Systems Biology - Tools, Strategies, and Companies Driving Integrative Biology 


A Bio-IT World publication
Thurs., February 14, 2008 | | Archives | Advertising | Your Account | CHI Conferences | Subscribe |
Sales Contacts
For advertising information contact: 

Alan El Faye
VP, Advertising Sales - CA, Western US, Canada, Pacific Rim

Kay O. Christopher
Regional Sales Manager, Advertising Sales -New England, North Eastern US

Tom Loughran
Regional Sales Manager, Advertising Sales -Midwest, South Eastern US, Europe

Contact the Editor 

We invite your comments and feedback for this edition of Systems Biology.
John Russell
Executive Editor

Link to Us! 
You are welcome to link to articles on our website. Contact Catherine Varmazis for details.

e-Prints & Reprints 
To post a full article from Systems Biology or Bio-IT World on your website (not just a link), or for paper reprints, please contact:
Becky Mullaney
The YGS Group
717-399-1900 ext.110

Q&A: Vijay Chandru Discusses Strand's 'Intel-Inside' Strategy 

GeneGo Launches Disease-Specific Platform

Montreal Researcher's Heart Model Has 2 Billion Elements
InforSense Launches VisualSense; Tackles Spotfire

Briefs from the Systems Biology Community


Executive Q&A: Inside Strand Life Sciences
By John Russell

Strand Life Sciences is hardly invisible, but its "Intel-inside" strategyVijay Chandru means that many users don't know Strand is the engine inside their informatics tools. Even a near-fatal terrorist attack on Strand Chairman and CEO Vijay Chandru didn't produce the typical coverage that suddenly raises one's profile. He and three others were wounded and another speaker was killed in an attack during a science conference in India. The attack, by a lone gunman wielding an AK-47, occurred on December 28, 2005, when much of the world was in holiday mode and not paying a lot of attention. (For two accounts of the attack, click here and here.)

Chandru missed nearly a year of work, but the company he founded labored on. He eventually resumed his responsibilities, which today call for Chandru to be in the U.S. a fair amount of the time. If you use GeneSpring or PathwayAssist, you are really using embedded Strand technology. Its strategy has been to develop solid technology and find partners to help bring that technology to market. Microarray tools were first, followed by pathway tools, then QSAR tools, and recently it's begun a solutions business that encompasses customized tools and research collaborations. Strand even has a system biology effort and has developed a liver model that's being evaluated by FDA and a few pharmas. Read more. 


GeneGo Launches Disease-Specific Platform
By John Russell

After just a few months of close collaboration with the Cystic Fibrosis Foundation Therapeutics (CFFT), GeneGo has launched MetaMiner CF, a disease-specific tool embedded in GeneGo's MetaCore pathway database and analysis platform. The new tool contains rich information about cystic fibrosis and represents an important expansion by GeneGo into disease-specific areas.

"CFFT approached GeneGo because we were looking for an informatics tool that would help integrate emerging data from biomarker and target identification projects with the known literature," says Diana Wetmore, VP of alliance management for CFFT (a non-profit drug discovery and development affiliate of the Cystic Fibrosis Foundation). Read more.


Montreal Researcher's Heart Model Has 2 Billion Elements
By Salvatore Salamone 

Researchers at the Université de Montréal (UdM) have run a two billion element model of the heart, which they claim is the largest mathematical simulation of a heart ever assembled. The model seeks to discover the electrical triggers and mechanisms of the various kinds of heart disease. Read more.


InforSense Launches VisualSense; Tackles Spotfire
By John Russell

InforSense introduced two products in January, VisualSense and Document Explorer, continuing to expand the analytics and collaboration capabilities embedded in its foundation product, InforSense Platform (IP). IP is essentially a middleware engine for data management and workflow into which various analytic applications from InforSense or third parties can be incorporated. Read more.


Briefs from the Systems Biology Community

Optimata Raises $1.5 Million
Bio-simulation specialist Optimata announced Wednesday the completion of a private placement of $1.5 million from a new group of private European investors. The company recently shifted its business emphasis from research collaboration to oncology drug repositioning. (See Optimata: Eyes on the Prize). Optimata will use the new funds to complete the evaluation process required for the selection of discontinued drug candidates most suitable for repurposing. The funding will also significantly enhance Optimata's computational capabilities.

"After closely examining more than 100 drug candidates, we have short-listed several that we believe have good prospects for repurposing and renewed clinical development," said Guy Malchi, Optimata's CEO, in a press release. "We plan in the next few months to make a final selection of one or two compounds and then to use our technology to significantly improve the compounds' safety and efficacy profiles. The in-licensing of drug candidates for in-house development represents an additional approach to our business development and one that we expect to substantially increase revenues."

Entelos Issues Guidance
Bio-simulation specialist Entelos recently issued financial guidance for the second half of its fiscal year that was in line with earlier forecasts. "The company has good contract visibility and has cash and accounts receivables of $9.9 million as at 31 December 2007," according a release.

"Since its interim report on 19 September 2007, Entelos announced expanding research in cardiovascular disease with Pfizer Inc., conducting additional research in diabetes with Johnson & Johnson Pharmaceutical Research and Development L.L.C., raising capital from Pfizer Ireland Pharmaceuticals and the Imperium Master Fund, repaying debt related to the acquisition of Iconix Biosciences, and initiating in silico research in rheumatoid arthritis with a new pharmaceutical customer, UCB Pharma," reported the company.

BioSeek Inks DSP Deal 
BioSeek struck a collaboration agreement with Dainippon Sumitomo Pharma Co. of Japan. BioSeek will use its BioMAP platform to support compound differentiation, lead development, and drug candidate selection activities for DSP discovery programs in inflammation and metabolic diseases. "[The BioSeek platform] deliver otherwise difficult-to-obtain human biological information, which will help us prioritize leads and candidates," stated Dr. Yuichi Yokoyama, executive director of DSP, in a release.

GTL to Support Bio-Hydrogen Research
The Genomics GTL program (U.S. Department of Energy) is seeking applications for research support in the following areas: i.) systems-level research to improve understanding of microbial regulatory and metabolic networks related to hydrogen production; ii.) development of new model organisms for microbial hydrogen production, and; iii.) targeted approaches for the identification and characterization of enzymes and biochemical pathways relevant to biological hydrogen production in genome and metagenome sequences.

Compugen Touts Early Results
Compugen announced promising results from initial in vivo validation studies of CGEN-855A and CGEN-855B, two novel peptide agonists of the FPRL1 G-protein coupled receptor (GPCR), which may serve as anti-inflammatory and cardio-protective drug candidates. CGEN-855A and CGEN-855B were discovered using the company's previously announced GPCR ligand discovery platform. In the study of acute myocardial ischemia-reperfusion injury, both compounds showed "significant dose-dependent protection against reperfusion injury and reduce infarct size by up to 36%.

Systems Biologist Wins 'Women in Science' Award
Naama Barkai of the Weizman Institute of Science in Rehovot, Israel, was selected as the first winner of the FEBS/EMBO Women in Science Award. Barkai receives the 2008 award for her contributions to the field of systems biology and the mathematical modeling of biological systems.

The FEBS/EMBO Women in Science Award is a joint initiative of EMBO and the Federation of European Biochemical Societies (FEBS). Launched in 2007, the aim of the award is to highlight the major contributions being made by female scientists to life sciences research. Each year the award will reward the exceptional achievements of one woman working in the life sciences in Europe. The winner will be honored at the annual FEBS Congress, where she will receive an award of EUR 10,000 and present a special plenary lecture. The first award will be made at the 2008 FEBS Congress in Athens, Greece.

Eisai Chooses Genedata Platform
Genedata announced an agreement with the Eisai Research Institute (ERI) for the company's Genedata Expressionist computational platform for biomarker discovery that integrates transcriptomics, proteomics, and metabolomics data within a single software system. "We are pleased to help Eisai Research Institute meet its bio-IT infrastructure needs for biomarker validation," said Jens Hoefkens of Genedata.

Lipomics and Joslin to Collaborate
Lipomics Technologies and Joslin Diabetes will initially tackle two research programs as part of a new collaboration. The first is a study on insulin-resistant patients with a family history of Type 2 diabetes to identify predictive markers of disease that can be translated into blood-based diagnostics. The second study hopes to clarify the effects of gastric bypass surgery on insulin sensitivity. Both programs originate from the laboratories of Mary Elizabeth Patti and Allison Goldfine at Harvard Medical School and Joslin. Lipomics will retain certain rights to develop diagnostic applications based on data emerging from these studies.

CombinatoRx Issues 2008 Guidance
CombinatoRx spelled out its goals and guidance for 2008 last month, and CEO Alex Borisy called it a "pivotal year" for the company with clinical data expected from CRx-102, 191, 197 and 401. CombinatoRx hopes to finish 2008 with revenue of $15-20 million, a net loss of $49-$55 million, and have cash/cash equivalents of $58-$64 million.

U.S. Army Extends MetaCore License
The U.S. Army has extended its license of MetaCore from pathway tool and database provider GeneGo. The US Army Center for Environmental Health Research will use MetaCore in its
Biomarker Discovery Program to identify novel biomarkers for exposure to toxic industrial chemicals and materials (TICs/TIMs) or as result of military activity.

Dancer Joins Cellzome
Cellzome appointed Dr. Jane Dancer as VP business development. Dancer had been in business development at MedImmune, where she was responsible for negotiating in- and out-licensing activity in relation to CAT's core technology and patents.

New Allergy/Asthma Enrollment Tool
KMR Group reports adding another set of Allergy/Asthma enrollment models to its services offering. KMR's Enrollment Forecasting tool is a predictive statistical model that simulates enrollment randomization in a given region and provides users with enrollment duration and site volume forecasts. The forecasts are based on thousands of clinical trial data, which is collected at the patient visit level. Other disease area models available on-line include: arthritis; cancers: advanced cancer, breast cancer, hematologic cancer, lung cancer, tumors; diabetes; neurodegenerative; viral: hepatitis and HIV.

BGM License Biomarker from CARIM 
BG Medicine reports it has obtained rights from ACS Biomarker to develop and commercialize a novel clinical diagnostic test for acute atherothrombosis based on a biomarker discovered by the Cardiovascular Research Institute Maastricht (CARIM). The test that BG Medicine plans to develop intends to use the biomarker to identify plaque rupture in patients early, for instance, when the blockage is temporary or not complete and has not yet caused the common signs and symptoms of heart attack or stroke. Under the terms of the agreement, ACS Biomarker granted BGM exclusive, worldwide commercial rights in exchange for milestone payments, royalties based on net sales, and sublicensing income of any products commercialized under the license. ACS was formed to commercialize biomarkers discovered by CARIM.

Who Says Black Boxes Are Bad?
An MIT team has used an engineering approach to show that complex biological systems can be studied with simple models developed by measuring what goes into and out of the system. Such an approach can give researchers an alternative way to look at the inner workings of a complicated biological system -- such as a pathway in a cell -- and allow them to study systems in their natural state.

The MIT researchers focused on a pathway in yeast that controls cells' response to a specific change in the environment. The resulting model is "the simplest model you can ever reduce these systems to," said Alexander van Oudenaarden, W.M. Keck Career Development Professor in Biomedical Engineering and Associate Professor of Physics and senior author of a paper describing the work in the Jan. 25 issue of Science.

A complex system can be treated as a "black box," where you don't know what's happening inside but can figure it out by analyzing the system's response to periodic inputs. This approach is widely used in the engineering disciplines but has rarely been applied to analyze biological pathways. The technique is very general and could be used to study any cellular pathway with measurable inputs and outputs, according to van Oudenaarden. Read full MIT article.



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:

Intrexon Corporation - Software Developer
The software developer will work in a close-knit team to build, develop and deploy advanced bioinformatics systems in concurrence with advancements in our gene-based technologies.  For a full description and application, please visit

GNS Biotech - Software Engineer, User Interfaces and Visualization
The successful candidate will work closely with the internal applications team and external customers to design and develop novel visualization approaches for ensembles of biological networks and to integrate GNS solutions with existing visualization tools.  The candidate must be capable of producing highly professional and interactive interfaces quickly and efficiently and will be familiar with a make of interface technologies including both web-based interfaces and stand-alone applications.  Must work fluidly with a fast moving, interdisciplinary team, have excellent communication skills and a passion for learning new science. For more information please visit

GNS Biotech - Software Engineer, Platform Development
The successful candidate will work closely with the algorithm development team to add newly developed algorithms into the production platform and the biological applications team to define and implement new functional requirements for the platform.  The candidate must be comfortable performing development on all aspects of the system, including the algorithms, data management and modeling, programmatic/scripting APIs, and user interface, as well as implementing automated tests for any of these components.  Major upcoming goals will be the optimization of algorithms to scale to larger computational problems and the development of infrastructure required for the application of the platform to different problem areas within biology.  The candidate will be responsible for design of new components and maintenance of existing platform code.  Must work fluidly with a fast moving, interdisciplinary team, have excellent communication skills and a passion for learning new science.  For more information please visit

GNS Biotech - Computational Scientist, Discovery Biology
The successful candidate will reverse engineer models from large coherent data sets.  In addition, the candidate will complete genome-wide association analysis of disease and drug-response and develop methods to deal with population genetic structure, pedigrees, missing data and computational scaling.  The candidate will be comfortable handing millions of marker and molecular phenotype data points using database management systems and statistical scripting, and will show familiarity with data issues regarding major genotyping platforms and external database resources.  Must work fluidly with a fast moving, interdisciplinary team, have excellent communication skills and a passion for learning new science.  For more information please visit

GNS Biotech - Computational Scientist, Biological Applications Candidates must have a combination of experience in the following areas: bioinformatics, microarray data analysis, algorithm development, statistics, machine learning, and network inference or reverse engineering methods.  Successful candidates will have a PhD (or be equivalently qualified) in Physics, Applied Mathematics, Computational Biology, Operations Research, or Engineering or have similar training thereof in the computational and biological sciences and 3+ years experience in the field.  Must work fluidly with a fast moving, interdisciplinary team, have excellent communication skills and a passion for learning new science.   For more information please visit

Software Engineer, Bioinformatician-  - ISB - Job #07-052
The Institute for Systems Biology's (ISB)
 Computational Core seeks qualified candidates to join its growing bioinformatics team.  For a full description and application instructions, please visit  ISB is an M/F/D/EOE. 

Bio-Informatics Scientist -Van Andel Institute - 
 opening at Van Andel Institute in Grand Rapids, Michigan.  Position supports collaborators using XB Bio-Integration Suite Software.  Qualified candidates will have Ph.D. in molecular biology or related discipline.  Two years post-doctoral training and experience in bioinformatics analysis of high throughput biological datasets.


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



GOT Summit: Getting Optimized Tools for Diagnostics May 19-21, 2008, Boston, MA CHI's 4th annual Summit offers the unique opportunity to learn about the newest developments and emerging technologies in genomics and proteomics for diagnostic applications.  A variety of interests are being covered such as: DNA and RNA microarrays as well as protein / tissue arrays; Genomics and proteomic sample preparation for further downstream processing and applications; Protein sample handling and further proteomic tools needed for diagnostics such as Mass spec, Lab on a Chip and biomarker handling. The four individual conferences of this summit provide well rounded information all the way from the sample collection to the sample handling to diagnostic tools from bench to bedside. Learn more and register at 


May 14-15, 2008 - The Post-Approval Summit at Harvard Focuses on strategies and best practices for demonstrating and improving the safety, effectiveness, value, and quality of healthcare products and services. Highlights will include: The Future of Safety Surveillance; Risk Minimization and RiskMAPs; Patient Registries, Real-World Data, and Decision-Making; Global Trends in Regulation and Reimbursement; Practical Issues and Solutions in Post-Approval for Drugs and Devices.

The 1st Symposium on Protein Tomography, May 1,2008,Boston,MA
Research and development of bio-therapeutics are hampered by inconclusive evidence of how a drug operates on a target. Present-day approaches fall short of proving the mechanism of action at the molecular level.  This problem is solved by Sidec research and Protein TomographyTM, which together provide exploratory insight for antibody development projects.  Sidec provides their partners with exclusive biological information by visualizing and interpreting real drug-target interaction events in situ and in vitro.  Sidec Research Collaborations enable our partners to:  Prioritize the most promising antibodies.  Locate the antibody-binding epitope.  Protect IP with evidence on the mechanism of action.  Expedite the drug approval process.  Promote therapeutic products to licensees.  To register for the Sidec Symposium please click here 

Med-e-Tel, The International Educational and Networking Forum
Telemedicine and Health ICT, offers opportunities to meet and network with qualified buyers, specialists, users, healthcare providers, industry representatives, researchers and policy makers from 50 countries around the world.  The event provides hands-on experience and an opportunity to discover and evaluate new products, systems and technologies and to hear about the latest ehealth/telemedicine news and trends. Med-e-Tel features an extensive educational and conference program with more than 150 presentations and workshops on a wide variety of telemedicine and ehealth topics. Med-e-Tel 2008 is scheduled for 16-18 April in Luxembourg.

TEPR 2008 - May 17-21, 2008
Mark your calendars for the premier EMR event of the year!  The 24th Annual TEPR Conference (Towards the Electronic Patient Record) will be held in sunny Ft. Lauderdale on May 17-21 of 2008.  Sponsored by Medical Records Institute, TEPR is an international conference which attracts over 3,500 decision makers interested in keeping up-to-date on all the latest EHR developments. With 22 parallel sessions each day and hundreds of industry exhibitors TEPR is widely recognized as the best annual educational conference and exhibition for health IT professionals and all others journeying Towards the Electronic Patient Record. With hundreds of vendor exhibits, world renowned speakers, and presentations by industry experts, this is an HIT event you don't want to miss!  For more information or to register,

Laboratory Informatics,
March 25-April 3, 2008 San Francisco CA.
IQPC's 3rd Laboratory Informatics conference is timed to influence developments in a rapidly advancing field by bringing together the major users and providers in the broad field of laboratory informatics. The conference is targeted at decision makers, policy strategists, problem solvers, advisors, researchers and consultants in the fields of chemical and laboratory informatics.
 click here for more information.

Lean Six Sigma for Pharmaceutical, Biotech, and Medical Device Excellence
February 25-27, 2008, Philadelphia, PA.  At the 5th Lean Six Sigma for Pharmaceutical, Biotech and Medical Device Excellence we will bring you case studies that tackle the problems you are encountering, provide you with real-world solutions to your problems and introduce you to industry peers who have been able to overcome many of the challenges that Lean Six Sigma presents. 
 Click here for more details

Best Practices Awards Program - April 29, 2008
Bio-IT World announces its 2008 Best Practices Awards Program and calls for entries. Established in 2003, this prestigious award program recognizes the innovative utilization of technology and business strategies to accelerate drug and clinical development and ultimately improve human health.
 Click here for complete details and submit your entry today!

Gain a competitive edge by taking a short course designed for industry application.  Spend 2-6 days at the MIT Professional Institute this summer learning about Controlled Release, Bioprocessing, Downstream Processing, Fermentation, Nanomaterials, FDA Regulatory Considerations, Data Modeling, Network Coding, Multicore Programming, Renewable Energy, or any of our other programs in Nano & Micro Technology, Lean Thinking, Supply Chain, Leadership and more. Over 40+ courses to choose from. Visit our website to register and view course descriptions.

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

 Email to a Friend


Bio-IT World's Sixth Annual Conference & Expo - April 28-30, 2008, in Boston.

Save up to $200 if you register by March 14.

Learn more and register.

CoSBi Course

The Microsoft Research - University of Trento Centre for Computational and Systems Biology (CoSBi) organizes a course for PhD students, advanced master students, early stage postdocs and interested junior researchers on methods and recent results on different aspects of computational and systems biology. Students with both experimental and computational/mathematical background are encouraged to apply.

Date: 10-14 March, 2008
Place: CoSBi, Trento, Italy

Applications accepted here with poster abstracts.


NuGenesis SDMS: Improving Data Accessiblity and Intellectual Property Managment 

Global pharmaceutical company improves the accessibility and intellectual property management
of drug candidate data with Waters® NuGenesis® SDMS software. Download the case study.
Download Now!

Absolute Software
A Layered Approach to Computer Security for Healthcare Organizations

With the widespread adoption of electronic health records and laptop computers, healthcare organizations face increased risk of data breaches. The loss of a computer compromises patient privacy, and exposes organizations to damaging publicity and HIPAA compliance challenges. This paper outlines a multilayered approach to computer security, complementing encryption with theft recovery and remote data delete capabilities to ensure the highest standard of protection. Download Now!

Master Control
How Effective Document Management Can Help Accelerate Time to Market

How Effective Document Management Can Help Accelerate Time to Market In the drug development process, time is indeed money. So it only makes sense to try to reduce delays in every phase of the process and speed up time to market. But how and where do you begin to save time? This white paper suggests that you start with the most basic activity-document management. This white paper discusses how effective document management can accelerate time to market  Click here to download whitepaper

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


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

Life Science Webcasts

Bio-IT World proudly introduces Life Science Webcasts -- a series of informal conversations with leading researchers and executives in the bio-IT and biopharma arena. This week, Dr. Jerald Schindler (VP, late stage clinical development statistics, Merck) discusses e-clinical research with Bio-IT World's Kevin Davies.

View the Webcast Now


View all SBNL archives.

Bio-IT World SB Links

Pathway Pioneers

Marvelous Models of Biological Systems

Pharsight Lands CRADA to Assist FDA with Modeling Initiative

Harvard Researchers Discuss Systems Biology

FDA Mulls Drug/Disease Model Library

Welcome MIRIAM: Researchers Propose Modeling Standard

Cambridge Healthtech InstitutePublished by Cambridge Healthtech Media Group, division of CHI, Copyright © 2008; All rights reserved. Systems Biology may not be reproduced, electronically or in print, by any means, mechanical or electronic, in whole or in part, without written permission of Cambridge Healthtech Media Group, 250 First Ave., Suite 300, Needham, MA, 02494. 
For reprints and/or copyright permission, please contact The YGS Group, 1808 Colonial Village Lane, Lancaster, PA 17601.  Phone: 717-399-1900, ext. 110. Email: