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Letter from the Editor 
PlayStation Cell Speeds Docking Programs 

Letter from the Editor

Dear Inside IT readers,

It saddens me to say that this is the farewell issue of Bio-IT World’s Inside IT.  For the past five years, Sal Salamone, one of the founding editors of Bio-IT World, has done absolutely sterling work reporting on the new trends and technologies from the IT space that impact the way life scientists gather, store, and analyze more and more data.  Sal remains a contributing editor of Bio-IT World, so his legions of fans in this space haven’t heard the last from him!

In place of Inside IT, starting this September, we are excited to announce the launch of a new e-newsletter from Cambridge Healthtech Media Group, devoted to the impact of informatics on the research/drug discovery value chain.  Edited by Bio-IT World’s John Russell, this fortnightly vehicle will provide compelling insights and commentary around the efficiency and “predictiveness” of modern biomedical research.  We hope that you will look for this new title when it debuts in the fall, and continue to turn to Bio-IT World for the latest on indispensable technologies driving the future success of the industry.


Kevin Davies PhD
Bio-IT World

PlayStation Cell Speeds Docking Programs
By Mike May

Last year, SimBioSys in Toronto, Canada, hit a software snag. Although it’s eHITS software produced great 3-D ligand structures, such as a potential drug docking with a receptor, the program needed to run faster. “A pharmaceutical company conducted a test comparing results from eHITS and other available packages,” recalls Zsolt Zsoldos, chief scientific and technology officer at SimBioSys. “eHITS provided the best docking accuracy and enrichment, but it was slow—too slow to purchase.” So Zsoldos and his colleagues set out in search of speed.

They tried field-programmable gate arrays (FPGAs) and graphics processing units (GPUs), but rejected both. “For the FPGAs, it would have required a lot of work to bring the complex algorithm down to the hardware-switch level. Also, practical throughput is much lower than the theoretical value on GPUs, because programming does not allow direct control of memory transfers and vector operations, and the performance gains are less than optimal,” explains Zsoldos.

Undeterred, they tried the Cell Broadband Engine, which was developed jointly by IBM, Sony, and Toshiba. Even though this processor powers Sony’s Playstation PS3, the Cell goes beyond games.

continues below



The Cell relies on two layers of hardware working in parallel. The power processor element—similar to an IBM Power 970—makes up one layer. The other consists of eight synergistic processing elements, which each contain a 128-bit vector processor with single-instruction, multiple-data architecture, a direct memory access controller, and 256 kilobytes of on-chip memory. In essence, this creates nine CPUs, all connected through an element interconnect bus with a bandwidth of 300 gigabytes per second. In all, the Cell turns out sustained power of 210 gigaflops (billion floating point operations per second)—70 times faster than an Intel dual-core 2.4 GHz processor.

Reorganizing the Algorithm
Beyond speed, other features enticed SimBioSys. For one thing, notes SimBioSys consultant Antony Williams, “There are multiple GPUs and FPGAs on the market, but the future of the Cell processor is stabilized by IBM’s multiyear development plan.” Zsoldos adds that pharmaceutical companies want to connect an accelerator to a server, and the IBM server blade, which includes two Cells, is ideal for that. Moreover, that piece of hardware pumps out 400 gigaflops. Read more



Lilly Singapore Center for Drug Discovery (LSCDD) - Associate Director of Informatics,
Lead and mentor a strong team for the Bioinformatics group at the Integrative Computational Sciences (ICS) department at LSCDD towards the development of novel algorithms, data analysis methods and software tools for drug discovery. Work closely with the Software Engineering group at ICS, and collaborate with the Discovery IT organization in Europe and USA. For additional information, or to apply visit:

Lilly Singapore Center for Drug Discovery (LSCDD)- Senior Bioinformatics Scientist,
Contribute to the development of novel algorithms, data analysis methods and software tools for drug discovery as part of the Integrative Computational Sciences (ICS) department at LSCDD.  Work closely with informatics and software engineering peers at ICS, and collaborate with the Discovery IT organization in Europe and USA. The successful candidate will offer hands-on insight and expertise in tailored therapeutic informatics and statistical analyses at the post-genomic era. For additional information, or to apply visit:

Lilly Singapore Center for Drug Discovery (LSCDD) - Manager, Software Engineering (Integrative Computational Sciences)
Join the Integrative Computational Sciences (ICS) department at Lilly Singapore Centre for Drug Discovery (LSCDD),as Manager Software Engineering.  Lead the development of integrated applications to process and visualize data from cutting edge technologies used by scientists at Lilly Research Labs (LRL) and the Drug Discovery Research (DDR) teams. Masters in Computer Science/Engineering or related discipline, 10+ years post graduation experience , 2 years management experience needed. For a complete job description and requirements or to apply visit: LSCDD 

Lilly Singapore Center for Drug Discovery(LSCDD) -Senior Software Engineer, 
Join a strong team of software engineers in our Integrative Computational Sciences (ICS) at LSCDD. Collaborate with, and help develop integrated applications to process and visualize data from cutting-edge technologies used by scientists at Lilly Research Labs (LRL) and the Drug Discovery Research (DDR) teams. The Software Engineering team provides computational tools and tailored software solutions that enable the global effort of Tailored Therapeutics; ‘The Right Drug, at The Right Dose for The Right Patient at The Right Time'. For additional information, or to apply visit:

Linguamatics, Applications Specialist, Life Sciences Text Mining Software - Northeast U.S.*
Linguamatics, a leader in semantic search and text mining for the
pharma/biotech industry, is looking for an experienced life science
focused applications specialist to demonstrate the value of our products and help drive the growth of our North American business.  For further information visit:

Memorial Sloan-Kettering Cancer Center - Linux Systems Administrator 
MSKCC Bioinformatics Core in Manhattan seeks Linux Systems Administrator. Install, configure and update monitor and troubleshoot HPC cluster, email and web servers.  Master's degree and 5 years experience with HPC, network security, Postfix, Apache, Tomcat, Grid Engine. Solaris, Email or #015429. EOE/AA 

Unilever - Mathematical Modeller (Research Scientist)
This research is leading to the requirement for integration of both biological and chemical data that may not be amenable to analysis through traditionally used techniques. The ability to work in multidisciplinary teams alongside biologists, chemists and statisticians plus enthusiasm for learning new science is critical for the role.   For a complete job description and to apply, please visit: 

More Life Science Jobs ~ Add a Job Listing



ELNs: Advanced Laboratory Solutions-September 15 - 17 2008 • Crowne Plaza, Brussels, Belgium 

Discovery Knowledge & Informatics - September 15 - 17, 2008 • Crowne Plaza, Brussels, Belgium 

Multiplexed Genomics Tools: Targeting the Missing Links
Between Health and Disease
 - September 21-23, 2008 •
 Providence, RI

Next-Generation Sequencing Data Analysis -September 22-23, 2008 • Providence, RI

Barnett Educational Services, 2008 Schedule

To have your event featured here, contact Lynn Cloonan for more information.

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Spain’s Emerging Biotech Revolution
The biotechnology sector is growing 10 percent faster in Spain than it is in the U.S. Driven by a culture, government and private sector that are open-minded and optimistic, Spain-based companies are emerging as leaders in this dynamic field. Discover how your business can capitalize on creative solutions from Spain-based enterprises. Download Now     

Will Healthcare IT Trends Standardize?
A new wave of activities are driving transformation within the healthcare market. One solution is found in a guide to PDF Healthcare Best Practices. This “Best Practices Guide” describes Portable Document Format (PDF) attributes and use to facilitate the capture, exchange, preservation and protection of healthcare information. This webinar will focus on trends in today’s healthcare market, the challenges in overcoming these issues, and finally how to use best practices to improve patient care, enhance productivity and eliminate paperwork. It’s hosted by Adobe and moderated by Digital Healthcare & Productivity Executive Editor, John Russell. Click here...  

Automate Method SOPs for Greater Efficiency and Fewer Errors with Waters® NuGenesis® Intelligent Procedure Manager
The Waters® NuGenesis® SDMS Intelligent Procedure Manager is a workflow software package designed to guide the laboratory analyst through a routine, comprehensive method standard operating procedure (SOP) and integrate results with a chromatography data system. The Intelligent Procedure Manager addresses the predominately manual activities required to perform an analytical method or test, reducing cycle times up to 50-75% as compared to a traditional paper trail with fewer opportunities for human error.  From late-stage development to final product quality control and lot release, Intelligent Procedure Manager can be applied to any lab environment where rigorous adherence to approved test methods and SOPs must be followed, including compliance requirements for cGMP operations.Download Now

This Bio•IT World Briefing On “Next-Generation Sequencing,”underwritten by GenomeQuest, Inc.,
presents a selection of feature stories, interviews,commentaries, conference reports, and editorials on the emergence, opportunities, and challenges posed by high-throughput sequencing. Covered in this collection: the launch of new platforms from Applied Biosystems and Helicos; new applications of nextgen sequencing; the rise of personal genomics; and informatics solutions to vexing problem of managing the vast volumes of next-gen data. Download now 

To have your white paper featured here, contact Lynn Cloonan for more information.


Life Science Webcasts from Bio-IT World and Cambridge Healthtech Media Group

Life Science Webcasts

Drug Discovery, Development and Commercialization: Evolving Challenges and Opportunities

Joshua Boger, PhD, president and CEO, Vertex Pharmaceuticals Inc., presents his keynote titled "Drug Discovery, Development and Commercialization: Evolving Challenges and Opportunities" at the 2008 Bio-IT World Conference & Expo, April 2008, in Boston.
View the webcast.

View all Bio-IT World webcasts.

Contact the Editor
We invite your comments and feedback for this edition of Inside IT.

Salvatore Salamone
Senior Contributing Editor

Salvatore Salamone is Bio-IT World's senior contributing editor for information technology. He has over 16 years' experience writing about networking technology and is the author of three books, including The Complete Guide to VPNs (published by InternetWeek, 1999), LAN Times Guide to Managing Remote Connectivity (Osborne McGraw-Hill, 1997), and Reducing the Cost of LAN Ownership (Van Nostrand Reinhold, 1995, co-written with Greg Gianforte).

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