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


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Wednesday, August 13, 2008 | | Archives | Advertising | Your Account | CHI Conferences | Subscribe |
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We invite your comments and feedback for this edition of Systems Biology.
John Russell
Executive Editor

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Systems Biology Becomes Predictive Biomedicine 
Entelos’ Bold Initiative:  
Briefs from the Systems Biology Community 
ISMB 2008
SBNL Highlights Reel

Predictive Biomedicine: Informatics Tools & Strategies Driving Decisions
By John Russell

In September, Bio-IT World’s monthly Systems Biology newsletter will become Predictive Biomedicine, a somewhat broadened newsletter with an increased, biweekly frequency, and a continued focus on the leading edge of computational biology.

John RussellWe understand that ‘predictive’ is a big word, and that biomedical research isn’t there yet, but ‘predictiveness’ is undeniably the direction in which the industry must move. Today, sophisticated informatics and computational tools increasingly enable researchers to understand experimental results and to make ‘reasonable predictions’ about everything from mechanism of action, target selection, useful biomarkers, toxicity, and clinical trial outcomes.

Predictive Biomedicine will cover the development and use of informatics and computational tools to manage, present, and interpret experimental data as well as those used in modeling and bio-simulation. Companies and thought-leaders; products and technologies; relevant research programs and their results will be covered. From data management challenges to systems biology initiatives, Predictive Biomedicine will report on industry’s efforts to reduce dependence on trial and error and to adopt more data-driven predictive methods to drive drug discovery and development and even healthcare delivery.

As a subscriber to Systems Biology you will automatically receive Predictive Biomedicine, and we hope you find its content useful and interesting; however you may also easily opt out when you receive the first (or any) issue. Write to me – -- with your suggestions for coverage topics or leads to important stories. Predictive Biomedicine also welcomes guest commentaries and letters and short papers so send your ideas for those as well. We’re especially interested in hearing of projects in which the informatics or computational tools drove key decisions.


Entelos' Bold Initiative:
By John Russell

Biosimulation specialist Entelos has launched an intriguing website – – that suggests the company is testing the waters for a major push into the consumer world of personalized medicine and health. This is a bold move.

Entelos is best known for its portfolio of PhysioLab computational disease models used in drug R&D. A year ago, the company acquired Iconix and its database of gene expression signatures. Now, the company seems to be leveraging its various technologies to create a ‘platform’ that would be able to take a variety of inputs – various biomarkers, SNP and genotype data, lifestyle attributes - from individual patients and produce a personalized risk assessment and, presumably, lifestyle and medication guidance.

The theme repeated throughout the site to visitors is: Know. Act. Achieve.  Read more.


Briefs from the Systems Biology Community

  • Ingenuity launches analysis services business 
  • Windber to collaborate with GenoLogics 
  • Harvard debuts “little b” language 
  • EU law may spur more pediatric simulations 
  • Ariadne inks Bayer CropScience deal 
  • Galapagos deposits data with EMBL
  • Metabolon works with UTHC diabetes researcher 
  • Cellumen collaborates with NCTR
  • GSK extends InforSense agreement 
  • Tissue of origin test gets FDA nod 
  • CRI, Pharsight strike an alliance . . . more 

SBNL Highlights Reel

During the past two and a half years, Systems Biology newsletter has covered many aspects of systems biology. On the eve of SBNL’s morphing into Predictive Biomedicine, it is perhaps worth singling out a few past articles that capture systems biology’s aspiration, challenge, and enthusiasm.

P4 Medicine: Lee Hood's Hopeful Vision of the Future

Exclusive Interview with David de Graaf, Pfizer's First Director of Systems Biology

GNS: Building a "SNPs-to-Outcomes" Engine

Entelos’ First Year as a Public Company

Systems Biology’s Awkward Adolescence



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:

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:

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

DIA 2nd Annual Clinical Forum: Data Driven Drug Development Decisions - October 20-23, 2008 | Ljubljana, Slovenia

Barnett Educational Services, 
2008 Schedule

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

 Email to a Friend
ISMB 2008
Sampling the Delights of
ISMB 2008

The 16th annual Intelligent Systems for Molecular Biology (ISMB) conference in Toronto features a “massively parallel” track structure to provide more opportunities for delegates. Read more…

Enabling Translational
 Research Informatics
Learn about the challenges facing life sciences research labs to manage their translational research data:
The trends for organizations to adopt informatics solutions for translational research.
The unique requirements with managing complex data and workflow. What labs should consider when reviewing informatics solutions for translational research.
Which life sciences research organizations are successfully adopting an informatics solution.Download Now

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

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 Expo
Video Highlights

Personalized Genetics: Advancements and Driving Change
Linda Avey, co-founder of 23andMe, delivers her keynote at the 2008 Bio-IT World Conference & Expo in Boston, April 30, 2008.
View the webcast.

The Future of Personal Genomics
A distinguished panel of personal genomics experts discuss the future of personal genomics at the 2008 Bio-IT World Conference & Expo in Boston, April 30, 2008.  They include Dietrich Stephan (co-founder, Navigenics); George Church (Harvard Medical School); Jeff Drazen (editor-in-chief, New England Journal Medicine); Fred Ledley (Bentley College); John Halamka (CIO, Harvard Medical School); and Linda Avey (23andMe). Bio-IT World Editor-in-Chief Kevin Davies moderates the discussion.
View the webcast.


See all past issues of
Systems Biology newsletter

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. 
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