven by industry
trends, technology innovation, implementation of past in-
vestments, and recognized need. An additional driver in
the post-Vioxx era will be regulatory requirements.
Companies are centralizing biomarker
research, to the point where it is
becoming a standalone function.
Clearly, spending in this area is driven by multiple fac-
tors and identification and validation of specific biomark-
ers, or an emerging new technology will lead to additional
investment. Closely tied to this is an increased need for in-
vestment in data integration and data-mining tools to or-
ganize the vast quantities of captured information.
With the potential of “early kills” before costly clinical
trial phases, companies can save in both money and re-
source prioritization. To help accomplish this, companies
are centralizing biomarker research, to the point where it
is becoming a standalone function. Although few compa-
nies currently have dedicated research solely for bio-
marker discovery, many incorporate biomarkers as
compounds move through the development process, es-
pecially markers for mechanism, toxicity, and efficacy.
The goal of having relevant markers that can be moved
from pre-clinical testing to clinical trials, as well as hav-
Featured Report:
“Molecular Biomarkers: Current Industry Sentiment and Future Trends”
(Life Science Insights #32694, Dec. 2004)
16 · BIO•IT WORLD March 2005 www.bio-itworld.com
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ing fewer, reliable markers to track as a drug goes into
the clinical setting are key to reduced spending.
The Critical Path Initiative, published by the FDA in
April 2004, outlines the agency’s goals in the coming
years, in cooperation with drug companies, to safely ex-
pedite drugs through clinical trials and increase the pre-
dictability of drug success. With half of all drugs entering
Phase III failing to emerge as new therapeutics, the avail-
ability of biomarkers early in clinical trials could benefit
attrition rates. Most companies surveyed have begun to
voluntarily submit unvalidated biomarkers to the FDA as
part of their new drug filings.
Game Change
In a recent Webcast update (see www.connectlive.com/
events/fdacriticalpath), the FDA discussed the potential
of an enrichment clinical trial design, where use of
prospectively identified biomarkers could reduce the
number of patients enrolled while decreasing the num-
ber of adverse events for patients. By understanding who
is likely to respond to which drug, biomarkers can
change the risk/benefit ratio for patients in clinical trials
by enriching the population of patients who will benefit,
as well as reducing the likelihood of adverse events. With
smaller enrollments, faster trials, and higher success
rates, companies can expect a greater market share for
successful drugs, and physicians will have clearer guid-
ance on better drug choices for their patients.
To date, successful inroads have been made in oncolo-
gy and AIDS, with recent reports showing promise for
biomarker discovery in autoimmune disorders such as
rheumatoid arthritis (RA). For example, Millennium
Pharmaceuticals recently announced the discovery, uti-
lizing mass spectrometry, of a panel of protein biomark-
ers that are elevated in patients with erosive RA. Early
detection of these biomarkers could ultimately alter
physician care management with earlier, more aggres-
sive treatment regimens. In January, ChondroGene and
researchers from UC-San Diego and Harvard published
findings that blood-derived RNA from patients with
schizophrenia and bipolar disorder expressed unique ge-
nomic signatures. This discovery could ultimately reveal
disease biomarkers as well as the potential for better dif-
ferentiating diagnoses for these two diseases.
Patricia Reilly is a research manager with Life Science In-
sights. E-mail: patricia_reilly@idc.com.
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b i o t e c h n o l o g y

P r o d u c t i v e. S e d u c t i v e. V i r g i n i a.

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© 2004 Virginia Economic Development Partnership

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18_18695_BIO0305 2/18/05 9:32 PM Page 18

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Tools • Equipment • Research

Science+ Technology
Reaching New Peaks 20 | DNA Chips Reveal Gene Activity 22 | Trekking Toward a Tricorder 24
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Nano Poised for Liftoff News Blast

NANOBIOTECH • First ‘nano’ technologies yield fruit in
HAPMAP GROWS
the lab and clinic with the promise of more to come The International HapMap
Consortium, boosted by an
By Salvatore Salamone additional $3.3 million in

F
ROM R&D ANALYSIS and public and commercial
pathogen detection to clinical funding, has announced
diagnosis and drug delivery, plans to create a map of
the biomedical applications human genetic variation five
of nanotechnology, while still in times denser than the 1 mil-
their infancy, are starting to yield lion SNPs originally planned.
real results. The consortium will take
While much of the work is the advantage of the rapid,
province of academia, increasingly high-throughput genotyp-
PAUL TROMBLEY, UNIVERSITY OF MICHIGAN CENTER FOR BIOLOGIC NANOTECHNOLOGY

clinical labs as well as biotech and ing capacity of Perlegen

pharmaceutical companies are get-
ting involved. Among several recent
notable announcements:
• Johnson & Johnson and Roche li-
censed Elan’s NanoCrystal tech-
nology, which enhances the
performance of drugs with poor
water-solubility.
• Researchers at Massachusetts
General Hospital announced in
PLoS Medicine that an injectable
solution of magnetic nanoparti-
cles can be used to track cancer in
patients, reducing the need for
surgery.
TINY TARGETS: Nanoparticles depicted here among cells (green)
• The FDA approved the nanoparti- show potential as targeted anti-cancer therapeutics.
cle-based drug Abraxane (the
first of what is called an albumin-bound
nanoparticle paclitaxel) for treatment of
metastatic breast cancer. Researchers say the
drug is a more effective, less toxic alternative EurekAlert, predicted that “many drugs that have
to Taxol.
Practical Applications
The recently published “2005 Nanomedicine,
Device & Diagnostic Report,” from NanoBiotech
News, finds 152 nanomedicine, nanodevice, and
nanodiagnostic products currently under devel-
opment in companies and academic research
centers. “There are already products based on
nanoscale materials that are being used in clini-
cal applications,” says James Baker, founder of
the Center for Biologic Nanotechnology at the
University of Michigan. He cites a nanocrystal
silver burn cream, which is unique because “the
small crystals have much more surface area than
Sciences to test another
4.6 million SNPs from pub-
licly available databases.
FIGHTING MDS
The University of Florida
has shown that Revlimid
treats myelodysplastic syn-
drome (MDS), a form of
pre-leukemia. The New
England Journal of Medi-
cine reported that Revlimid
simultaneously blocks the
growth of new blood ves-
sels that nourish tumors
(anti-angiogenesis) and
stimulates the immune
larger particles and, as such, are more effective system to fight cancer cells.
in their antimicrobial action.”
Baker, speaking in an online chat hosted by YIN AND YANG
Engineers at the University
been either stabilized or delivered with nanopar- of Washington have com-
ticles will start appearing in the clinics.” In some bined an ancient Chinese
cases, the technology offers an alternative to the folk remedy with a natural
traditional methods of attacking disease targets. blood protein. The resulting
By presenting drugs to the body in different molecule, a combination of
ways using nanotechnology methods, “we may artemisinin and transferrin,
be able to use compounds that previously weren’t could be a cancer drug. In a
therapeutically useful,” says Jeffrey Schloss, who paper published in Life Sci-
coordinates strategic nanotechnology develop- ences, researchers exposed
ment for the NIH through his work with the Na- human leukemia cells and
tional Human Genome Research Institute. white blood cells to the
A key advantage for the technology is the compound. The leukemia
ability to target specific cells, which could “im- cells quickly died; the white
prove the efficacy of the therapy while decreas- blood cells remained
ing the toxicity,” Baker says. Conventional drugs unharmed.

18 · BIO•IT WORLD March 2005 www.bio-itworld.com

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19_18695_BIO0305 2/18/05 9:32 PM Page 19
Å Previous Page Contents
Craig Venter: In Darwin’s Wake
DISCOVERY • Beach (and
sea) combing today, data
analysis tomorrow; Venter
talks about his voyage
By Melissa Trudinger
SINCE LEAVING CELERA GENOMICS in
2003, J. Craig Venter has turned his atten-
tion from mining the human genome to ex-
ploring the life forms of the oceans, the
beginning of what he calls a “full systematic
survey of the planet.” (See April 2004
Bio•IT World, page 1.) Melissa Trudinger,
of Bio•IT World’s sister publication Aus-
tralian Life Scientist, caught up with Venter
on the Australian leg of his round-the-
world voyage of discovery.
Q: How much time do you get to spend
on the trip itself?
VENTER: I fly in and out, and do all the
major ocean passages — the goal isn’t to
watch my boat from my office sail around
the world. Not too many people get to sail
around the world doing world-class sci-
ence, so I try to do as much of that as possi-
ble. But I still have to run an institute and
things, so I definitely fly back and forth.
What are your goals for the project?
I’ve done a lot of interviews, including one
in the Galapagos on Darwin’s birthday,
comparing [what we’re doing] to what
Darwin did. At this stage of the game, what
Darwin was doing was collecting samples,
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are typically taken up by many cell types,
risking damage to normal tissue.
Nanobiotech is increasingly getting the
attention of government agencies and the
vendor community. The National Nan-
otechnology Initiative (NNI) funds nan-
otech research at various agencies.
The proposed budget for FY2005 is $982
million — about a 2-percent increase. While
this increase is modest for an emerging
technology, agencies that fund life science-
related nanotech research are expected to
get substantially higher percentage increas-
es: A further $400 million has been ear-
marked for the NSF and the Department of
Health and Human Services.
Some two-thirds of NNI funds are for
university-related research spanning a
wide range of topics. Additional govern-
ment funding efforts provide further sup-
port for basic research into nanobiotech.
For instance, last fall the National Cancer
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Science+ Technology
GIANT WET LAB: Craig Venter (l) monitors
ocean sampling during Sorcerer II’s round-
the-world voyage.
and it wasn’t as though he came up with
his theory of evolution while sitting on the
beach in the Galapagos ... That’s one of the
challenges we have, to see if we can come
up with a new view of biology from being
the first to have this massive gene collec-
tion — a gene-centric view of the world to
see what the data actually say. One aspect
is collecting the data, and part of it is try-
ing to make some intelligent findings out
of them, and that’s a big challenge.
How many scientists do you think are
using the data that are out there so far?
All we hear is that it’s the most used data-
base now out there, and the diversity in it
Institute launched a $144-million, five-
year NCI Alliance for Nanotechnology in
Cancer. Andrew von Eschenbach, NCI di-
rector, said at the time: “Nanotechnology
has the potential to radically increase our
options for prevention, diagnosis, and
treatment of cancer.”
Growth of Consortia
There is growing interest on the vendor
side, too. Lucent teamed with the state of
New Jersey and the New Jersey Institute of
Technology to create the New Jersey Nan-
otechnology Consortium (NJNC; see April
2003 Bio•IT World, page 18). The goals of
the NJNC, which started operations in
2003, are to speed the development of
nanotechnology-based drug discovery and
diagnostic devices and to work with phar-
maceutical companies to develop commer-
cial products in these areas.
Last summer, Accelrys launched the Ac-
www.bio-itworld.com
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is far greater than the rest of Genbank put
together, so I have no idea, but I’m sure it’s
in the thousands ... I’m finding more gen-
eral interest with our environmental ge-
nomics work than I’ve found collectively
for everything we’ve ever done in the hu-
man genome.
It would seem that the Human Genome
Project was just the tip of the iceberg, if
you put in scale and context?
Without the genome project, it would have
been maybe 100 years to find all the human
genes, if ever — just looking for things one
function at a time. Somehow, biologists
have proceeded quite nicely up to [2005]
without knowing who is in our environ-
ment. People had the notion there was
more there than they thought, but one of
the peculiar things about science is that if
you can’t measure something, it largely
doesn’t exist.
Where do you think this sort of project
will go from here?
We’re hoping our global expedition will be
the catalyst for governments around the
world, scientists around the world, adopt-
ing this approach and doing a full systemat-
ic survey of the planet. So going from an
idea [that] people were sure couldn’t possi-
bly work, to showing that even if we go from
less than 1 percent of the biology of the
planet to 5 to 10 percent, that at least gives
us a window on what we’re missing. ●
MORE ONLINE
The full interview can be found at
www.bio-itworld.com/news,
DocFinder 7394.
celrys Nanotechnology Consortium, which
aims to extend existing tools and create
new software tools to aid the design of
nanomaterials and nanodevices.
“The [idea] for the consortium is to
bridge between chemistry and engineer-
ing,” says Scott Kahn, Accelrys’ chief sci-
ence officer. “[We] focus squarely on the
chemistry and extending computational
methods.” He notes that the types of tools
currently used in nanotech development
include modeling, simulation, and infor-
matics tools. For example, Accelrys’ Mate-
rials Studio suite includes a variety of
tools used to test and validate nanotech
research ideas.
Kahn says some researchers use the
tools to “visualize or explore the energetics
of interactions.” For example, a researcher
can put together two molecules and see if a
test nano-sized molecule and drug target
stay together or fall apart. ●
March 2005 BIO•IT WORLD
· 19
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Science+ Technology

ABI Machine Reaches New Peak

EQUIPMENT • New mass spec instrument billed as
world’s most sensitive for small molecules
By Mark D. Uehling
MANY A CLINICAL TRIAL turns on a sim-
ple scientific question. Is that a toxic
metabolite in a patient’s blood sample? A
drug? Or bits of benign detritus? It is hard-
ly uncommon for a long-sought chemical
signal to be too faint to be detected confi-
dently and reproducibly.
Applied Biosystems believes its new API
(atmospheric pressurization ionization)
5000 will set a new threshold of detection
for small molecules. Other competitors, of
course, will have their own salty interpre-
tations of that claim. But for now, Applied
Biosystems machines seem to be the ones
to beat, with Bear Stearns on record in a
2004 report that they are the standard
throughout the contract research organi-
zation (CRO) industry.
In the case of the 5000, ABI bills the in-
strument as the world’s most sensitive
LC/MS/MS system. It was designed for ab-
sorption, distribution, metabolism, excre-
tion and toxicity (ADMET) projects, as well
as studies to identify dystrophia myotonica-
protein kinase (DMPK), a proxy for healthy
muscle, heart, and brain cells. The API
5000 is basically a small-molecule quanti-
tative analysis tool, the company says.
‘Out of the Grass’
Tamara Bond, an Applied Biosystems
product manager for the company’s
quadrupole instruments, notes that cus-
tomers in pharma and CROs have been
keen to test-drive the new machine. “They
brought in their hardest samples, the ones
they’re really struggling with,” Bond says.
“What we’ve been able to do is run them
on the API 5000 and see a signal. What
they say is, ‘This pulls it out of the grass.’”
2.50E+06
Getting a nice, sharp peak on a piece
of paper is not the only benefit of the new
machine. It’s designed to run unat-
tended, at high throughput. The key
isn’t only one nice peak, but lots of
them, with minimal human inter-
vention. A proprietary algorithm op-
timizes the peaks, minimizing the
need for scientists to play with the parame-
ters to get a perfect result. In one in-house
test, just 28 of 360 peaks needed manual
re-integration.
ABI reports the machine is approxi-
mately 10 times more sensitive than its
predecessor, the API 4000, which was in-
troduced in 2001. Because of an orifice
that is twice as large and other tweaks,
however, the signal-to-noise ratio on the
5000 works out to be four times better
than the API 4000.
Sensitivity Training
With the new API 5000, Applied Biosys-
tems says it has taken pains to maintain as
much of the process logic of the earlier ma-
chine. That was intended to make the tran-
sition to the new machine easier and
cheaper, mainly by minimizing downtime
due to re-training staff, recalibrating ma-
chines, and revalidating methods and
workflows.
“All of the improvements are internal to
the instruments,” Bond notes. “All of the
SOPs you currently have in place and the
source parameters and the compound-de-
pendent parameters are all virtually identi-
cal. There is no learning curve with this
instrument.”
Bond says ABI is hoping the new ma-
chine is so sensitive that it will let cus-
tomers stretch out the supply of precious
2.5
Internal Standard Area Ratio
NOZZLE MAGIC: This QJet ion guide, part of
the API 5000, uses only radio frequency (RF)
to help focus the sample being measured
and is designed to be relatively contami-
nant-free.
analytes by using less in each run. She sug-
gests the greater sensitivity of the machine
could be a factor in helping industry move
selected compounds into humans earlier —
even at microdosages. While these sorts of
instruments are often used in clinical re-
search, the company expects that some of
the units could find their way into the dis-
covery process as well, helping to keep poor
compounds out of trials in the first place.
With a list price starting at $450,000, of
course, the API 5000 is not an impulse buy.
But for project teams struggling to detect a
faint signal of efficacy or toxicity, it could
produce answers faster.
Included with the purchase price: ver-
sion 1.4.1 of Applied Biosystem’s Analyst
software, which is used on a variety of oth-
er quadrupole instruments. But this time,
the software and the instrument were im-
proved together. “Many of the improve-
ments with the software are directed
toward customers who would be quanti-
tive, regulated lab customers,” Bond says.
The law under 21 CFR Part 11, she
notes, requires that only one live copy of
the data be extant at one time. In the past,
that required cumbersome saving and

2.00E+06 2.0 deletion of data off the PC attached to the

instrument — and onto the company net-
work. Now that can happen in one step, in
Response

1.50E+06 1.5
a fully auditable manner.
1.00E+06 Alprazolam 2.5 pg/µL MRM transition 308 281➔CV 3.1% 1.0 The software also has highly adjustable
settings for 21 CFR Part 11 compliance, al-
0.50E+04 0.5 lowing managers to determine which proj-
ects and events to track. New projects can
0.00E+00 0.0 be set up based on an “audit map” that was
0 100 200 300 400 500
used previously. Security can be handled
Injection Number
based on the user, the project, the comput-
COMPLETE CONSISTENCY: In a two-day test, the new machine reproducibly and reliably gen- er, or all three.
erated data with little noise in analyzing 500 injections that contained Xanax at a few The new machine was produced in a
picograms per microliter. partnership with MDS/Sciex of Canada. ●

20 · BIO•IT WORLD March 2005 www.bio-itworld.com

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21_18695_BIO0305 2/25/05 10:55 AM Page 21

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Science+ Technology
DNA Chips Reveal Gene Activity
LAB TECHNIQUES • Broad-Affymetrix collaboration
examines chromatin and histone roles in gene regulation
By Kevin Davies
RESEARCHERS FROM the Broad Institute
of Harvard and MIT have used DNA mi-
croarrays to reveal patterns of chemical
modifications of chromatin, the complex
of protein and DNA that makes up chro-
mosomes. Writing in Cell, Broad re-
searchers Bradley Bernstein, Stuart L.
Schreiber, Eric Lander, and co-workers say
they have produced “an unprecedented
long-range view [of chromatin modifica-
tion], three orders of magnitude greater in
scale than prior studies, that reveals a se-
ries of insights into the structure and func-
tion of vertebrate chromatin.”
Chromatin is composed of spools of
DNA wrapped around proteins called his-
tones. Chemical modifications of the his-
tones lead to conformation changes that
have profound effects on gene activity in
health and disease.
The Broad researchers collaborated
with Affymetrix to survey the chromatin
modifications along chromosomes 21 and
22. They first isolated DNA regions in
which one of the histones (H3) had been
chemically tagged either with methyl or
acetyl groups. Next, the Affymetrix mi-
croarrays were used to identify the DNA
sequences associated with the tagged his-
tones. The Broad Institute’s Michael Kamal
led the computational data analysis.
Not surprisingly, most of the mapped
tags lie close to the known starting points
of active genes. However, Bernstein’s
group also found tags sitting in regions
near the same genes in both humans and
mouse chromosomes, suggesting impor-
tant functions. The researchers also sur-
veyed the HOX genes, key developmental
regulators, finding “huge stretches of
genome, many thousands of base pairs in
length, that are completely covered by
tags,” Bernstein says. These unique chro-
matin structures could be activating sets
of HOX genes for specific developmental
programs.
The chromatin data “will be an invalu-
able resource in our effort to define the
regulatory network of the genome,” Kamal
says. Future studies of these tags may shed
light on the molecular basis of cancers, in-
cluding leukemia. “We’re finding that
there may be much less unimportant DNA
in the genome than we thought,” said
Thomas Gingeras, Affymetrix vice presi-
dent of biological sciences. ●
Featured Paper:
Bernstein, B.E. et al. “Genomic maps and comparative
analysis of histone modifications in human and
mouse.” Cell 120, 169-181; 2005.

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embedded (FFPE) samples and other samples Profiling Drug Efficacy
containing partially degraded RNAs. The DASL as-
say enables researchers to measure RNA abundance Pathway Profiler, developed by Upstate Group, is a new service that measures
of over 5,000 genes in parallel per sample. The assay cell-based signaling cascades and, by doing so, provides drug development
probes three unique sequences per target gene, and companies with a unique assessment of their drug’s efficacy inside the cell.
PCR amplification is limited to genes of interest. Ac- Pathway Profiler is able to make these evaluations at various concentrations
cording to the compa- simultaneously on multiple targets in a single sample and on multiple cell
ny, this results in high types or cells derived from various disease
Vendor: Illumina
specificity and sensitivi- Products: DASL assay
states. It offers greater ease and convenience for
Vendor: Upstate Group
ty when hybridized and and DASL cancer panel quantitative investigation of cell signaling in a Product: Pathway Profiler
detected on Illumina’s Availability: Now native cellular environment for customer-speci- Availability: Now
Sentrix Arrays. The For more information: fied analytes. Used primarily by pharmaceutical For more information:
company has also re- (800) 809-4566; companies engaged in cancer research, Pathway (800) 233-3991;
leased a standard DASL www.illumina.com Profiler service is also appropriate for diabetes, www.upstate.com
cancer panel. inflammation, angiogenesis, and other research.

22 · BIO•IT WORLD March 2005 www.bio-itworld.com

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23_18695_BIO0305 2/16/05 9:37 PM Page 23

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ROBUST OBJECTS
AND ROBUST SQL

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24_18695_BIO0305 2/17/05 8:55 PM Page 24
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Science+ Technology
Fully Equipped · Robert M. Frederickson
······························································································································
Trekking Toward a Tricorder
I GREW UP ON A STEADY DIET OF STAR TREK. The
portrayal of the modern medical clinic aboard the Enter-
prise was of particular interest to me, with such wonders
as instant inoculations and vaccines, and biosensors that
could provide readouts following a mere touch to the
skin. Of course, this was pure science fiction, but in some
ways, we are moving toward these fanciful ideas.
An example of this march to the future can be found
in the collaboration between Vanderbilt University’s In-
stitute for Integrative Biosystems Research and Educa-
tion (VIIBRE) and Pria Diagnostics, a privately held
California company that specializes in miniaturized med-
ical diagnostics. The agreement, announced late last
year, aims to develop a portable device similar to today’s
home pregnancy tests that could quickly detect the pres-
ence of infectious diseases, including HIV and measles,
as well as biological agents such as ricin and anthrax.
VIIBRE has developed special elec-
trodes that have been customized to
measure the concentrations of the
metabolites that cells consume and ex-
crete in extremely small volumes. It
has also developed microfluidic de-
vices that enable the electrodes to
move and manipulate small numbers
of cells reliably. Meanwhile, Pria has
developed a micro-optical fluorescence
spectroscopy system and used it as the
basis for a portable male fertility detec-
tor that measures sperm motility with
accuracy comparable to laboratory
MPTV.NET
analyses. The device includes an opti-
cal MEMS component together with an
LED to read fluorescent chemicals that bind to a sample of
sperm. The groups plan to work together to prototype
portable instruments for clinical diagnosis and biodefense.
Portable HIV Monitor
Treating AIDS patients is expensive, and healthcare pro-
fessionals have the problem of deciding when to start
and stop anti-retroviral therapy. According to CTO Jason
Pyle, Pria is developing a device that it hopes will allow
medical professionals and HIV patients to manage the
disease in a way similar to how diabetes patients monitor
their condition with home blood-glucose detectors. A
goal of the collaboration is to produce the first portable
HIV monitor within two years.
24 · BIO•IT WORLD March 2005 www.bio-itworld.com
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Front Cover Search Issue Next Page Å
A key VIIBRE technology is an electrode-based sensor
capable of simultaneously measuring the concentrations
of key chemicals and metabolites that cells consume and
excrete — oxygen, glucose, and lactic acid — with suffi-
cient sensitivity to monitor the health of a few thousand
cells. Called a four-channel microphysiometer, the device
is a modification of Molecular Devices’ decade-old Cy-
tosensor, which was designed to measure changes in acid-
ity in a small chamber holding 100,000 to 1,000,000
cultured cells. The VIIBRE group added three additional
sensors, allowing the device to simultaneously chart vari-
ations in the concentrations of oxygen, glucose, and lactic
acid, in addition to pH, in real time. Described in an arti-
cle last year in Analytical Chemistry (76, 519-27; 2004),
the added capability is important because monitoring
variations in these four parameters allow researchers to
quickly assess the impact that exposure to different chem-
icals has on the metabolic activity and
health of small groups of cells.
Vanderbilt researchers have recent-
ly further miniaturized the customized
sensors to record rapid changes in the
metabolism and signaling of individ-
ual cells. To handle such small num-
bers of cells, they adapted a method
for molding microchannels and valves
from a plastic similar to that used in
soft contact lenses. This has given
them the capability to capture, manip-
ulate, grow, and study single living
cells in volumes that are barely larger
than the cells themselves.
While most sensors identify a sin-
gle toxic agent or group of agents, the ability to monitor
the health of small groups of cells makes it possible to de-
tect the presence of unknown poisons as long as they af-
fect cell metabolism. Furthermore, by examining the
impact an unknown agent has on different cell types the
approach may provide insights into its mode of toxicity.
The device may also find application as a high-through-
put screening system to determine the biological activity
of large numbers of compounds.
Clearly not science fiction, but devices that might
have come in handy while exploring new worlds!
Robert M. Frederickson is a science writer based in Seattle.
E-mail: rfreder@yahoo.com.
Front Cover Search Issue Next Page Å
25_18695_BIO0305 2/16/05 9:42 PM Page 25

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26_18695_BIO0305 2/18/05 9:35 PM Page 26

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A PERFECT

REVENGE IS SWEET FOR APPLE, NOW

SAVORING THE RISE OF MAC OS X AND

XSERVE IN THE LAB, BUT THIS IS STILL THE

PLANTING. A DIFFICULT GROWING SEASON

LIES AHEAD. By John Russell

Master gardener Philip Schiller,

Apple senior vice president of
worldwide product marketing,
says X’s rise in life sciences was
ANNE HAMERSKY

part plan and part luck. Either

way, he’s not complaining.

26 · BIO•IT WORLD March 2005 www.bio-itworld.com

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27_18695_BIO0305 2/18/05 9:37 PM Page 27

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FORGET, FOR A MOMENT, the

Apple faithful’s fanatical love
for the Mac — declared with
numbing monotony during the
reporting for this story. (It’s
truly amazing.) The real ques-
tion is: Can Apple Computer’s
growing presence in the life
sciences transform it into more
than an afterthought in main-
stream computing and per-
haps a dominant player in all
of science?
To that question, no one yet
has an adequate answer.
However, there is no question-
ing the strengthening rise of
Apple in life science. Apple
stalwarts have been lurking in
the shadows for more than a
decade and watching with de-
rision as the world went Win-
dows. They suffered lasting
estrangement from IT depart-
ments and learned to fend for
themselves while Apple’s self-
inflicted market missteps
threatened them with extinc-
tion in the mid-1990s.
Now they’re fighting back
with some needed help from
Apple. >>>

www.bio-itworld.com March 2005 BIO•IT WORLD

· 27

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28_18695_BIO0305 2/18/05 9:38 PM Page 28

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In the past five years, the introduction

of Mac OS X, the G5 processor, the rack- AT A GLANCE
mounted Xserve line, and recently Xserve Sales in millions
RAID, Xsan, and Xgrid have fanned new
flames in Apple hearts. A small army of iPod: Apple’s $9,000
8,000 Total
1990s graduate students who tackled all
things ’omics by writing and using open- Little Rocket 7,000
Sales**
source applications — many on the Mac — 6,000 iPod
are now moving into lead positions in aca- THE MAC PACK is hoping the
5,000 Sales
demia and industry, where they are busily spectacular success of Apple’s
writing grants and drafting budgets that iPod — up 279 percent in sales 4,000 Mac
make room for Apple. and 370 percent in units last Sales *
A PERFECT “I’ve been waiting a year — rubs off on Macs, whose
3,000

long time for this, since unit sales have been somewhat 2,000
they first started talking flat. In fact, the sale of 4.6 mil- 1,000
about Copeland (Mac OS lion iPods helped Apple start 0
8 upgrade) around 1994,” FY2005 with its most profitable 2001 ’02 ’03 ’04
says Michael Barmada, as- quarter ever ($295 million at the
sistant professor in the end of CY2004).
Department of Human Ge- First-quarter Mac sales were Unit Sales in thousands
netics at University of Pittsburgh’s Gradu- also strong surpassing a million 5,000
ate School of Public Health. Just four units. Last year, poor iMacs sales 4,000 iPod
months ago, he powered up a 121-node (down 23 percent in 2004) tem- 3,000 Mac*
Xserve cluster that was originally going to pered strong PowerBook sales
be a 200-node Linux system — before he (up 22 percent) and modest 2,000
changed his mind. PowerMac growth (15 percent). 1,000
Copeland, of course, was a minor flop. The recently introduced, sleeker 0
But the return of Steve Jobs to the Apple new iMac and hot new Mac mini 2001 ’02 ’03 ’04
helm in September 1997 was followed may reverse the trend.
with his announcement in 1998 of the Mac One unanswered question is Net Income in millions
OS X roadmap. Mac OS X Server, a version how well Apple will deal with
$300
for developers, was introduced in 1999, its splitting personality. iPod
followed quickly by a desktop version, Dar- sales have zoomed past $1 bil- $200
win 0.1, in 2000. It was essentially the lion while Apple computers lost
same OS that Jobs had developed at NeXT ground in terms of worldwide 100
Computer, built on bulletproof Unix. Since market share. If iPod sales keep
then have come Cheetah, (release 10.0), soaring at the same rate — per- 0
Puma (10.1), Jaguar (10.2), and Panther haps unlikely — they would sur- 2001 ’02 ’03 ’04
(10.3). And Tiger (release 10.4) is expect- pass Apple computer sales in
ed to pounce on the scene soon this year. less than two years. J.R. * Power Macintosh, PowerBook, Xserve product line,
iMac, eMac, and iBook sales
** Includes Mac, iPod, other music products,
peripherals, software, and services
X MARKED THE SPOT
X made all the difference, Barmada says:
“We have a lot of software, and it’s all Source: Apple SEC filings (10K, 12/04; 10K, 12/03)
home-grown stuff. No one in the field is re- Mac relatively easily was very helpful.” main mostly neutral to hostile to the Mac.
ally a professional programmer, and so it’s There were other advantages, too. It is Suddenly, life science is Apple’s fastest-
code that’s cobbled together and very easy to use both office productivity tools growing business market.
poorly annotated and, you know, is an and life science applications on the Apple “It wasn’t so much that we went after
amalgam of Pascal, Fortran, and C and platform. (Cutting and pasting from Word that community, [but] I wouldn’t call it
C++. You name it, and we’ve probably got to informatics applications is mostly a serendipity,” says Philip Schiller, Apple
it. I think there’s actually some old Cobol breeze.) Security is excellent — in part be- senior vice president of worldwide product
code floating around somewhere. So the cause fewer hackers have targeted the marketing, who has a B.S. in biology from
fact that I could bring that all over to the Mac, but mainly because of its security- Boston College. “We were very specific
rich Unix underpinning. Mac OS X about what Mac OS X should be. We knew
rarely crashes. And ease of manage- that we needed to build it on the reliability
ment is a huge plus, Mac OS X users say, and open-source nature and performance
not least because IT departments re- (CONTINUED ON PAGE 30)

“We have a lot of software, and it’s all home-

PATRICIA NAGLE/UNIVERSITY OF PITTSBURG

grown stuff. You name it, and we’ve probably

got it. So the fact that I could bring that all over
to the Mac relatively easily was very helpful.”
Michael Barmada, University of Pittsburgh

28 · BIO•IT WORLD March 2005 www.bio-itworld.com

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29_18695_BIO0305 2/18/05 9:50 PM Page 29

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30_18695_BIO0305 2/18/05 9:39 PM Page 30

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(CONTINUED FROM PAGE 28)

of Unix, and, not coincidently, the scientif-
ic community saw the value as well.”
The analyst community has also taken
Mounting a Mac Attack on Instruments
note. “It’s the dual nature. I can be in a
APPLE LOST GROUND to Microsoft and Linux in the rush to computerize lab
Unix environment and pretty easily port
equipment during the past decade. Many more instruments now come bun-
my Linux open-source applications with-
dled with PCs for control, and more Windows-based interfaces and devices
out rebooting. That’s an attractive conven-
drivers are being written.
ience,” says Michael Swenson, research
“It is something that we are aware of and have a strong interest in turning
manager at Life Science Insights. “The G5
that around,” says Philip Schiller, Apple senior vice president for worldwide
processor has been designed to improve
product marketing. “We’re looking at a relationship with some key players. We
f loating-point perform-
A PERFECT ance, which the G4 wasn’t. have a relationship with Becton Dickinson, and they sell their flow cytometers
with Apple computers as the
Also, when you think
instrumentation control.”
about small clusters, one
It wasn’t always this way.
issue is ease of use and,
Apple had the early lead,
clearly, the other issue is
says Jay Caprioli of the
access to the right applica-
Whitehead Institute. Even
tions. Apple has a pretty
now, “there’s a large num-
good story to tell on both.”
ber of instruments in the lab
Don’t be misled. Big hurdles remain.
running on really, really old
Apples’ worldwide market share has dwin-
Macs,” he says. “We’re
dled to around 2 percent (3-plus percent in
pushing 10 years on some
the United States), and Mac unit sales are
and using System 7 and Mac
fairly flat (see “iPod: Apple’s Little Rocket,”
OS 8. One frustrating point
page 28). Macs are still more expensive
for IT is there’s no upgrade
than PCs on the desktop. Technical issues
for these systems other than
persist — it is a computer, after all. The
buying new instruments.”
rush to “free” Linux remains in full force.
Apple is making selective
In-house and third-party Mac technical
headway. “We have a really
support is relatively scarce. Power users
deep buy with the micro-
and developers grumble that Apple pro-
scope companies,” says Eliz-
vides few details about its long-term tech-
abeth Kerr, Apple’s director
nology plans. Moreover, Apple has made
of science and technology
slower progress in convincing laboratory
ANNE HAMERSKY

markets. Caprioli readily

instrument makers to write drivers and in-
terfaces for the Mac.
CURSE OF REDMOND
Then there’s Microsoft Windows. It’s
everywhere, and supported by virtually
everyone (developers, IT departments, re-
tailers, etc.). Only the graphics arts com-
munity has stubbornly resisted Window’s
onslaught, staunchly remaining the single
biggest market segment for the Mac.
“I think we are still an underdog in
many places,” Schiller agrees, but that is
clearly changing. “Our goal isn’t to be the
world’s biggest supercomputer company —
that’s not who we are. But we do see a mar-
ket for taking these Xserves and providing
department-level clusters so people can
now have access to high-performance com-
puting and cluster computing that is easy to
set up and easy to use in any department.”
Indeed, Apple clusters are sprouting up
all over academia, though market share
numbers for that segment are difficult to
come by (Swenson declined to estimate for
this article, as did Apple). And Schiller’s
comments notwithstanding, Virginia Tech’s
massive 1,000-plus-node, 12.2-teraFLOPS
Apple cluster has grabbed most of the re-
cent headlines by virtue of its spot among
the top 10 supercomputers in the world. But
agrees: “They have done a
very good job in microscopy.
Apple has always lent itself UNDER THE MICROSCOPE. Apple has won big
to doing imaging analysis with Microscopy venders but struggles in other
and manipulation, and I’m categories, Elizabeth Kerr says.
seeing a lot of newer micro-
scopes hooked to Macs and to cinema displays. We have a couple here hooked
to a big flat-panel display running on a dual-processor Mac.”
Robotics control is Mike Barmada’s big headache at the University of Pitts-
burgh’s Apple cluster. “They (robotics suppliers) only have drivers available for PCs.
It would be nice if Apple could make headway into that area, but I have a hard
time envisioning just how because there are so many vendors. It would be great if
Apple could get some of the big ones to at least write cross-platform drivers.”
Says Kerr, “We’re trying to do more, but [instruments] is a challenging
opportunity simply because a lot of that comes from people using white-box
clone products.” J.R.
there are many more modest installations. users so people who developed their own
Idaho State University is a good exam- programs and their own tools and were
ple. Molecular evolution researcher pretty much the ones who had access to it.
Michael Thomas arrived in the summer of Apple was a drop in the bucket there,”
2003 to take an assistant professorship, Thomas says.
and promptly built a 10-node Xserve clus- Searching for something more broadly
ter serving 30 faculty and student users. accessible, Thomas read about the iNquiry
“Before that, I was working at a bioin- package (cluster configuration and infor-
formatics center (Medical College of Wis- matics toolset for Xserve). “It wasn’t for
consin, Milwaukee) that had a huge cluster sale yet, [so] I called BioTeam (iNquiry de-
of Linux machines but also Compaq and velopers), and talking with them is what
Sun clusters — really high-end stuff — and clinched it.”
most of the users on those were power (CONTINUED ON PAGE 32)

30 · BIO•IT WORLD March 2005 www.bio-itworld.com

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31_18695_BIO0305 2/22/05 1:29 PM Page 31

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ADVERTISING

Charting a
Web Course
No IT executive looks forward to asking upper management
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© REDLINE NETWORKS 2005 —Henry Svendblad, VP of IT

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32r1_695_BIO0305 2/22/05 4:47 PM Page 32

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(CONTINUED FROM PAGE 30)

As it turns out, Thomas — or, perhaps
more accurately, his bioinformatics pro-
grammer, Luobin Yang — added fuel to Ap-
ple’s spreading fire. iNquiry is intended to
make it easy to configure and administer an
Apple cluster and also has about 200 open-
source informatics applications. It was not
ready for prime time, Thomas says, and he
and Yang helped work out its kinks.
“I worry a lot, especially when he’s on
the phone chatting with
A PERFECT iNquiry and the BioTeam
and telling them the latest,
greatest thing he’s put in
there. My nightmare is that
one day he’ll be moving to
FURNALD & GRAY

Cambridge,” Thomas says,

adding quickly that Yang’s
wife is a nursing student
and gets free tuition while he works there. BENCHTOP BATTLE. Macs hold a slight edge over PCs on the lab benchtop at the Whitehead
“So I’ve got at least three more years.” iN- Institute, say informaticist Robert Latek and desktop support’s Jay Caprioli.
quiry is now bundled in Apple Workgroup
Cluster for Bioinformatics. they’re doing,” Thomas says. from departmental desktops.
Ease of management was critical to Thomas has growing plans of his own. Today, the Mac presence on the re-
Thomas’ Xserve choice. He receives little or He is remodeling the current IT space to search desktop varies widely. At the White-
no support from central IT. “I’ll get tenure accommodate more machines, and plans head Institute, Macs hold a 55-percent to
or not (in roughly four years) based on my to swap older G4s for G5 systems. Also, 45-percent edge over PCs, and that has
science, not the cluster. I didn’t want to be whenever one of his colleagues plans to been steady for about a year, says Jay
tied up administering it, and I wanted Lu- submit a grant, he writes a little section for Caprioli, a desktop support team member
obin to be writing programs, not adminis- them to add in, supporting the purchase of at Whitehead. Similarly, about half the fac-
tering it.” It took six weeks to gather all the more nodes where needed. The mi- ulty at Idaho State have Macs on the desk-
equipment, but just a day or so to get the croscopy center has also inquired about top. At Pitt, Barmada buys Macs “for all of
cluster up and running — not counting iN- adding a couple of nodes for its use. our students and postdocs within the divi-
quiry troubleshooting. Thomas’ research sion because they need the Unix utilities.”
on alternative splicing in genome evolu- Once inoculated with the Apple bug,
tion requires multiple searches and ho- IN VOGUE users are seldom cured. Barmada was in-
molog alignments between species. It seems a little ironic that Apple’s resur- fected in 1986 while a student at Carnegie
Last summer, members of the Universi- gence is reminiscent of the PC revolution. Mellon. “I was writing papers and surfing
ty of Idaho informatics group visited the Departments in corporate America, unable what little Web there was,” he says. For
Idaho State cluster, liked what they saw, to get what they wanted from central IT or- Thomas, addiction occurred at Penn State,
and are now setting up their own 250-node ganizations, had sufficient budgets to go where much of the molecular evolution
Xserve cluster. “They actually didn’t like out and buy PCs themselves and use them software ran on the Mac.
iNquiry and have been griping about it for office productivity tools — primarily Says Whitehead’s Caprioli, “A couple of
quite a lot. But they really liked Xserve, word processing, spreadsheets, and later years ago, one of our faculty switched to
and it fits in really well with the other stuff for presentations. The PC spread outward Windows for a particular application
(voice recognition) and found that the
whole platform experience of moving to
Windows wasn’t worth it, and now he’s
It Ain’t Over ‘Til It’s Over ... switched back to the Mac.”
Robert Latek, a senior Whitehead bioin-
APPLE’S RENEWED VIGOR in life science hardly means it has no competition.
formaticist, adds, “From our perspective in
Opinions vary on who’s ahead, but there is some consensus around the follow-
the lab, it’s definitely more expensive to
ing picture of the competitive landscape. Dell Computer, with extremely
purchase an Apple system and an Apple
aggressive pricing, is making headway in life science and has high awareness.
laptop than getting some sort of PC sys-
Niche supplier Linux Networx seems to be gaining traction with its cluster
tem; however, it really pays off in the long
expertise and riding the Linux movement.
run. The machines last a long time, the
Recently, IBM has started paying more attention to the small workgroup
quality of the equipment and the displays
environment and reaping some benefits there. Sun does well wherever Oracle
is phenomenal, it makes up for the price,
is the database of choice but has occasionally been criticized for flip-flopping
and just its ease of use.”
on support of Linux.
“We’ve got people out there who are
HP’s presence in the enterprise remains substantial despite ending devel-
still running on PowerMac G3s going on al-
opment of the Alpha chip. HP recently hired a vice president of life sciences
most six years now, and as much as we’d
and is expected to clarify its strategy soon. The company is perceived to be
like them to upgrade to newer hardware,
strong in larger clusters based on Intel’s Itanium microprocessors. No supplier
some of them are pretty happy with what
yet has a clear lead in Opteron (Advanced Micro Devices)-based clusters. J.R.
they’ve got,” Caprioli says.
(CONTINUED ON PAGE 34)

32 · BIO•IT WORLD March 2005 www.bio-itworld.com

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33_18695_BIO0305 2/24/05 12:36 PM Page 33

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Å Previous Page Contents Zoom In Zoom Out Front Cover Search Issue Next Page Å
35_18695_BIO0305 2/18/05 9:40 PM Page 35
Å Previous Page Contents
(CONTINUED FROM PAGE 32)
Conquering the Whitehead server room
may be more challenging. It’s all Linux. “A
few years ago, we had everything from SGI,
Solaris, Linux, to other flavors of Unix. It
just became too difficult to maintain all
those different systems,” Caprioli says. “We
chose at the time what we thought was
best, and that was Linux. Also, the enter-
prise side of our IT department was very
comfortable running Linux systems.”
Still, Whitehead re-
A PERFECT cently bought a single G5
Xser ve and is experi-
menting with NetBoot
for managing its Macs.
“Apple’s got some great
tools on the server level
for moving off the net-
work, system deploy-
ment off the network, and update
installation that’s all through NetBoot.
We’re going to investigate where we can go
with other things,” Caprioli says.
Although not directly involved, Caprioli
reports Whitehead has performed compar-
ison tests on different 32-bit and 64-bit
platforms for a new cluster. Apple’s costs
weren’t significantly higher, he says, but
installing open-source software on the
Xserve posed a challenge. Administrators
had a difficult time gathering needed li-
braries and installing them.
“I think that’s something that will im-
prove over time. Right now, it seems to be
one of those things that’s sort of opposite
of the desktop. It is a little bit harder to ad-
minister the Xserves for scientific purposes
than to manage the desktops,” he says,
sounding a somewhat contrary note to Ida-
ho State’s Thomas.
CULTIVATING PHARMA
Cracking Big Pharma is also likely to be dif-
ficult for Apple. Cost is one obstacle. En-
trenched corporate IT is another. The
industry’s legendary conservatism is a
third hurdle. At Novartis, George Morris,
chief operating officer for informatics, says
Macs are welcome in the lab but not active-
ly courted (see July 2004 Bio•IT World,
page 36). Smaller biopharmas are some-
what more receptive.
Alan Goates, Isis Pharmaceuticals’ direc-
tor of bioinformatics, took a tiny step into
the Apple orchard with a single Xserve to
support a biosurveillance database project
developed for the FBI. The database has
about 50 tables, and comprises a few giga-
bytes of data about organisms, diseases, and
host-pathogen relationships. More recently,
he’s been looking at a small Apple cluster.
“When I got here about seven years
ago, this place was strictly a PC-only shop.
The IT department wouldn’t let you have a
Mac, and I had to fight tooth and nail to
Å Previous Page Contents
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use one myself,” Goates recalls. “That poli-
cy fortunately changed as my boss became
a vice president and informatics [fell] un-
der his umbrella. He also uses a Mac.”
Linux still rules the roost at Isis. Its Linux
cluster of about 200 nodes handles all inter-
nal R&D (RNAi therapeutics). Apple servers
are used only for the collaborative govern-
ment programs that Goates oversees. Still,
this small toehold is a start, and in the past
five years, Goates says, Apple desktops have
grown from roughly 3 percent to 10 percent,
with several executives adopting 17-inch
PowerBooks as their main desktop.
Schiller is refreshingly candid. “I don’t
want to underestimate [the challenge]. The
difficulty in trying to turn some of those
more established IT departments running
large enterprise solutions in pharma and
other places is tough. We’re not stupidly
thinking we can knock them all down easily
and quickly. And there is still so much to be
done in life sciences — so many seats to
win; so many server farms to win.”
Rev up the tractors and let the harvest
begin. ●
Xserve Tech Specs
Introduction of the rackable Xserve
moved Apple into the high-
performance computing club, and
introduction of the Workgroup Cluster
for Bioinformatics (8 to 32 processors,
rack, iNquiry cluster configuration tool
bundled with 200 informatics
applications) has made it easy for
researchers to set up shop fast.
VITAL STATISTICS
Size and weight: 1U (1.75 in x 17.6 in x
28 in); 33 to 37 pounds (pending
number of drives)
Processors: Single G5 running at 2.0
GHz or dual G5s at 2.3 GHz
Frontside bus: 1 GHz (single processor);
1.5 GHz (dual processors)
Slots: Two full-length 64-bit PCI-X
slots
Memory: 8GB RAM maximum
Storage: 80GB serial ATA drive plus two
more drive bays
I/O: Two onboard gigabit ethernet; two
Firewire 800; one Firewire 400; two
USB 2.0, one DB-9 (RS-232)
OS: Mac OS X 10.3
Cost: Roughly $3,000 to $4,000
pending configuration (list price)
Source: www.apple.com
www.bio-itworld.com March 2005 BIO•IT WORLD
· 35
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Å Previous Page Contents
TUESDAY, MAY 17 AGENDA
IT Solutions for Drug
Discovery
Sponsored by HP
IT Solutions for Drug Discovery
Scott McClelland, HP
Jeff Miller, HP*
Technologies for Small
Molecule Drug Design
Juswinder Singh, Biogen Idec
Discovery Informatics:
Biomarkers & Chemogenomics
John Reynders, Eli Lilly
Semantic Web for Life Sciences
Andy Palmer,
Infinity Pharmaceuticals
How to Make Effective Use of
Knowledge from Information Systems
Eric Neumann, Sanofi-Aventis
Insilico Biology
Jeremy Gunawardena,
Harvard Medical School
Applying Predictive Biosimulation and
Virtual Patient Populations to Biomarker
Identification and Clinical Trial Design
Alex Bangs, Entelos
Computational Systems Biology for
Determining Biological Drug
Mechanism of Action
Iya Khalil, Gene Network Sciences
Systems Biology Model
for Type II Diabetes
Keith Elliston, GenStruct
Keynote: Tim Berners-Lee, Director, W3C; Sponsored by Life Science Insights
Networking Reception on Exhibit Floor: Sponsored by Life Science Insights
WEDNESDAY, MAY 18 AGENDA
Apple and Mac OS X v 10.4 Tiger:
Energize Your Workflow
Elizabeth Kerr, Apple
Oracle’s Solutions
for Systems Biology
Susie Stephens, Oracle
Effective Tools for Global
Federated Drug Discovery
Simon Smith,
Johnson & Johnson
Pharmaceutical R&D
Blue Gene: Computationon a
New Scale for Life Sciences
Ajay Royyuru, IBM Research
IT Infrastructure at NIBR
George Morris, Novartis
Lessons from the African American
Bio•IT World Best of Show Awards Ceremony & Reception on the Exhibit Floor
Visit www.bio-itworldexpo.com for the most up-to-date session information and agenda.
Å Previous Page Contents
Zoom In
Advances in Genomic
Medicine
Featured Speaker:
The Impact of Genetic Research
on the Future of Healthcare
Allen Roses, GlaxoSmithKline
The Possibilities of
Whole Genome Sequencing
Kelly Frazer, Perlegen Sciences
Using High-throughput Genetic
Analysis for Target Validation
Alisoun Carey, Oxagen
Addressing Complex Diseases
Through Biomarker Discovery
Michael Paul, LineaGen
Clinical Proteomics in Cancer
Emanuel Petricoin, CBER
Quantitative Analysis
Erwin Bottinger,
Mount Sinai School of Medicine
Interpreting Higher-
Dimensional Datasets
John Quackenbush,
Dana-Farber Cancer Institute
Beyond 25,000 Genes:
The Next Generation
of Pharmaceutical Genomics
Jason Johnson, Merck
Genomic Research in
Velcade Phase II
Myeloma Trials
George Mulligan,
Millennium Pharmaceuticals
Lunch/Exhibit Floor
Genotyping Technologies Used
in Pharmacogenomics
Keith Johnson, Pfizer
Global Research and Development
Information-Based Medicine
Michael Svinte, IBM
Treasure Your Exceptions —
Keys to Novel Targets and New
Approaches to Drug Development
Michael Hayden,
Aspreva Pharmaceuticals/
Xenon Pharmaceuticals
Heart Failure Trial (A-HeFT)
Manuel Worcel, NitroMed
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eClinical Trials Workshops
+ Research + Special Sessions
Sponsored by CRF
Featured Speaker: Think What’s Workshop WA:
Possible, Do What You Dare eClinical Trials: Planning
Sylva Collins, and Implementation
Novartis Pharmaceuticals
Technologies & Standards – Workshop WB:
Usage and Adoption Enterprise Information Management
Ken Getz, CISCRP for BioPharma
Dave Iberson-Hurst, Assero Sponsored by netNumina
Rebecca D. Kush, CDISC
Workshop WC: Predictive
Modeling in Drug Discovery
Lunch
New Considerations for the
Biopharmaceutical Industry
Ed Helton, SAS Institute
Gary Lubin, Merck Capital Ventures
Michael Martorelli,
Fairmount Partners
eClinical Case Studies and
Standards in Use
Michael Kilhullen, SAS Institute
James Langford, DataLabs
Bob Lyons, Nextrials
Rick Piazza, etrials Worldwide
Bill Qubeck, Pfizer*
Keynote
Safety Surveillance in Clinical Trials — Workshop WD: Integrating
New Technologies to Assess Safety Toxicogenomic Databases
Jonathan Morris, ProSanos into Drug Development
Paul Bleicher, Phase Forward
Speakers TBA
Technology Implementation Workshop WE:
for Clinical Trials – Integrating Visualization
Security Issues Security Advisor with Data Mining for Discovery
Cathy Tilton, SAFLINK
Joon You, Target Health
eClinical Vendor Panel Discussion
Moderator: Jerry Schindler,
Wyeth Research
Accommodating “eSource”
Processes and Technologies Within
the Regulations for Clinical Trials
Landen Bain, Top Sail Technologies
Dave Iberson-Hurst, Assero
Steve Schwartz, Allscripts Healthcare
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Å Previous Page Contents Zoom In Zoom Out Front Cover Search Issue Next Page Å

THURSDAY, MAY 19 AGENDA

IT Solutions for Drug
Discovery
Sponsored by HP
Keynote: J. Craig Venter, PhD, President, The J. Craig Venter Institute
The Benjamin Franklin Award presented to Ewan Birney, European Bioinformatics Institute. Presented by Bioinformatics.Org
Featured Speaker
Systems Development
to Support UK Biobank
Steve Walker, UK Biobank
The Biomolecular Interaction Network
Database and Its Related Tools:
Enabling Drug Discovery and
Systems Biology Research
Christopher Hogue,
The Blueprint Initiative
Developing Robust Computational
Platforms for Gene Discovery
Jean-François Levesque,
Genizon BioSciences
Biological Application Integration
Paul Donachy,
Belfast e-Science Centre
Lab Automation Enabling
Drug Discovery
Anu Acharya, Ocimum Biosolutions
Venture Forum
Venture Forum
Industry Overview
Bryan Pearce, Ernst & Young
Overview of the
Bio-IT Landscape:
Segmenting and Analyzing
the Life Science Opportunity
Jim Golden, SAIC
Lunch/Exhibit Floor
Putting the Industry
in Perspective
Buyer’s Panel:
A Frank Discussion
eClinical Trials
+ Research
Sponsored by CRF
National Health Information Technology
Initiatives (HIT, NHII) and NIH Roadmap
Sue Dubman, NCICB
Meredith Nahm, Duke Clinical
Research Institute
Ron Marks, Clinipace
Trial Registries
Alan Breier, Eli Lilly*
Ida Sim, UCSF*
Alexa McCray,
National Library of Medicine*
Workshops
+ Special Sessions
Workshop WF:
Text Mining — Knowledge
Discovery in Life Sciences
Special Session —
OPEN TO ALL CONFERENCE ATTENDEES
Regulatory Compliance Issues
Within the Life Sciences,
Brock Reeve, Vice President,
Life Science Insights
Special Session — Bioinformatics.Org
OPEN TO ALL CONFERENCE ATTENDEES
Open-source Bioinformatics
Software & Development Projects

Visit www.bio-itworldexpo.com for the most up-to-date session information and agenda.

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40_18695_BIO0305 2/18/05 9:42 PM Page 40

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Data • Computing • Infrastructure

IT + Informatics
Microsoft Invests in EuroScience 42 | InforSense Approach to Risk Sharing 44 | Relief for File Servers 46
··········································································································································
··········································································································································

J&J Teams with United News Blast

Devices for Global Grid FDA’S NEW GATE
The FDA this week
GRID COMPUTING • Departmental grid pilot of 450 nodes announced that it has
selected GlobalNet
will expand companywide to 3,000 nodes by year-end Services, in conjunction
with Cyclone Commerce,
By Salvatore Salamone for the FDA Electronic Sub-
Grid Power

J
OHNSON & JOHNSON is expanding its mission Gateway project.
R&D computational grid efforts from Once completed, the gate-
discrete departmental projects into a J&J Pharma R&D’s grid, once fully deployed, will way will provide a single,
companywide initiative. allow researchers to submit computational jobs centralized point for the
that will run on desktop PCs and clusters
This new initiative is a major expansion submission of new drug
throughout the company.
of the company’s grid work. For about two applications. The project
years, European and U.S. departments has an initial rollout date
within J&J Pharmaceutical Research & De- of June of this year.
velopment (J&JPRD) have used computa-
tional grids based on United Devices Grid FINCH TAKES FLIGHT
MP technology. These research efforts were Applied Biosystems and
independent of each other. User Grid MP software Geospiza will develop and
The new effort is for the deployment of submits a schedules the job market a joint informatics
job to the and sends it out Compute job runs on a mix
a single global grid that will host many ap- platform. At the heart of
grid to run on the grid of available PCs and clusters
plications, be centrally managed, and be of- the partnership is an
fered to researchers as a service. agreement to integrate
“One business driver [for the grid] is to Project Summary Applied Biosystems’ LS*LIMS
get maximum use of our current computers,” Software with Geospiza’s
says David Neilson, senior director, J&JPRD Current State: About 450 nodes Finch Suite, which is a
IM (information management). The system Project Goal: About 3,000 nodes by the 3rd or Web-based platform for
would tap the unused processing power of 4th quarter of this year analyzing and managing
desktop PCs and some Linux clusters. Technology Partner: United Devices the data associated with
Neilson notes that the grid is still in the Grid Software Used in the Project: United DNA sequencing and geno-
ramp-up stage and will go from about 450 Devices Grid MP typing experiments. ABI
nodes to 3,000 nodes by the third or fourth Current Applications Supported: Virtual docking, announced it will become a
quarter of this year. virtual high-throughput screening, and worldwide reseller of
The new initiative “will make applica- pharmacokinetic clinical trial data analysis Geospiza’s Finch software.
tions available to multiple business units Additional Applications Being Added:
and multiple geographies,” says Ben Rouse, BLAST, HMMer FUJITSU WINS ONE
United Devices’ CEO. He notes that for the GPC Biotech has licensed
past year United Devices has been working in a what was available. Here, United Devices en- Fujitsu America’s BioMed-
partnership arrangement with J&JPRD, devel- hanced its existing offerings to give J&JPRD a CAChe suite of automated
oping high-level management systems that unified job scheduler system that runs on top of docking and molecular
would help run this global grid. local job schedulers. The scheduler can take a modeling software. GPC
For example, the two companies worked on a high-priority job and, for example, switch it over Biotech scientists in the
capacity-management application to give to a high-performance cluster as that cluster be- company’s Waltham, Mass.,
J&JPRD insight into the grid’s operations. Using comes available. and Martinsried/Munich,
this application, administrators can look at grid The enhanced management tools are also seen Germany, facilities will use
utilization and define and measure service-level as the key to future use of the grid. “We’re asking the software to predict and
agreements. [ourselves] how might we provide service offer- select better quality leads
Job scheduling was the other area addressed. ings around this [grid],” Neilson says. “We work to help the company’s can-
From a scheduling point of view, there was a de- with lots of sites and departments, all of which cer drug discovery and
sire to develop a more sophisticated tool than have business leaders we have to satisfy.” ● development work.

40 · BIO•IT WORLD March 2005 www.bio-itworld.com

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41_18695_BIO0305 2/18/05 9:58 PM Page 41

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Your lab is smarter

When you store all of your data in one system

To get ahead these days you have to work smarter, not harder.
Now Agilent offers a solution that enables your laboratory
to work smarter than ever, delivering substantial gains in
productivity and efficiency with significant cost savings.
Agilent’s Cerity Enterprise Content Management System (ECM)
streamlines the collection, organization, search, and review of
all your data, regardless of format.

Cerity ECM delivers complete data integration by combining

analytical data management with document management in
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• Total content solution all major analytical data systems and standard desktop
• Secure data archiving and retrieval software applications such as Microsoft® Office and Adobe®
• Regulatory and quality compliant Acrobat®. This secure, Web-based application gives you instant
• Seamless integration with existing IT infrastructure access to all of your data for faster, better-informed decision
• Virtually unlimited scalability
making, and shorter time-to-market. Cerity ECM also provides
• Integrated business process management features
• Document management functionality regardless of format security and traceability for your Microsoft Excel spreadsheets
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© Agilent Technologies, Inc. 2005 MC 10587

Microsoft is a U.S. registered trademark of Microsoft Corporation

Adobe and Acrobat are trademarks of Adobe Systems Incorporated

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42_18695_BIO0305 2/18/05 9:43 PM Page 42
Å Previous Page Contents
IT+ Informatics
Microsoft Invests in EuroScience Centers
SYSTEMS BIOLOGY • Italian
university receives first of
several investments
EPA PHOTOS
GLOBAL HEALTH: Gates hopes EuroScience
centers will provide insight to his other
efforts to promote health.
··········································································································································
··········································································································································
Birney Wins Franklin Award
INFORMATICS LEADER • Ensembl project leader to
be honored at Bio•IT World Conference + Expo in May
By Kevin Davies
EWAN BIRNEY, a prominent scientist in
the Human Genome Project from the Euro-
pean Bioinformatics Institute (EBI), has
won the 2005 Benjamin Franklin Award
from Bioinformatics.Org. The young
British bioinformatician will be presented
with the award at this year’s Bio•IT World
Conference + Expo, on May 19, in Boston.
The Benjamin Franklin Award in Bioin-
formatics is a humanitarian award that
recognizes scientists who advocate open
access to programs and other materials in
the bioinformatics arena. Birney was laud-
ed by his peers for his vigorous defense of
open access to the human genome se-
quence data.
As co-leader of the EBI’s open-source
Ensembl project, Birney has done more
than most to ensure free access to premi-
um-quality genome annotation data via
the Web. Ensembl provides comprehensive
annotation data on 16 vertebrate and other
large genome sequences, including chim-
42 · BIO•IT WORLD March 2005 www.bio-itworld.com
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By Scarlet Pruitt, IDG News Service
MICROSOFT HAS LAUNCHED an initia-
tive to invest in scientific research centers
in Europe, heeding a call by the European
Commission for increased technology re-
search. The EuroScience initiative was un-
veiled by Microsoft chairman Bill Gates at
the company’s Government Leaders Forum
in Prague, in January.
The first research center is at the Uni-
versity of Trento, Italy, and will focus on
using computational tools for biological re-
search. Gates selected Trento’s Computa-
tional and Systems Biology center because
the university is on the frontier of biologi-
cal sciences and will hopefully produce
useful medicines. “There is a great level of
innovation in European universities, and
software has become a great vehicle for re-
search,” he said.
EuroScience operates as a public-pri-
vate sector partnership, and, in the case of
Trento, the Italian government is con-
tributing 60 percent of funds, and Mi-
crosoft the remainder. Microsoft will
provide software, and its computer re-
searchers in Cambridge, England, and the
United States will work with the lab. It will
panzee and dog. As Birney and
colleagues wrote in a recent re-
view of the portal, “The Ensem-
bl software system is being
increasingly widely reused in
different projects, showing the
benefits of a completely open
OPEN ACCESS: Ewan Birney is lauded for his efforts to
approach to software develop- ensure wide access to premium genome annotation data.
ment and distribution.”
Birney trained as a biochemist at Ox-
ford University, and did his Ph.D. with
Richard Durbin at the Wellcome Trust
Sanger Institute. He is the author of valu-
able programs, including Ensembl compo-
nents GeneWise and GenomeWise.
GeneWise predicts gene structure using
protein sequences, while GenomeWise
provides gene structures from cDNA and
EST data. In addition, Birney serves as co-
leader of the open-source bioinformatics
toolkit Bioperl, and is president of the
Open Bioinformatics Foundation, an or-
ganization that supports the development
of several bioinformatics toolkits.
Zoom In Zoom Out Front Cover
Search Issue Next Page Å
also be offering postdoctoral fellowships,
scholarships, awards, and workshops
through the program.
The initiative will focus on computa-
tional science, intelligent environments,
and new computing paradigms that draw
from nature, chemistry, and biology. The
software giant will be able to generate in-
tellectual property (IP) from advances in
computing, while the research institutes
will gain scientific IP. “We are at a great
point where computing and software can
advance science,” Gates said.
Additional centers will be announced in
the coming months, with discussions un-
der way with institutes in France, Ger-
many, and the United Kingdom. Gates left
the door open for expansion of the pro-
gram into the United States and Asia. “I’m
sure we will be in other regions,” he said.
Although EuroScience is a Microsoft
initiative, Gates expressed hope that the
research could one day be fed into his oth-
er activities to solve global health prob-
lems. The Bill and Melinda Gates
Foundation has dedicated hundreds of mil-
lions of dollars toward vaccinating chil-
dren in developing nations. ●
Most recently, Birney played a key role
in the assembly of the draft sequences of
the rat and chicken. Other current inter-
ests include the Reactome database — a
knowledge base of human biological path-
ways; the Encode project — detailed gene
anatomy of a specified region of the hu-
man genome; and the Biosapiens Network
of Excellence — a Europe-wide network
for genome annotation.
Bioinformatics.Org solicited nomina-
tions for the 2005 award from its more
than 12,000 members. The previous win-
ners were Lincoln Stein (2004), James
Kent (2003), and Michael Eisen (2002). ●
Search Issue Next Page Å
43_18695_BIO0305 2/18/05 9:54 PM Page 43

Å Previous Page Contents Zoom In Zoom Out Front Cover Search Issue Next Page Å

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Å Previous Page Contents Zoom In Zoom Out Front Cover Search Issue Next Page Å
44r1_695_BIO0305 2/22/05 12:16 PM Page 44
Å Previous Page Contents
IT+ Informatics
InforSense Approach to Data Sharing
WORKFLOW • CEO Yike Guo discusses Shanghai’s
giant grid computing project to link scientists
By Kevin Davies
INFORSENSE, WHICH WAS SPUN out of
Imperial College London six years ago by
computing science professor Yike Guo,
made two noteworthy deals in the past six
months — one with Shanghai to build a
grid computing network uniting research
scientists, the other with GlaxoSmithKline
to develop an open workflow platform for
enterprise chemoinformatics. But as Guo
explains to Kevin Davies, both deals have,
at their core, a common goal: sharing data,
software, and expertise effectively among
large, diverse user communities.
Q: How did you get involved with China?
Guo: Our initial involvement was to create
a software development base in China —
it’s where we develop our workflow com-
ponents, especially for bioinformatics and
protein informatics. We have a joint lab
with the Shanghai Center for Bioinforma-
tion Technology (SCBIT), and with IBM,
which provides the hardware facilities.
InforSense provides the development proj-
ects, including development of compo-
nents for advanced integrative studies of
biological information.
China not only has cheaper develop-
mental costs than Britain, but also has a
very good scientific base — plenty of
young scientists looking for good places to
work. Shanghai has the best bioinformati-
cians in the whole country. Another reason
is that China has big projects in life science
research, such as the Human Genome Pro-
ject, and now the Human Proteome Pro-
ject. So they need software for large-scale
integrative analytics.
What is the new grid computing project
in Shanghai?
InforSense was spun out of Imperial Col-
lege (where Guo is on the faculty) and still
has an IP pipeline with the university, so
we are deeply involved in grid computing.
I’ve been working with China in the field of
high-performance computing and its appli-
cations. [Our] software is used extensively
in Chinese bioscience, chemistry, and in-
formatics fields.
The Shanghai municipality is advanced
in grid computing, and its infrastructure al-
lows Shanghai’s scientists in research and
industry to share four things: information,
computation, instruments, and expertise.
It’s an extremely ambitious project, which
will last about 15 to 20 years. Phase 1 is
44 · BIO•IT WORLD March 2005 www.bio-itworld.com
Å Previous Page Contents
Zoom In Zoom Out Front Cover
three years, with 200 million yuan (£15
million) investment. In addition, there will
be ongoing research collaborations be-
tween Europe and Shanghai in grid com-
puting. The focus isn’t about scheduling
CPUs but understanding, on a higher level,
service-based computing environments to
utilize information, computation, instru-
ments, and expertise — that is, to build a
virtual research community.
SILO SMASHER: Guo (center) plans to help provide
Shanghai scientists with ready access to software appli-
cations, data resources, and automated analytic work-
flows over the Web.
How will this architecture empower the
Shanghai scientific community?
The goal is to establish a virtual organiza-
tion for Chinese scientists in Shanghai for
collaborative research. Efficiency is one
priority. If you put your people and re-
sources in silos, it’s very inefficient. The
key to improving research efficiency is to
share, across the organization and across
domains, resources, information, and
knowledge ...
Our discovery workflow is mechanized
to dynamically integrate analytical servic-
es, including software applications, data
sources, and instruments in a dynamic and
personal way to form protocols or work-
flows. This workflow is in fact a plan or
record of what kind of protocol a scientist
has created. It can be stored, optimized,
and reused.
We provide the analyst portal approach
for publishing workflows as reusable end-
user applications. Web portal deployment
technology allows scientists to automati-
Zoom In Zoom Out Front Cover
Search Issue Next Page Å
cally turn an analytic workflow into a Web
application. This is achieved by a simple
click, so you don’t need scientists to write
Web applications themselves. Scientists
can easily publish their research results to-
gether with the protocols from which the
results are derived.
Tell us about your recent partnership
with GSK.
The GSK partnership is a micro view of our
integrative analytical computing. They
have exactly the same problems as Shang-
hai — sharing data, instruments, expert-
ise, etc. The only difference is
vertical. GSK is focused on one
area: drug discovery.
The major problem in any
pharma is integration — from
data to applications and finally
to expertise ... In discovery sci-
ence, how one integrates infor-
mation is very task driven and
personal. It reflects an individ-
ual scientist’s method of doing
a particular scientific job.
On the other hand, in the IT
world, after many years, soft-
ware integration has finally
come to a solution using Web
services architecture: Publish
everything with standard Web
service protocols; software can
then adopt an SOA (service-
oriented architecture). If we
put this together, whether in-
formation or application, so
long as it gets published in a
standard way, then we can join them to-
gether and provide an environment so
that each scientist can also connect them
in a flexible way. This is our Open Discov-
ery Workflow concept: We allow scien-
tists to define discovery protocols for a
particular task.
GSK Chemistry adopted this concept
— they put all their algorithms, perhaps a
couple of hundred, even in library design,
developed over the past 20 years into
databases and into Web services and used
us to join them together. Moreover, all the
integrative workflows can be stored in
our workflow warehouse so they become
the company’s knowledge base of infor-
matics processes. This is an enter-
prisewide deal with GSK. Within 10 years,
I expect that every scientist can do their
job using this mechanism. ●
MORE ONLINE
Read the full interview online at
www.bio-itworld.com/currentissue.
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46_18695_BIO0305 2/18/05 9:46 PM Page 46

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IT+ Informatics

Inside the Box · Chris Dagdigian

······························································································································

Lab Notes: Relief for File Servers

BIOTEAM REGULARLY EVALUATES emerging technology
products to find better, cheaper, or more practical tools
for handling vexing research computing infrastructure is-
sues. Current and emerging IT products are brought into
our lab facilities for two main reasons: to see if they work
as advertised, and to determine via hands-on usage if
they are something BioTeam would feel comfortable rec-
ommending to others. The subject of this column is a
storage product that falls into the “clever” or “why didn’t
I think of that?” category.
BioTeam first became aware of Montilio in early 2004,
when the company was in stealth mode and keeping
product plans tightly held. Initial talks about the yet-to-
exist item were interesting enough that both parties
maintained contact until
late-beta hardware was
available for initial testing
in January 2005. By the
time this column is pub-
lished, Montilio will have
exited stealth mode with
shipping product released
for general availability. The
hardware made available
for our testing is expected
to closely match the ship-
ping product.
What is it? Montilio
calls it “RapidFile,” and it is
nothing more than a full-
CLEVERLY SIMPLE: The RapidFile PCI-X length PCI-X card intended
card relieves network file server conges- for use in network-attached
tion and boosts performance.
file servers. Nothing about
RapidFile is exceptionally new or revolutionary: Montilio
has cleverly combined several existing and well-known
technologies with a custom chipset and some driver soft-
ware. The end result is a PCI card that can turn a cheap
single- or dual-CPU server into a network file-serving
monster capable of standing toe to toe against much
larger and more expensive systems.
OK, enough teasing and beating around the bush. The
RapidFile PCI card combines dual QLogic Fibre Channel
storage host bus adaptors (HBAs) with dual Silverback
gigabit ethernet network interfaces augmented by TCP
offload engines. The Fibre Channel and gigabit ethernet
devices integrate seamlessly with the host server system
while the Montilio ASIC chip and driver software work to
accelerate file-serving operations.
The value in this is pretty compelling for people who
need inexpensive yet high-performance NFS from net-
work-attached storage systems. By combining storage
controllers and network interfaces on the same PCI card,
Montilio is able keep utilization of both the storage and
network data paths high without placing a significant
load on the file server itself. File operations and data tra-
verse only the PCI card — there is no need to pass traffic
up through the system bus to the CPU and operating sys-
tem. The Montilio ASIC chip and driver software sepa-
rates data payloads from control commands, and only
the control commands are passed along to the host oper-
ating system and CPU.
Cost Cutter
Two immediate advantages seen with RapidFile are the
removal of the PCI bus as a potential rate-limiting per-
formance bottleneck and the financial savings realized
by using cheaper server configurations than what would
normally be required.
A third distinct advantage that BioTeam sees is rela-
tive transparency of the hardware and lightweight sys-
tem requirements. We prefer to let scientific and research
needs drive our IT planning, and generally frown upon
vendor products that demand rigid system and software
configurations in order to function. RapidFile has no re-
quirements or special software for clients at all, and
when the card is placed into a Linux server the operating
system merely sees additional well-known devices, in-
cluding the PCI Bridge, the QLogic Fibre Channel HBAs,
and the gigabit ethernet interfaces. As for the driver soft-
ware and daemons that must run on the server, Montilio
says its code is straightforward enough that the company
can build versions for the common Linux distributions
and kernel combinations. Support for Windows-based
servers and CIFS file services is forthcoming.
The January 2005 tests were conducted in the labs of
Cambridge Computer, a well-known company specializ-
ing in complex storage and backup situations. In addi-
tion to lab space, Cambridge Computer provided the
Fibre Channel switch and IBM storage arrays. BioTeam
provided IBM e325 Opteron and Sun V60 Xeon client
computers, and Montilio provided the RapidFile card
and the file server.
To highlight the ability of RapidFile to run on inex-
pensive hardware, the file server machine had only a

46 · BIO•IT WORLD March 2005 www.bio-itworld.com

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47r1_695_BIO0305 2/22/05 12:19 PM Page 47

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single 2.8GHz Xeon CPU and 2 GB of
physical memory, and was running
RedHat 9 as an operating system. In
one of our simple tests, we were able
to observe the file server reporting a
utilization level of less than 5 per-
cent while our client nodes were
nearly saturating the gigabit ether-
net links with long NFS read and
write requests.
So is BioTeam recommending
RapidFile? The short answer is “not
quite yet,” as we need to re-test with
the shipping version of the card as
well as deploy it in a larger and more
realistic research computing setting.
As it stands, RapidFile is certainly in-
teresting enough for us to continue
evaluating.
Is this sort of “combo card” packaging
merely a niche product or something
that actually addresses a current prob-
lem, or cost or performance issue? Let
me know what you think at
chris@bioteam.net.
IT+ Informatics
Evolution of New Genes Studied
DATA MINING • EMBL researchers use comparative genomic
analysis to identify new primate-specific gene family
By Kevin Davies
IN ANOTHER EXAMPLE of the power of
comparative genomics, scientists at the Eu-
ropean Molecular Biology Laboratory
(EMBL) in Heidelberg, Germany, have
identified a new primate-specific gene
family that spans about 10 percent of hu-
man chromosome 2 and illustrates how
genes have evolved and acquired new
functions during evolution.
Gene duplication is known to be a
strong driver of evolution. Acquiring extra
copies of genes can be detrimental to an
organism’s health, and evolution frequent-
ly counters the dosage problem by convert-
ing the extra copies into nonfunctional
“pseudogenes.” However, in some cases,
this gene redundancy also provides the op-
portunity for extra copies to potentially ac-
Featured Report:
Ciccarelli, F.D.; von Mering, C.; Suyama, M.; Harrington,
E.; Izaurralde, E.; and Bork, P. “Complex genomic
rearrangements lead to novel primate gene function.”
Genome Research 15, 343-51; 2005.
quire new functions, and hence confer a se-
lective advantage to an organism.
Reporting in the online edition of
Genome Research, Peer Bork and col-
leagues set out to find examples of this
phenomenon by systematically comparing
the genomes of several species for exam-
ples of single genes that are present in mul-
tiple copies in primates.
The EMBL bioinformaticians found 22
genes that fit those criteria, including a
gene called RanBP2. This gene codes for a
large protein that regulates traffic of nucleic
acids and proteins in and out of the nucleus.
In humans, the new gene family spans a
striking 10 percent of human chromosome
2, which was formed millions of years ago
by the fusion of two ape chromosomes.
The gene family acquired a domain from
the neighboring GCC2 gene, which has a
function in the cytoplasm. The new gene
family has eight members, and is named
RGP (for RanBP2-like, GRIP domain-con-
taining proteins). ●

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· 47

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48_18695_BIO0305 2/22/05 1:47 PM Page 48

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IT+ Informatics
NEW PRODUCTS

HP Boosts Integrity Sun Rolls Out Pay-

Per-Use HPC Services
Line’s Performance
Sun Microsystems rolls out the Sun
HP has upgraded its Integrity line of Grid service, an on-demand high-per-
servers, which are designed for use in formance computing service that al-
high-performance computing environments. The product lows life science companies to quickly
line now incorporates Intel’s newly enhanced Itanium-2 9M Vendor: HP apply computing resources to new
processor. As a result, according to HP, the new Integrity sys- Product: HP Integrity projects or to meet periodic surges in
tems deliver up to 25-percent better performance than their server line demand during busy times. The serv-
Availability: Now
predecessors. Additionally, HP Integrity servers running Lin- ice includes the Sun Grid compute
For more
ux can now support more processors. Specifically, Linux- information: utility, which will cost $1 per CPU per
based Integrity servers can now support up to 16 CPUs, as (800) 282-6672; hour to use, and the Sun Grid storage
opposed to eight before. This is due in part to the general www.hp.com utility for $1 per gigabyte per month.
availability of the new Linux 2.6 kernel. Sun says a number of life science ap-
plications, including protein folding,
would benefit from the new grid
service.
AccuSoft Upgrades VisiQuest Analysis Software
AccuSoft has announced VisiQuest 4.0 for Windows, a native Vendor: Sun Microsystems
Windows version of its imaging and data analysis software Vendor: AccuSoft
Product: Sun Grid compute and storage
that includes new programming and data-handling features. Product: VisiQuest 4.0
services
for Windows
One enhancement is a new user interface that lets re- Availability: Now
Availability: $1 per CPU per hour, $1 per
searchers organize and place commonly used analysis tools GB per month/Limited availability now
For more information:
in a customized pattern. Additionally, there is a new method For more information: (800) 555-9786;
(800) 525-3577;
to search for glyphs, and VisiQuest now supports more than www.sun.com
www.accusoft.com
75 file formats, including new support for TWAIN.

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Our unequaled functionality is just the tip of the iceberg.

What’s below the surface?

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 50_18695_BIO0305 2/18/05 9:48 PM Page 50

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The Russell Transcript · J o h n Ru s s e l l

······························································································································································
······························································································································································

Entelos’ Lofty Aspirations

JUST AS THE SYSTEMS BIOLOGY LABEL is falling out of
vogue, a few companies in that space are showing signs
of sustainable life by winning repeat pharma business
and that holiest of grails — the promise of a piece of the
action for compounds they help develop.
Last month, model-maker Entelos announced that its
“research” collaboration with Organon Pharmaceuticals
had been extended to include co-promotion and com-
mercialization rights for rheumatoid arthritis (RA) thera-
peutics. That’s a significant change, as noted by Organon
senior vice president of research David Nicholson: “This
transition from a strictly research effort was the next step
in our growing relationship.”
Near the end of 2004, another systems biology compa-
ny, Ingenuity Systems, deepened its deal with Merck. In-
genuity subscribers generally access its Pathways
Knowledge Base and Pathway Analysis tool over the Web.
Merck thought enough of the technology to bring the en-
tire system inside its firewall and deploy it companywide.
Meanwhile, startup
want to be drug companies when they grow up — even if
most won’t say so. Entelos is a good example of how the
survivors have held on, and it is a little more daring in
outlining its aspirations.
Ducking Arrows
Founded in 1996, Entelos was an early systems biology pi-
oneer. Since then, its staff has grown to 70. The compa-
ny’s bread-and-butter technology is its line of PhysioLabs:
custom mathematical models, first designed around spe-
cific diseases, such as RA, and now being extended to
general physiology systems such as inflammation.
Initial efforts were focused on discovery, which helped
build scientific credibility. Collaborators have included
Pfizer, Bristol-Meyer, the American Diabetes Association,
and others. Recently, Entelos has shifted focus to pre-clin-
ical and clinical opportunities because that’s where the
money is. Pharma has plenty of targets.
The way in which Entelos derived income has also
evolved. The Organon collaboration has included royal-

“We’ve started to use Genstruct used its in silico

platform to identify mech-
our technology to anism-of-action hypothe-
ses on promising
look at in-licensing compounds that had
stumped Pfizer. “Obvious-
opportunities.” ly, there was enough ma-
terial in there that we’ve
James Karis, Entelos extended our collabora-
tion,” says Enoch Huang,
director of molecular informatics at Pfizer Research
Technology Center.
For good or ill, Entelos, Ingenuity, and Genstruct —
and others — happily sailed under the systems biology
banner. There was definitely market buzz around the la-
bel. However, there was also confusion, and Entelos pres-
ident and CEO James Karis complains that pharma still
has a difficult time differentiating among the players.
Whatever they are called, companies developing com-
putational predictive biology platforms have begun de-
livering enough value — biomarkers, prioritized targets,
novel pathways — to prompt pharmaceutical companies
to cough up cash and commitment. That’s emboldening
the systems biology crowd to want more.
“The mega trend is pretty good,” Karis says. The chal-
lenge these companies face is growth. Many of them
ties, milestones for the targets, access to abandon com-
pounds, and technology transfer for screening assays
before ascending to the co-development and commer-
cialization plateau.
Now, Karis says, “We’ve started to use our technology
to look at in-licensing opportunities, and we have been
evaluating — we haven’t done one yet — opportunities.
That’s the evolution of the business model: revenues and
services fees as well as product participation.”
Adds Entelos chief business officer Michael French,
“We may very well come out and say, ‘This disease area
we’re going to own.’ It might a disease where pharma
may or may not be interested, but where we believe our
technology puts us in a stronger position.”
One competitor dismisses in-licensing as too expen-
sive. Another is intrigued by the idea. They’d all like to
link payment to direct participation in the IP their pre-
dictive platforms produce. A few are succeeding to
some extent.
This is an interesting period for systems biology’s
wing of predictive biology companies. The label’s luster
is fading, but buoyed by pharma’s growing interest, they
are trying to figure out how to grow.
Will Entelos play Daedalus or Icarus? What’s your predic-
tion? Write me at john_russell@bio-itworld.com.

50 · BIO•IT WORLD March 2005 www.bio-itworld.com

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