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


A Bio-IT World publication
Wednesday, January 16, 2008 | | Archives | Advertising | Your Account | CHI Conferences | Subscribe |
Sales Contacts
For advertising information contact: 

Alan El Faye
VP, Advertising Sales - CA, Western US,Midwest, South Eastern US, Europe, 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

India Is Connexios' Competitive Advantage 
Toward a Predictive Model for a Cell
SB Agenda 2008: Survey Says... 
 Short News and Analysis
India Is Connexios' Competitive Advantage
By John Russell

Suri VenkatachalamAll biotech start-ups wrestle with raising capital, proving their science, and navigating unforgiving markets. Suri Venkatachalam, CEO and managing director of Bangalore-based Connexios, believes that being in India is a competitive edge that will enable Connexios to survive where other worthy companies might not, and to become one of the first successful systems biology-based drug companies.

Lower cost is clearly the biggest advantage. He estimates Connexios' costs are one sixth to one eighth of what they would be in the U.S. Given that his young company has already raised roughly $20 million and that its primary investor is patient, India's lower cost of operation has allowed Connexios to grow headcount to 120, to substantially expand the scope of its activities, and to still enjoy the luxury of a long runway to success.

"Even in the context of Indian costs, this is a very reasonable amount of money. We've spent maybe $5 or $6 million to build this up. So, we have a reasonable amount of money to carry a few programs into the clinic, a couple of programs at least," he says.

Add to this financial strength India's glut of technical talent, its growing life science ecosystem of companies, ready access to clinical trial participants, and a national hunger for equal footing on the world stage, and you understand why Venkatachalam likes his chances for success. Read more.


Toward a Predictive Model for a Cell
By John Russell

Nitin BaligaLast month, a really nice piece of systems biology work was published in the journal Cell in which researchers developed a predictive model for a free cell, in this case the Archea organism, Halobacterium salinarum NRC-1. What's more, the authors suggest that even though their model is for a relatively simply organism (~2400 genes), the approach used to build it can probably be used to tackle complex organisms.

The authors of the paper, "Environmental and Gene Regulatory Influence Network (EGRIN): A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell," say they used a data-driven discovery approach to determine regulatory and functional interrelationships among roughly 80 percent of NRC-1's genes. Read more.

Short News and Analysis

NanoString Wins Second Order
NanoString Technologies landed a second Early-Access Agreement for its nCounter Analysis System, this one with the Genome Sequencing Center at the Washington University School of Medicine. This is the second deal in as many months for the young company. The nCounter Analysis System uses a novel digital technology that enables direct multiplexed measurement of gene expression and offers high levels of sensitivity and precision, including detection of fractional fold change differences, a feature unique to this platform. The technology uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction. CalTech ordered the first one in December.

The nCounter system will be used first for a large scale diabetes study by Dr. James Cheverud to validate the expression of over 50 genes across 15 tissues in over 900 samples. "We chose the nCounter Analysis system because of the high quality of data generated from the system and the fact that we couldn't do this study with competing methods," said Dr. James Cheverud "If we wanted to perform this study with QPCR it would have been over 55, 000 individual reactions. We can complete the entire study on the nCounter Analysis System in about 900 reactions and in a fraction of the time."

Compugen Lands Roche RA Deal
Compugen signed a collaborative discovery and license agreement with Roche covering the identification and validation of genetic variations for the prediction of response to drugs used for the treatment of rheumatoid arthritis. Compugen will use its proprietary GeneVa platform to analyze DNA samples and clinical data provided by Roche to identify and validate non-SNP genetic variations that could serve as biomarkers for selected drugs for treatment of RA.

The GeneVa platform incorporates an in silico database of approximately 200,000 predicted non-SNP genetic variations, including insertions, deletions and copy-number variations in the human genome. "This agreement is both the first based on our GeneVa platform and also our first collaboration with Roche," stated Alex Kotzer, Compugen CEO in a release. "We believe that our GeneVa platform will prove to be a key addition to ongoing worldwide efforts towards more personalized medicine and tools for the accurate assessment of individual predisposition to various diseases and other medical conditions, thereby allowing earlier and more appropriate intervention."

BGM IPO Delayed?
 BG Medicine was unable to excite investors and has delayed its IPO plans according to a report in The Boston Globe. In its prospectus BGM laid out aggressive plans to develop a portfolio of diagnostic biomarkers. (See BG Medicine to Take the IPO Plunge). BGM had reduced the proposed price of its offering from $14-$16 down to $8-$10 but still ended up delaying the IPO.

Morphotek signs research agreement with Ludwig Institute
Morphotek Inc. announced the signing of a collaborative research agreement with the Ludwig Institute for Cancer Research (LICR).  The multi-year agreement will fund research at LICR to develop model systems that can validate the role of novel pathways for human disease and conduct preclinical proof-of-concept studies to demonstrate the feasibility of employing antibodies to block these disease pathways, potentially leading to the development of novel therapies. Morphotek and LICR have collaborated for several years on programs that have led to clinical candidates.  The precursor antibody to Morphotek's lead therapeutic antibody, MORAb-003,  currently in Phase II trials for ovarian cancer, was originally discovered by LICR researchers and optimized using Morphotek's Morphodoma  technology.

FDA's NME Approvals Down...Again
The FDA approved just 19 novel drugs last year, the lowest number since 1983 according to reports in
 The Wall Street Journal and Seventeen were NMEs and two were biotech drugs. Novartis and GlaxoSmithKline reportedly led the industry with two approvals a piece. There's really not much more to say.

Industry complains the FDA has become tougher. FDA disagrees. The more prosaic truth seems to be that given today's standards for safety and efficacy and the state of our knowledge, drug discovery and development remains inherently messy and unpredictable. Even a doubling in the approvals rate, though welcome, would hardly constitute a game-changing leap. We're just not there yet.

UCBerkeley Expands Use of Metacore
GeneGo reports UC Berkeley will expand its use of GeneGo's MetaCore/MetaDrug Discovery Platform in their Computational Toxicology course, a required component for Molecular Toxicology majors, and in undergrad honors research programs. "When we designed our Computational Toxicology course a few years ago we anticipated a shift in the future toward 'systems biology' that is, looking at the complex interactions of metabolic, genetic, protein, and cellular elements with the goal of modeling entire systems in relation to chemical stresses," said Dale Johnson, adjunct professor, who designed and teaches the Computational Toxicology course.

"The complexity of these chemical/biological interactions resulting from environmental exposures, food sources, or pharmaceutical compounds, highlights our thinking that an overall systems approach will be necessary if relevant advances are to be made in applying computational solutions. We are extremely pleased to be able to utilize MetaCore/MetaDrug as the core part of our coursework."

Prtizter Renews Ingenuity Deal
Pritzker Neuropsychiatric Disorders Research Consortium (PNDRC) has renewed and expanded its licensing agreement for access to the Ingenuity Pathways Analysis (IPA) software application, assisting the PNDRC's efforts to understand neuropsychiatric disorders. Consortium members will utilize the newest release of IPA to illustrate significant differences in gene expression and to determine impact in neuronal pathways, circuits, and target systems.

The PNDRC focuses on the discovery of neurobiological and genetic causes of severe psychiatric disorders such as major depression, manic-depressive illness or bipolar disorder, and schizophrenia, with a concerted effort to identify novel targets for the treatment of these diseases. IPA is being used in the creation and analysis of customized pathways, which can then help correlate gene expression profiles to functions, diseases, pathways, and molecular mechanisms in order to better elucidate novel targets. PNDRC is comprised of scientific groups at the University of Michigan, Weill Medical College of Cornell University, Stanford, UC Irvine, and the UC Davis.

Progress for Physiomics
Physiomics, a U.K.-based modeling company, recently signed an MOU with the Institute of Life Science of Swansea University ('ILS') which among other things will provide Physiomics with access to "Blue C" one of the most powerful supercomputers dedicated to Life Science. Blue C is the result of a joint-effort by ILS, the Welsh Government and IBM. Collaborative research projects with ILS oncology groups are planned, and will focus on the effect of anticancer drugs. Physiomics will contribute modeling expertise and simulations expertise. Physiomics COO Christophe Chassagnole says pilot studies have already shown 'Blue C's potential shorten some tasks from many hours to "just a couple of minutes."

Separately, ValiRx, a cancer therapeutics company, announced completion of the first phase of its collaboration with Physiomics, begun last February. The effort combines Physiomics simulation technology with ValiRx's GeneICE technology to generate a cancer cell death model - the Apoptosis Model. This model, which ValiRx plans to patent, will be used to accelerate ValiRx's internal development as well as be available for licensing to third parties. ValiRX says the model helped it reach key decisions regarding which new cancer cells to target.

Entelos Adds Financing 
Entelos struck a debt financing agreement with Imperium Master Fund in which Imperium will provide $6.5 million in total cash loan proceeds to Entelos. The modeling and bio-simulation specialist says it intends to use $1.5 million of the proceeds to repay certain debt of Iconix Biosciences resulting from the acquisition by Entelos of Iconix, and to use $5 million as long-term working capital.

Nycomed Expands Genedata Deal
Genedata announced a multi-year contract extension for the use of the Genedata Screener lead discovery product suite with Nycomed, a global manufacturer of pharmaceuticals. Genedata will create a global scientific computing infrastructure for the lead discovery and drug research programs at Nycomed sites worldwide.
Genedata Screener will enable the interdisciplinary teams at all sites to rapidly capture, visualize, analyze and manage large volumes of assay data. Dr. Werner Stürmer, Head of HTS at Nycomed, said in a release, "Genedata Screener not only improves the efficiency and quality of our screening campaigns, but also has a catalytic impact on our global information network - increasing the number of users and promoting accurate and timely decisions across departments and countries. "   

Oxford Announces Systems Biology Scholarships
The U.K.'s University of Oxford is accepting applications for up to 24 "studentships" within the Systems Biology (Sysbio) Doctoral Training Centres. The four-year program consists of two terms of taught courses plus extended projects and laboratory rotations that will provide students with the necessary biological, experimental, and theoretical background before they choose to specialize by undertaking a substantive research project. The project is affiliated with the Oxford Centre for Integrative Systems Biology, and applicants selected to participate will conduct research in one of four main research areas covering chemosensory networks and whole organism behavior; signaling pathway modeling; molecules to cells; and integrative biology. Deadline for applying is Feb. 1, 2008. Full details of the programs and how to apply can be found on the
 University of Oxford website.




Van Andel Institute - Bio-Informatics Scientist
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.

Director of Strategic Business Management - SAIC-Frederick, Inc.
SAIC-Frederick, Inc. is seeking a leader to manage strategic business opportunities, initiatives, partnerships, alliances, and joint ventures associated with the Advanced Technology Partnerships Initiative (ATPI). The newly created ATPI seeks to accelerate delivery of effective therapeutic and diagnostic modalities to cancer patients using advanced technology platforms and public-private partnerships. Learn more at or or contact Mary L. Siegle at

 Director of Information Systems - SAIC-Frederick, Inc.
SAIC-Frederick, Inc. is seeking expert in all areas of information services, including security, disaster recovery, remote access, database administration, operations systems design, programming, and communication. Direct a staff of 40+ within the Advanced Biomedical Computing Center (ABCC) the National Cancer Institute's fully integrated supercomputing facility for biomedical research. Competitive salary/benefits package.  Learn more at or or contact Mary L. Siegle at . 

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



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, visit

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

The Association for Laboratory Automation (ALA) presents LabAutomation 2008, January 26-30, in Palm Springs, CA. LabAutomation2008, the world's largest conference and exhibition focused exclusively on the rapidly growing field of laboratory automation, brings together a diverse group of academicians, scientists, engineers, business leaders, post-docs and graduate students from around the globe. For more details clicks here

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!

MIT Advanced Study Program  - Register for Spring 2008
Put MIT to work for you. The MIT Advanced Study Program (ASP) is now accepting applications for the Spring 2008 term.  ASP provides full and part-time certificate programs to working professionals at any stage of their careers. The program includes a flexible curriculum of MIT courses designed around the goals of participants and their sponsors.  Visit our website to view participant profiles & comments, watch our program video, and find out if MIT is right for you.


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

 Email to a Friend
Letter from the Editor
SB Agenda 2008: Survey Says....
By John Russell

We're seeking guidance in defining a research report on the State of Systems Biology. To that end, Bio-IT World and its sister division, CHI Insight Pharma Reports, have drafted a brief online survey to capture readers' thoughts on what such a report should contain to be useful. The planning survey is deliberately quite short and its results will help inform the direction of the report and kind of research conducted during its preparation.    

As an added incentive, survey takers will be offered a 10 percent discount off the price of any report listed on the Insight Pharma website and a 15 percent discount off the price of the Systems Biology report when it publishes. To take the survey click here: Survey Link.

Producing the SB report is one major agenda item this year. Another is doing a substantial article on the multitude of efforts to better understand and predict liver toxicity issues. The range of technologies tackling this problem - in silico, cell-based, microarray, etc. - is truly expansive. The article is tentatively scheduled for late spring.

Nearer-term, we plan an in-depth look at Genstruct's evolution and strategy as well as a report on the DREAM2 conference. I welcome input on any of these projects or suggestions for others. Write to me at


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.

Streamlining the Chromatographic Method Validation Process
Chromatographic method validation is a critical step in the workflow of pharmaceutical, food safety, chemical, and environmental laboratories. It can adversely impact regulatory compliance, product development, and ultimately product release and availability. Empower 2 Method Validation Manager is a business critical software that reduces the time and costs required to perform chromatographic method validation by as much as 80%. This whitepaper discusses how.
Reduce time/cost to perform chromatographic method validation-Download Free whitepaper!

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


Bring On 2008!
Dec. 13, 2007

Sunlight and Systems Biology in Seattle
Nov. 14, 2007

Optimata Shifts Business Emphasis
Oct. 10, 2007

Systems Biology's Awkward Adolescence
Sept. 12, 2007

BG Medicine to Take IPO Plunge
August 15, 2007

P4 Medicine: Lee Hood's Hopeful Vision of the Future 
July 19, 2007

A Tour of the Systems Biology Landscape 
June 13, 2007

Entelos' First Year as a Public Company 
May 9, 2007

Lilly: Why Singapore Is Right for Systems Biology 
April 18, 2007

Towards a Cancer Interactome 
March 21, 2007

Entelos Strikes Deal with J&J
February 14, 2007

Burning Questions in SB; Executives Look Ahead; Trends
January 10, 2007

The Novartis Conjurer; Outlook 2007: SB Execs Survey; Trends
December 13, 2006

Systems Biology DREAM(s) Big
November 13, 2006

Pfizer SB Chief David de Graaf Looks Back and Ahead
October 18, 2006

SB in the Hot Seat; Regulomics Conference 
September 13, 2006

Pfizer's Progress, GNS Growth, and more
August 24, 2006

Conversation with Genstruct's Keith Elliston 
July 27, 2006

Sunrise for Systems Biology 
June 15, 2006

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 © 2007; 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: