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Bio-IT World Bio-IT 50

Bio-IT World editors pick the top life sciences firms, including some promising newcomers.

March 14, 2006 | Selecting any kind of “top 50” list is an exercise fraught with subjectivity and sometimes outright dissent. When a popular magazine selects its 50 most beautiful people, we suspect there is widespread agreement with the first 30 or so selections, even if some choices are “safe” and predictable. But then puzzlement and confusion creep in with the final selections.

BioIT50logo.jpgOr pity the selectors of the NCAA basketball tournament. Who do they pick for that 15th seed? The seventh team in the Big 10, or the winner of some obscure conference that few have ever heard of?

With that said, and knowing full well that our selections won’t please everyone, we felt this was an appropriate time to sit back and appraise the world of technology providers without which biopharma couldn’t exist. And so we undertook to identify 50 companies that provide the most indispensable, enabling technologies.

The task wasn’t easy by any means: indeed, we could pick another 50 firms who are invaluable partners to the industry, or show the potential to become so. We did not judge strictly by market cap or revenues, although commercial considerations were a factor. But there are many companies that receive liberal coverage in this magazine that we simply did not have room for, much to our chagrin.

We opted not to rank these companies in any sort of hierarchical order, although we might be tempted next time around. But when all is said and done, we believe the 50 companies profiled here have driven and continue to drive the future of biomedical research and drug discovery. You may agree, but if you don’t, just tell us where we messed up. 
                             — Kevin Davies, John Russell, Sal Salamone, Mark D. Uehling, and Steven Withrow

HQ: San Diego; CEO: Mark Emkjer; Sales: $69.6 million
Simple choices, easy integration
Accelrys has essentially reworked its product line, adopting an open-platform architecture allowing individual products to work more easily with others. The company also launched its “Solutions for” approach that groups tools into bundles for specific job functions. Seeing potential in a nascent research field, Accelrys launched the NanoBiology Initiative. And the company was one of several Microsoft partners showcased for its software’s ability to run on Windows Compute Cluster Server. The company’s acquisition of SciTegic continues to push forward — SciTegic added its 20th partner at the start of 2006.
Challenge: Face crowded analysis tool and workflow market
Opportunity: Leverage synergies between tool architecture and SciTegic’s workflow infrastructure

HQ: Santa Clara, Calif.; CEO: Steve Fodor; Sales: $364 million
Microarray leader takes on genome
Affymetrix remains the dominant fixture in the microarray market. New whole-genome arrays and a bevy of open-source software analysis programs are helping customers extract maximum value from gene expression arrays. Spin-off Perlegen was a major partner in the HapMap and struck a $50 million deal with Pfizer. Affymetrix chips continue to help demystify the function of “dark” DNA and provide the platform for Roche’s FDA-approved Amplichip diagnostic test. Affymetrix beefed up its own platform by acquiring ParAllele for $120 million. But the company faces tough competition — not to mention ongoing legal challenges — from bead array rival Illumina.
Challenge: Expand microarray markets in face of stiffening competition
Opportunity: Capitalize on demand for high-throughput genotyping

HQ: Santa Clara, Calif.; CEO: William Sullivan; Sales: $5.1 billion
Lab-on-a-Chip and more
Spun off from Hewlett-Packard in 1999, Agilent provides products in gene expression, proteomics, informatics, and pharmaceutical analysis. Its portfolio was buoyed by the 2004 introduction of the Lab-on-a-Chip system, and the recent acquisition of Molecular Imaging, premier manufacturer of electron microscopes. In January, Agilent launched the first dual-mode microarray platform. It also announced the biggest refresh of its HPLC and mass spec instrument line in 10 years. The stock has climbed 75 percent from its mid-2005 low, spurred by the sale of Agilent’s semiconductor unit (for $2.5 billion).
Challenge: Make impact in molecular diagnostics market
Opportunity: New focus reaps dividends for mass spec, microarray business

: Cupertino, Calif.; CEO: Steve Jobs; Sales: $13.9 billion
Once-mighty mighty again
Miracle worker Steve Jobs resuscitated Apple on the lab bench top with Mac OS X — researchers love its Unix underpinning and think the shiny laptops are cool. By introducing the Xserve and Xraid product lines, Jobs mounted an effective invasion of the server room. Surely the incorporation of Intel chips into Apple products will splash more fuel onto this bonfire. Even the iPod has a life sciences play, being used to port informatics software, configure clusters, and download the human genome! It’s hard to see much downside at the moment.
Challenge: Keep momentum and ensure X products stay price competitive
Opportunity: Sell larger clusters to biotech, migrate beyond pharma research lab

 Applied Biosystems
HQ: Foster City, Calif.; CEO: Catherine Burzik; Sales: $1.4 billion (2004)
Expanding; sequencing challenges
Under Cathy Burzik’s first year at the helm, ABI’s stock price jumped 40 percent — taking in revenues, ABI posted solid growth in instruments (PCR, mass spectrometry), consumables, and informatics — and closed out the year by snapping up RNAi company Ambion for $273 million. While diversification into areas such as forensic science and biosecurity is a plus, ABI is acutely aware of imminent challenges to its two-decade monopoly in the DNA capillary sequencing market, recently investing in Visigen, one of several upcoming single-molecule sequencing startups.
Challenge: Fend off intense competition in the next generation of genome sequencing
Opportunity: Build integrated “one-stop” online shopping network

 Beckman Coulter
HQ: Fullerton, Calif.; CEO: Scott Garrett; Sales: $2.5 billion
Integrated molecular biology tools
Founded in 1934, Beckman Coulter is a large and diversified manufacturer of instruments and software for hospitals, laboratories, and biomedical research. The company’s portfolio includes robotic systems; cell analysis; DNA sequencers; genotyping systems; liquid chromatography; microarrays; and cellular imaging. Two-thirds of its annual sales come in the form recurring supplies, kits, and services. Beckman spends intensively to help customers automate and integrate their workflows, investing in software (like electronic lab notebooks) as well as instrumentation.
Challenge: Deal with ongoing consolidation of industry; continued shift in investment strategy by biopharma
Opportunity: Integrate complex systems and expand automated applications to meet customer needs

Becton Dickinson
HQ: Franklin Lakes, N.J.; CEO: Edward Ludwig; Sales: $5.4 billion
Ubiquitous lab presence
BD Biosciences (one of three divisions of Becton Dickinson) offers a broad range of lab equipment and assay products for R&D and drug discovery applications, such as the robotic BD Viper system. From flow cytometers and cell culture to molecular biology kits and drug screening systems, the company is a ubiquitous presence in research labs. Last year, the company sold its Clontech subsidiary, acquired in 1999, to Japan’s Takara Bio for $60 million. It recently took a major step towards the molecular diagnostics market with the purchase of clinical microbiology company GeneOhm Systems for $230 million.
Challenge: Increase pace of R&D spending; drive molecular diagnostics strategy
Opportunity: Drive growth and expand margins by improving operating effectiveness

Bio-Rad Laboratories
HQ: Hercules, Calif.; CEO: Norman Schwartz; Sales: $1.2 billion
Dedicated to detection
A large and diversified manufacturer of instruments for hospitals and research. In its life sciences division, Bio-Rad delivers electrophoresis, image analysis, molecular detection, chromatography, gene transfer, sample preparation, and amplification. In one peer-reviewed publication, the authors praised Bio-Rad’s PROTEAN system for 2-D protein gels, citing its “highly reproducible reference maps, as well as separate milligram quantities of protein for micropreparative purposes.” The company is in a significant legal battle with Applied Biosystems over patents on PCR and thermal cycler technology and has a deepening partnership on a microfluidics system with Caliper Life Sciences.
Challenge: Strengthen customer relationships to advance R&D efforts
Opportunity: Maintain leading roles in both existing and niche markets

HQ: San Jose, Calif.; CEO: Mike Gustafson; Sales: Undisclosed (private)
Storage maverick
Many storage vendors focus on scalability, but BlueArc also addresses performance. Its Titan system architecture performs many file server functions in hardware and the unit parallelizes most operations - ideal for the computational demands of bioinformatics and drug discovery research, and helping BlueArc systems gain popularity in many life science organizations. Moreover, the high performance and scalability of BlueArc’s products are attracting clients in a number of industries including digital media and entertainment.
Challenge: Differentiate product from established players, other storage mavericks
Opportunity: Fill high-performance storage needs to complement increasingly more powerful computing systems

Bruker Biosciences
HQ: Billerica, Mass.; CEO: Frank H. Laukien; Sales: $303 million
Proteomics powerhouse
Bruker BioSciences has two separate divisions focused on the life sciences and specializing in instruments and software for detection and analysis. The company just won another award from Frost & Sullivan for innovation in its ClinProt mass spectrometry solution, used in biomarker analysis and other tasks. Bruker also makes a variety of molecular detection and analysis systems, including platforms for protein microarrays, liquid chromatography, X-ray crystallography, nuclear magnetic resonance, and FT-ICR. Though the parent company maintains most operations in the United States, several acquired companies and major research projects are in Germany.
Challenge: Expand leading position in clinical proteomics biomarker and biomarker panel detection, localization, identification, and validation
Opportunity: Pursue advancements in MALDI imaging; forensic drug screening by LC-MS

Caliper Life Sciences
HQ: Hopkinton, Mass.; CEO: Kevin Hrusovsky; Sales: $86 million
Tide turning for microfluidics
Caliper Life Sciences has enjoyed steady growth over the past two years since its acquisition of Zymark in 2003. The company combines microfluidics and laboratory automation to deliver research tools in the field of genomics, proteomics, and drug discovery. Caliper’s LabChip technology for diagnostic assays is used in 75 percent of Big Pharma companies. The company has diversified its partnerships, adding Affymetrix and Bio-Rad to Agilent among its best partners. The company recently acquired NovaScreen BioSciences and Xenogen Corporation in an $80 million deal. Xenogen’s in vivo imaging expertise helps Caliper offer a range of techniques from test tube to live subject.
Challenge: Maximize synergies with Xenogen and other acquisitions
Opportunity: Expanded customer base promises double-digit growth

HQ: Nottingham, U.K.; CEO: Steve Kent; Sales: Undisclosed (private)
Calling all patients
With 600 employees, ClinPhone is the largest vendor exclusively devoted to technology of clinical trials. It uses the telephone to dominate interactive voice response (IVR), randomization, and supply management, having helped on 1,400 trials at 90,000 sites in 71 languages. Without separate hardware, some of its solutions are appealingly priced lower than those of handheld patient diaries. The company also provides systems for electronic patient-reported outcomes (ePRO) and clinical trial management (CTM). ClinPhone recently reported a 218 percent increase in sales since 2001.
Challenge: Continue to grow, collaborate with EDC vendors, and validate device-free approaches to ePRO
Opportunity: Exploit cost, logistical disadvantages for handheld patient-reported outcome solutions

Elsevier MDL
HQ: San Leandro, Calif.; CEO: Lars Barfod; Sales: $9.27 billion (Reed Elsevier; 2004)
Cheminformatics muscle
Elsevier MDL spent the last year introducing new products or enhancing its existing informatics offerings. It introduced the MDL e-lab Notebook, part of an initiative that builds on MDL’s expertise in chemical reaction databases and workflows. There were also major upgrades to the MDL Isentris informatics platform and the cheminformatics MDL server product line. To help make its products easier to use in R&D workflows, the company undertook or strengthened partnerships with a number of vendors including InforSense, Tripos, and Spotfire.
Challenge: Get lab notebook recognition in a large, fractured market
Opportunity: Leverage partnerships and its own workflow technology to help R&D labs

HQ: Hopkinton, Mass.; CEO: Joseph Tucci; Sales: $8.23 billion (2004)
Storage leader, software focus
EMC has undergone a metamorphosis, shifting greater attention to its software, while maintaining a strong position in the storage hardware market. Last year, the company launched the first significant upgrades to Documentum content management system and eRoom collaborative software. Additionally, it acquired Captiva Software and Acartus, companies whose technology help capture, convert, and manage data. In 2005, EMC moved ahead of HP in sales of external disk-based storage for the first time since HP acquired Compaq.
Challenge: Deal with competition from new high-performance storage vendors
Opportunity: Leverage synergies between software and hardware

HQ: Foster City, Calif.; CEO: James M. Karis; Sales: Undisclosed (private)
Perseverance pays off
Established in 1996, Entelos is the granddaddy and a leader among biosimulation platform providers. Acquisition of Discovery Innovations last year brought IT/KM expertise that may allow Entelos to transform its PhysioLab platform, usually customized for a particular disease, into a more generalized tool. A deal with Unilever will move Entelos into the cosmetics market. Entelos is the only systems biology company to win full co-marketing rights for a joint development program with a partner (Organon). Other promising model-makers include Genstruct and Gene Network Sciences, who both emphasize inference engines over the mechanistic modeling used by Entelos.
Challenge: Making mechanistic models is expensive, time-consuming
Opportunity: Leverage DI acquisition to enable selling to a larger market

HQ: Morrisville, N.C.; CEO: John Cline; Sales: $12.8 million
Linking EDC and diaries
With 90 employees, etrials has perhaps a third the staff of rivals Phase Forward or Medidata in the electronic data capture (EDC) market. But etrials offers something those companies can’t: patient diaries and interactive voice response (IVR), sparing customers the headache of setting up additional databases and trial parameters. Through a merger, etrials will likely become a public company in 2006 and, like all participants in the market niche, is courting contract research organizations (CROs). etrials hopes that computer-driven efficiency gains will be attractive to such companies, which traditionally place greater emphasis on service than IT.
Challenge: Maintain service level, market share as growth continues
Opportunity: Pitch partnerships to tech-averse CROs forced to use technology by their clients

454 Life Sciences
HQ: Branford, Conn.; CEO: Chris McLeod; Sales: Undisclosed (private)
Accessible sequencing solutions
454 — a spin-off of Curagen founded by Jonathan Rothberg — captured headlines last year with a landmark publication of its next-generation sequencing platform in Nature. 454 claims its Genome Sequencer 20 system offers 100-fold reduction in cost over conventional automated Sanger sequencing, sequencing 20 million bases in a few hours. Systems were sold to leading genome centers. In October, 454 entered a five-year strategic partnership with Roche Diagnostics for worldwide distribution of its instrument. CEO McLeod predicts that “personal genome sequencing has the potential to become as critical to healthcare as the MRI.”
Challenge: Steal a march on competition in single-molecule sequencing platforms
Opportunity: Clinical diagnostics may become an important revenue stream down the road

HQ: Tokyo, Japan; CEO: Naoyuki Akikusa; Sales: $44.28 billion
Stepping up U.S. efforts
Fujitsu has more than 20 years experience developing informatics applications. But not many in the United States know about this, even though its products, such as MOPAC and CAChe, are widely sold domestically under resellers’ names. To boost its U.S. presence, researchers in the company’s relatively new BioSciences Group (part of the Fujitsu subsidiary Fujitsu Computer Systems) are tackling life science problems to highlight the company’s offerings. One such effort demonstrated a new approach to in silico ADME/Tox predictions. Fujitsu is also showcasing its BioServer, a massively parallel grid supercomputer, in its research work.
Challenge: Overcome lack of name recognition in U.S. life science market
Opportunity: Apply informatics and supercomputing expertise to life science problems

GE Healthcare
: Chalfont St. Giles, U.K.; CEO (elect): Joe Hogan; Sales: $15.15 billion
Good things to life sciences
GE Healthcare, the leader in the medical imaging market ahead of Siemens and Philips, reckons its $9.5 billion acquisition of Amersham Biosciences will broaden its global reach and accelerate its vision for personalized medicine — detecting disease before the onset of physical symptoms. That’s the party line, anyway. That vision will be directed by Joe Hogan, who succeeds former CEO Sir William Castell, who retires this year. Another priority is electronic health records, exemplified by the recent merger with IDX Systems, which Hogan believes will be available for consumers within a few years.
Challenge: Maintain strong leadership after departure of Sir William Castell
Opportunity: Enable “early health” model of care focused on detection and prevention

HQ: Mountain View, Calif.; CEO: Eric Schmidt; Sales: $4 billion
Search for life science impact
 “The Ethernet,” says inventor Bob Metcalfe, “provides the plumbing for the Internet, which provides the plumbing for the World Wide Web, which in turn provides the plumbing for Google!” Well put. Since its 2004 IPO, Google’s spectacular success was reflected in its share price, which quintupled in 12 months before dipping recently. But can Google’s search prowess do for life science and medicine? While Google directs more people to medical journals than any other source, Google Scholar is outpacing PubMed. Founders Sergey Brin and Larry Page have met with Craig Venter to discuss potential collaborations in Googling genomic information. The British Medical Journal recently called for the launch of “Google Medicine.” Stay tuned.
Challenge: Sustain astonishing momentum while honoring mandate to “do no evil”
Opportunity: Leverage information retrieval for global human health benefits

HQ: Palo Alto, Calif.; CEO: Mark Hurd; Sales: $86.7 billion
Building on HPC tradition
HP’s position in the scientific computing market, greatly enhanced with the acquisition of Compaq, continues. The company is one of many systems vendors jumping on the Itanium bandwagon, offering users a 64-bit alternative to even its own proprietary systems. Targeting the life sciences, HP sells preconfigured systems that bundle HP servers or clusters with a choice of Accelrys’ Materials Studio, the BioTeam’s iNquiry, or AMBER. HP conducts its life sciences work under a broader healthcare umbrella that addresses data management, security, regulatory compliance, and storage needs.
Challenge: Continued competition from IBM, others on consulting services front
Opportunity: Analysts think HP’s product mix puts it on right track to grow its business

HQ: Armonk, N.Y.; CEO: Samuel Palmisano; Sales: $96.29 billion (2004)
HPC domination
IBM’s life science reach is enormous, covering middleware and database software, collaborative software (Lotus Notes), server and workstation hardware, and integration and consulting services. Increasingly it is taking a partnering role leading the charge on biobanks, information-based medicine, even teaming with National Geographic in a global genealogy survey. The world’s top two most powerful supercomputers are IBM Blue Gene systems, being used by scientists to perform molecular interaction simulations.
Challenge: Deal with an SEC investigation into 2005 first-quarter earnings announcements.
Opportunity: Expand availability of its superior technology (e.g., Blue Gene) and data and project management skills

IBM Global Services
HQ: Armonk, N.Y.; CEO: Sam Palmisano; Sales: $49.3 billion (Services, 2004)
In praise of heft and deft(ness)
IBM is the gazillion-pound gorilla in IT services and consulting. Gargantuan, well funded, and made smarter about pharma by its acquisition of PricewaterhouseCoopers in 2002, IBM has a portfolio of products and services that dwarfs most competitors. Big Blue has worked hard to integrate its healthcare and life sciences initiatives. It currently leads one of three federally funded coalitions developing prototypes for an interoperable national health-IT network.
Opportunity: Drive and sell into the transformation of U.S. healthcare systems
Challenge: Avoid trampling customers with good but heavy-handed intentions

HQ: San Diego; CEO: Jay Flatley; Sales: $50 million
Increasingly popular bead platform
Founded in 1998, Illumina is finally delivering commercial systems based on its innovative bead-based array technology. Its growing popularity has led to a near-120-percent stock growth in the past 12 months. CEO Jay Flatley predicts “explosive growth” in the SNP whole-genome genotyping and genetic diagnostics space in the next few years. Illumina partnered with Invitrogen in oligator core technology. Introduced in early 2004, Illumina has already installed almost 100 BeadStations. The company has just released its HumanHap300 Genotyping BeadChip, containing 300,000 “tag SNPs” used to monitor human populations. Its latest Infinium genotyping arrays should have 1 million SNPs. Acquired last year, Cyvera is now “Illumina East.”
Challenge: Establish as main rival to Affymetrix
Opportunity: Capitalize on high-throughput genotyping explosion

HQ: London; CEO: Yike Guo; Sales: Undisclosed (private)
New customers, partnerships
2005 was a coming-out year for InforSense, as its KDE integrative analytics platform was selected as the underlying workflow infrastructure by several life science organizations. These include Bayer, which is using KDE to enhance its drug discovery cheminformatics infrastructure; the National Cancer Institute for its NCI Core Genotyping Facility for high-throughput genetic data analysis; and the Windber Research Institute in its translational medicine work. The company continues to work with existing clients GSK and AstraZeneca, while striking new alliances with The BioTeam, Elsevier MDL, and Spotfire.
Challenge: Distinguish itself from commercial and open-source workflow competitors
Opportunity: Tap into growing demand for industrialized processes in life science R&D

Ingenuity Systems
HQ: Redwood City, Calif.; CEO: Jake Leschly; Sales: Undisclosed (private)
Status no guarantee of success
Much like GeneGo, Ingenuity is making hay in the pathway analysis market, relying on proprietary, manually curated databases. Acceptance and demand for pathway analysis tools is clearly growing. “We’ve been able to gain new insights, substantiate hypotheses, and identify biomarkers with these tools,” says Steve Howes of Wyeth, which expanded its Ingenuity relationship. Ingenuity’s list of customers is impressive, and its early-mover advantage may be critical, as the market doesn’t seem to require an army of pathway tool providers.
Challenge: Fend off lower-cost competitors who argue manual DB curation adds cost, not value
Opportunity: Sell more enterprisewide deployments; incorporate high-end modeling capabilities

HQ: San Diego; CEO: Gregory Lucier; Sales: $1.2 billion
Building one-stop consumable shop
Invitrogen continued its aggressive shopping program in 2005 by acquiring Zymed (antibody manufacturer), Dynal (magnetic bead technology), and Quantum Dot, bold steps toward CEO Greg Lucier’s vision of becoming “the preeminent partner for organizations performing disease research and drug development worldwide.” But those acquisitions have not necessarily impressed the market — Invitrogen’s stock price is flat from 12 months ago. The company launched iPath, a pathway resource, and signed a proteomics deal with rival Applied Biosystems. Frost & Sullivan selected Invitrogen as recipient of the 2005 Drug Discovery Technologies Company of the Year Award.
Challenge: Increase profitability in tricky pharma climate
Opportunity: Develop luxury suite of molecular biology tools and platforms

HQ: Pittsburgh, Pa.; CEO: Doug Engfer; Sales: Undisclosed (private)
So patients can’t make it up
Invivodata’s has extensive peer-reviewed publications showing — at times in hilarious detail — the inadequacy of paper patient diaries. Having assisted 130 trials involving over 50,000 patients, invivodata is the only e-diary company that can identify two FDA approvals that depended on its technology. But picking a leader among a handful of e-patient diary companies is somewhat arbitrary, as all suppliers have generally satisfied customers and all typically custom-program Palm handhelds. The company claims its revenues tripled from 2004 to 2005.
Challenge: Surmount doubts about patient-diary space due to potentially crippling lawsuit brought by Boston’s PHT
Opportunity: Continue to (quietly) build on access to friends at FDA

Isilon Systems
HQ: Seattle, Wash.; CEO: Steve Goldman; Sales: Undisclosed (private)
Showing big boys how to do it
The glut of experimental data and data analysis requirements are causing many headaches, with storage systems often the weakest link. Isilon has combined high performance, low management, and high scalability into its storage systems, winning customers such as the Cedars-Sinai Medical Center’s Louis Warschaw Prostate Cancer Center. The system meets the center’s expected growth in storage needs and offers high performance, without increasing management burden. Non-life-science customers include Kodak EasyShare Gallery, Sony Pictures Imageworks, and Myspace.Com.
Challenge: Battle storage giants and high-performance storage competitors
Opportunity: Leverage showcase clients using systems to get more customers

Medidata Solutions
HQ: New York, N.Y.; CEO: Tarek Sherif; Sales: Undisclosed (private)
Specializing in EDC
Medidata Solutions is arguably the world’s leading electronic data capture supplier, and the vendor most feared by competitors. Unlike the tools of some competitors, its technology was always designed to work via the Internet. It has aggressively hired senior executives from rival companies. Major customers include Bayer and Johnson & Johnson. Some customers believe Medidata’s growth has been so explosive that service has suffered; others continue to praise the staff’s flexibility. In preparing for a future stock offering, Medidata recently claimed a 9,000 percent increase in revenues from 2000 to 2004.
Challenge: Maintain service level, identify affordable acquisition targets in CTM and drug safety niches
Opportunity: Build on early efforts to integrate company technology with hospital, physician IT systems

HQ: Redmond, Wash.; CEO: Steven Ballmer; Sales: $39.79 billion
The giant roars
In 2005, Microsoft made a multi-front push into the life sciences. It launched its Digital Pharma Initiative, an effort to provide hardware vendors, software developers, and systems integrators with a framework they can use to deliver life-science-specific solutions to the pharmaceutical industry. And it took aim at Linux clusters with the launch of the beta 2 version of Windows Compute Cluster Server 2003 - announced in person by Bill Gates at the Supercomputing 05 conference. Both efforts already have an impressive list of well-known life science customers and vendor partners.
Challenge: Convince users its HPC software is an alternative to Unix and Linux
Opportunity: Leverage client software as an entrée into life science HPC applications and workflows

Network Appliance
HQ: Sunnyvale, Calif.; CEO: Daniel Warmenhoven; Sales: $1.6 billion
Storage pioneer keeps pace
The pioneer of network-attached storage continues to work from a position of strength. The NetApp systems, widely used in the life sciences, are admired for their ability to handle the explosive growth in data. Additionally, NetApp (alone and through partnerships) continues to enhance its offerings to ensure stored data meets security and regulatory compliance requirements. NetApp has reaped the benefits of an IBM reseller partnership and just opened a regional headquarters in Hong Kong.
Challenge: Keep its stock price high after talk of an (unlikely) IBM buyout sent it up
Opportunity: Combat challenges from storage startups by leveraging its distribution and reseller channels

HQ: San Ramon, Calif.; CEO: Jim Rogers; Sales: Undisclosed (private)
Small but powerful
Nextrials has an unusually full-featured EDC application that works across multiple phases of trials. Just two weeks are needed to set up a database; the fact that its code runs on Unix servers means Nextrials inflicts almost no downtime on customers. The company’s EDC tools can also manage multiple trials (CTM) and drug safety data management and reports. Nextrials has pioneered the electronic transfer of laboratory in accordance with the formats of the Clinical Data Interchange Standards Consortium (CDISC). Novacea is a major customer.
Challenge: Build greater visibility in Europe, northeast U.S.
Opportunity: Clinical trial sponsors already using CDISC and don’t want to integrate multiple databases, applications

HQ: Redwood Shores, Calif.; CEO: Larry Ellison; Sales: $12.9 billion
Life-science goliath
Oracle’s databases remain the standard in pharma, where they are used throughout drug discovery and development. The company’s latest database, 10g, handles monstrously big scientific data sets. It includes new functionality specifically for the life sciences that has been exploited by industry, academia, and instrument manufacturers. Oracle also has a broad suite of tools for clinical trials: systems for standardizing terminology; for managing clinical data (CDM); for managing trials (CTMS); and for assessing drug safety. With Pfizer as a supporter, Oracle developed a controversial application for collecting clinical trial data that emulates the paper forms that still bedevil the industry.
Challenge: Digest large acquisitions; convince life science customers their needs are on Oracle’s vast corporate agenda
Opportunity: Uniquely able to integrate drug discovery, clinical trial data — and electronic health records in hospitals and physician offices

HQ: Wellesley, Mass.; CEO: Gregory Summe; Sales: $1.47 billion
Financials pave way for growth
PE’s Life & Analytical Sciences (LAS) division accounts for on the order of $1 billion in revenue. Its diverse equipment portfolio encompasses everything from liquid handlers to HPLC and GC/MS systems. Equally diverse are LAS’ services such as genetic screening and protein analysis. Early last year PE struck a major collaboration with Waters to deliver newborn screening solutions and distribute certain Waters products. The sale of its aerospace and fluid-testing businesses have strengthened PE’s balance sheet and should fuel future growth.
Challenge: Manage its diverse portfolio instruments and services
Opportunity: Leverage technology expertise to provide innovations in health sciences

HQ: Mountain View, Calif.; CEO: Shawn M. O’Connor; Sales: $22.5 million
Taking the trial out of trials
When Pfizer was trying to decide if a combination therapy project should move forward, it used Pharsight simulation technology to speed the decision-making process, shutter the project six months early, and save $2 million. In the world of clinical trial simulation, Pharsight is the leader. It’s also profitable ($2.7 million net in 2005 versus $2 million loss in 2004). Few aspects of drug development are as costly as clinical trials.
Challenge: Most modeling providers previously focused on discovery are now targeting clinical trials
Opportunity: Grow with the market and maintain its leadership position

Phase Forward
HQ: Waltham, Mass.; CEO: Bob Weiler; Sales: $87.1 million
Clinical tools for Big Pharma
The leading e-clinical suite provider, Phase Forward offers three main products: tools for EDC; clinical data management (CDM); and analyzing drug safety, in part using its own software and that acquired in the purchase of Lincoln Technologies. Some customers happily build their clinical trials around Phase Forward; others struggle to integrate the company’s applications. Phase Forward has a strong global presence. Major customers include Lilly and Glaxo. In the EDC niche, where it is trying to appeal to smaller sponsors and CROs, Phase Forward faces robust competition from cheaper and more Web-based rivals.
Challenge: Reduce cost structure, help industry understand EDC value proposition
Opportunity: Use financial strength, marketing to crush smaller companies

HQ: San Diego; CEO: Ken Dahlberg; Sales: $7.2 billion
Chasing the gold — SAIC plans IPO
SAIC will relinquish its status as the largest employee-owned research and engineering company with a planned IPO later this year. The 43,000-employee company’s operating income jumped 23 percent last year, and its win rate on re-compete projects was an impressive 95 percent. SAIC executes roughly 9,000 contracts annually and has its fingers in virtually every technology pot. One life sciences example is long-term work at NCI, including participation in the cancer Biomedical Informatics Grid (caBIG) project. A rare hiccup was poor financial results from its Greek Olympics contract. That delayed the public offering but won’t prevent it.
Opportunity: Grow more rapidly using IPO funds for acquisitions
Challenge: Allay investor worries over disappointing Greek Olympics contract

HQ: Cary, N.C.; CEO: Jim Goodnight; Sales: $1.5 billion
Setting high standards
The leading statistical software company makes analytical tools for all industries. But its applications for the life sciences are considered indispensable in pharma and academia alike, where SAS-savvy programmers remain in high demand. The company controls the file format for data submitted to the FDA — but, to its credit, the company has been a steadfast contributor to development of nonproprietary formats developed by CDISC. Few technology vendors can honestly claim, as SAS does, to support the import, export, and processing of XML documents and content in CDISC-defined formats.
Challenge: Make SAS tools easier to use for nonprogrammers, nonstatisticians
Opportunity: Supply analytics for increasingly complex genetic, clinical data sets in life science companies of all sizes

HQ: Mountain View, Calif.; CEO: Dennis McKenna; Sales: $730 million
Needed technology makeover
For years, SGI was a leader in the scientific computing and visualization workstation market. But its products, built on proprietary 64-bit technology, were falling out of fashion. To address this, the company has shifted to a new class of systems based on Intel Itanium2 processors and SGI’s NUMAflex shared memory architecture. The new Altix computing and Prism visualization systems, while pricey, quickly garnered the interest of researchers. SGI also teamed with the NCI to develop an automated imaging workflow and analysis process for studying cancer cells. (This project won a 2005 Bio•IT World Best Practices Award.)
Challenge: Compete with lower-cost 64-bit systems flooding the market
Opportunity: Gain more clients by leveraging visualization and systems expertise

HQ: Kyoto, Japan; CEO: Shigehiko Hattori; Sales: $2.1 billion (2004)
Venerable, tough, and lasting power
Founded in 1875, Shimadzu is a massive manufacturing conglomerate spanning medical devices, science instruments, aircraft equipment, and industrial machinery. Its diverse scientific instrument business is more than double the size of other LOBs, including HPLC, GC, and mass spectrometers. Japan’s troubled economy has hampered growth, but overseas sales are strong and the company is mounting an aggressive effort in China. Shimadzu has targeted pharma and plans to accelerate new product launches.
Challenge: Manage global expansion while navigating Japan’s troubled economy
Opportunity: Ride expected demand wave for mass spec in all things omic

Siemens AG
HQ: Munich, Germany; CEO: Klaus Kleinfeld; Sales: $91 billion
Care without boundaries
President Bush’s increasing focus on healthcare underscores Siemens Medical Solutions’ array of efforts to bring medicine into the 21st century with offerings such as the Soarian health information solution (an integrated system for patient-centered care), the REMIND data-mining platform, and a full suite of imaging solutions, including syngo RIS/PACS and the Biograph 16. Siemens will partner with Nucletron BV to expand its oncology care portfolio. In the health-IT area, COO Janet Dillione states: “Building a national health information network will be a formidable task, but it can be done and we already have the technology to help make it happen.”
Challenge: Help to build a national health information network for electronic health records
Opportunity: Innovate in widespread adoption of interoperable health-IT solutions

HQ: San Francisco; CEO: John West; Sales: Undisclosed (private)
Single molecules to $1,000 genome
Solexa begins shipping its flagship 1G Analyzer sequencing machine this year, capable of sequencing DNA for 1/100 the current cost — or $100,000 for a human genome for a few months on a single instrument. Solexa merged with Lynx Therapeutics last year and attracted nearly $100 million in financing. CEO West, formerly a VP with Applied Biosystems, foresees a $1 billion market, particularly if the Cancer Genome Project is funded, and reckons Solexa can maintain its lead in cost-effectiveness over rivals 454, Helicos, and PacificBio. In January, Solexa completed the second and final closing of a $65 million private equity financing.
Challenge: Convince customers to step away from traditional capillary sequencing
Opportunity: Grab early lead in $1,000 genome sweepstakes

HQ: Somerville, Mass.; CEO: Christopher Ahlberg; Sales: Undisclosed (private)
Keeps going and going and going...
Spotfire’s analytic and visualization tools are a mainstay in virtually all drug discovery organizations. The company continues enhancing DecisionSite with new analytic and management features, recently adding gene expression and functional genomics software. In a sign of how applications will work in the future (integrated into workflows using Web services), Spotfire teamed with InforSense and GlaxoSmithKline in a rapid application development project. Stephen Calvert, vice president of cheminformatics at GSK, says the work allowed GSK to “deliver applications to end-users at the pace of discovery.”
Challenge: Highlight its life science expertise to differentiate its software from generic analysis tool vendors
Opportunity: Team with partners to tightly integrate DecisionSite into analytic workflows

HQ: Zurich, Switzerland; CEO: Thomas Bachmann; Sales: $230 million (2004)
The substance of discovery
This longtime robotics and life sciences supply company has branched out to create high-throughput automation platforms that encompass all aspects of the discovery process — liquid handling, analysis, sample tracking, storage, etc. — including enhancements for its Freedom EVO liquid-handling platform and the introduction of a sample storage and retrieval system for smaller laboratories. Last year Tecan struck deals with Promega and Dynal, as well as the installation of the REMP BioBank (Tecan acquired REMP in June 2005), a large-scale automated repository for biological samples at Pfizer’s facility in Groton, Conn.
Challenge: Continue to improve operational efficiency; maintain growth momentum
Opportunity: Build on current success to improve profitability to reach industry benchmarks

HQ: Seattle, Wash.; CEO: Joseph Duncan; Sales: Undisclosed (private)
Lab automation, data management
Teranode links the computational and experimental worlds by allowing researchers to quickly model, automate, and manage experiments. With its software, researchers use a graphical pallet to model experimental steps and procedures. The software automatically converts the model to programming code. Teranode offers a number of preconfigured applications, including one for pathway analysis. The company has partnered with major pathway model providers and other software vendors, allowing easier import of data and existing models. The company is also a leading proponent of Semantic Web technology.
Challenge: Demonstrate its approach scales to accommodate very large data sets
Opportunity: Promote use of its tools to meet the data management, lab automation needs of many companies

HQ: Waltham, Mass.; CEO: Marijn Dekkers; Sales: $2.2 billion (2004)
Managing data a new priority
Long known for its analysis and lab equipment, Thermo has focused its efforts over the last year on commercial off-the-shelf laboratory information management systems (LIMS). This year, Thermo introduced the Darwin LIMS, which manages manufacturing, quality assurance, and quality-control data required to bring a drug to market. Last year, Thermo introduced the Galileo LIMS 3.1 for high-throughput in vitro ADME/Tox labs and Retriever 3.0, a Web-based data extraction tool for secure access to lab data. Even when the company introduces new hardware, a key feature is the accompanying data management software.
Challenge: Vie with numerous competitors in a very fractured LIMS market
Opportunity: Leverage equipment customers in need of better data management

HQ: St. Louis, Mo.; CEO: John McAlister; Sales: $64.8 million (2004)
Informatics heavyweight
Tripos started the year with the timely announcement of a new $5 million deal with Wyeth. That’s a far cry form its expired four-year, $90-million collaboration with Pfizer, which coincided with news of lay-offs at its UK research center. Last year, Tripos acquired the molecular discovery software company Optive Research, introduced a laboratory information product suite called Benchware. It also released new versions of SYBYL, its molecular modeling suite, and LITHIUM, the computational chemistry decision support platform.
Challenge: Refocus strategy while battling pressures to cut staff and break company apart
Opportunity: Leverage its new service-oriented architecture approach to work more easily with other applications

United Devices
HQ: Austin, Texas; CEO: Ben Rouse; Sales: Undisclosed (private)
Tapping unused resources
Grids have been eyed for years for their promise to harness computing power, but it took United Devices, with its easy-to-manage software, to get companies to take a serious look at the technology. UD’s Grid MP software is the underlying infrastructure powering several philanthropic PC grids (e.g., FightAids@Home and World Community Grid) and many commercial grids such as those used by Novartis and Johnson & Johnson Pharma R&D. Recently, the company has been bulking up its cluster solutions through new software releases and has focused on partnerships to certify its program for use on various systems.
Challenge: Overcome PC-grid-only perception and get recognition of its cluster support
Opportunity: Leverage its success in corporate grids to attract new customers

HQ: Milford, Mass.; CEO: Douglas A. Berthiaume; Sales: $1.1 billion (2004)
Critical mass and momentum
Having passed the $1 billion sales mark, Waters is poised to challenge bigger rivals. It aggressively added lab informatics to its portfolio of instruments (chromatography, mass spec, thermal analysis) and is betting big on selling integrated lab solutions. The Acquity UPLC platforms made substantial inroads last year, and Waters recently launched a major upgrade of NuGenesis SDMS software. It’s not all rosy: Lab-on-a-chip technologies pose a threat. But FDA’s push for more information about on- and off-target activity (can you say Vioxx?) should boost overall demand for instruments.
Challenge: Monitor competitive, chip-based microfluidic offerings
Opportunity: Leverage its complete solution capability

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