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


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David de Graaf Leaves Pfizer for Boehringer-Ingelheim 
DREAM3 Challenges Have Been Posted 
Entelos Issues Update, Wins Patent, Makes Perpetual Friend 
Make Your Data Sing -- Literally 
IO Informatics Puts Semantic Web Ideas to Work
Briefs from the Systems Biology Community 

DREAM3 Challenges Have Been Posted

Plans are already afoot for DREAM3 which will be held in conjunction with 5th Annual RECOM Satellite on Regulatory Genomics and the 4th Annual RECOM Satellite on System Biology next October 29-Nov 2. The meeting is jointly organized by the Broad Institute of MIT and Harvard, and the MIT Computer Science and Artificial Intelligence Lab (CSAIL).

The DREAM -- Dialogue for Reverse Engineering Assessments and Methods -- project is intended to held advance methods for inferring true biological networks from experimental data. DREAM3 is a competition in which scientists are invited to use their favorite methods to solve blinded data sets. DREAM2 was the first such exercise, and the results indicated we still have far to go on the path to accurate network predictions. For more, read Making DREAM(s) Come True Isn’t Easy.

Last week, co-organizers Gustavo Stolovitzky (IBM) and Andrew Califano (Columbia) announced all the challenges for this year’s exercise were posted and available for downloading. The text of their letter follows:

“We would like to alert you that the last challenge (Challenge 1) that completes the series of 4 challenges for DREAM3 has just been posted on our website. Please take a look at the challenge description. In this challenge we are asking the predictors to infer some information on the molecular species that participate in a signaling cascade from real flow cytometry data.

To access the other data sets and descriptions of the challenges, please go to this link. The best performers in these challenges will be invited to present in the joint RECOMB Systems Biology/Regulatory Genomics/DREAM3 conference.

To learn more about the DREAM3 conference, please go to this link. To learn more about the DREAM project, please go here."

I like the description offered by the co-organizers: “DREAM3 is part of a project we call the DREAM (Dialogue for Reverse Engineering Assessments and Methods) project. Its main objective is to catalyze the interaction between experiment and theory in the area of cellular network inference. The fundamental question for DREAM is simple: How can researchers assess how well they are describing the networks of interacting molecules that underlie biological systems, and how well can they predict the results of a biological experiment? The answer is not so simple. Researchers have used a variety of algorithms to deduce the structure of very different biological and artificial networks, and evaluated their success using various metrics. What is still needed, and what DREAM aims to achieve, is a fair comparison of the strengths and weaknesses of the methods and a clear sense of the reliability of the network models they produce.”


Entelos Issues Update, Wins Patent, Makes Perpetual Friend

“Trading has been in line with management expectations. The Company has good contract visibility and has approximately 70% of its 2008 annual revenue expectation under contract as at 30 June 2008. Cash, investments, and accounts receivable totaled $8.5 million as at 30 June 2008 versus $5.7 million at the end of the same period one year ago,” reported Entelos in a market update delivered ahead of its pre-close period for the six-month period ended June 30, 2008

The company also reported a new multi-million dollar research contract focused on cardiovascular risk reduction, joined a three-year consortium funded by Pfizer to find new targets in diabetes and obesity, and entered into an agreement with Eli Lilly to conduct in silico research in diabetes with the Entelos Metabolism PhysioLab.

Lilly also exercised its option to purchase a perpetual license to Entelos’ proprietary DrugMatrix database, the “world’s largest” reference database linking gene expression profiles of over 630 drugs to results from traditional preclinical pharmacology, safety, and toxicity tests.

Separately, Entelos said it was granted a U.S. Patent No. 7,396,645, for “Cholestasis Signature.” This technology helps researchers to screen novel compounds more rapidly and efficiently during preclinical studies for cholestasis, a specific type of drug-induced liver damage.

“We are pleased to add this new patent to our growing portfolio of patents that strengthen our leadership position in both disease simulation and predictive technologies focused on safety and toxicity testing,” stated James Karis, president and CEO of Entelos. “… In addition, this patent complements Entelos’ ongoing effort with the FDA to build a model of drug-induced liver injury to identify patients at risk for developing rare side effects.”


Make Your Data Sing--Literally

Human hearing is wonderfully discriminating. Most of us effortlessly notice when a musical instrument drifts out of tune or a piece of music breaks out of harmony. The ‘bad’ notes stick out. What’s more, the simple tones we hear are actually many overtones blended together – in this sense music acts as a kind of natural integrator of complex data.

Gil Alterovitz, a research fellow at Harvard/MIT Division of Health Science and Technology (in Children's Hospital Informatics Program) and a research affiliate, MIT Computer Science and Artificial Intelligence Laboratory, has been pioneering efforts to turn data – gene expression levels, for example – into musical applications that could be used in biomedical research, diagnostics, and for an endless variety of monitoring systems. To a significant extent the secret sauce is made of clever algorithms for data compression and transduction into notes. More.


IO Informatics Puts Semantic Web Ideas to Work

The founders of IO Informatics adopted semantic web ideas early and incorporated them into a scientific data integration and management platform: Sentient Suit. More.


Briefs from the Systems Biology Community

  • Ingenuity/CHDI work on Huntington’s disease tool 
  • Genomatix releases Genome Analyzer 
  • Physiomics expands support of Lilly's oncology programs 
  • ISMB kicks off in Toronto 
  • Finnish Red Cross licenses Ariadne’s Pathway Studio 
  • Linguamatics joins BioIT Alliance 
  • Genego works with Yale Microarray Center 
  • Compugen reports in vivo study results 
  • Genedata inks deal with Axxam 
  • Pharsight added to Russell Microcap. . .more. 


Friedrich Miescher Institute for Biomedical Research - Part of the Novartis Research Foundation
Basel, Switzerland is looking for a Head of IT Systems & Infrastructure. You will manage a cutting-edge core server and network infrastructure, comprising Linux and Solaris, as well as a robust Windows and Macintosh environment. We look forward to receiving your application: click for more information

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:

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-15 - 17 September, 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

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David de Graaf Leaves Pfizer for Boehringer-Ingelheim

Roughly three years after becoming Pfizer’s first director of systems biology, David de Graaf is leaving to become the VP of Biotherapeutics and Integrative Biology at Boehringer-Ingelheim. It’s not immediately clear what, if anything, de Graaf’s departure means about Pfizer’s enthusiasm for systems biology. One insider suggested not reading too much into the move. It does seem like a promotion for de Graaf.

Pfizer recently assembled a three-year, US$14-million systems-biology consortium to improve the understanding of diabetes and obesity. The consortium is called the Insulin Resistance Pathways Project (IRP Project). There have been reports that Pfizer systems biology group, currently based at Pfizer’s Research Technology Center, Cambridge, MA, would focus more on diabetes and metabolic disease plus house an RNAi group.

Carolyn Cho had already been promoted to director of the Systems Biology Target Group. She said in an email, “Yes, it’s a real loss to us, but a great move for David. He’s built quite a group here, and helped craft our role as part of Pfizer’s new Biotherapeutics and Bioinnovation Center (BBC).  We’re soldiering on, here, with our new BBC mission and not anticipating any major changes.”

Many biopharmas have struggled with how best to adopt and use systems biology (See System Biology’s Awkward Adolescence) and with managing their technology centers generally. Indeed, the RTC’s role has been changing and is now coming more directly under the leadership of Corey Goodman who is building the BBC organization on the West Coast.

Last year, Lilly changed the name of its Singapore Lilly Systems Biology Center to Lilly Singapore Centre for Drug Discovery. It’s interesting to note the system biology label has again become fashionable among many biotechs. Conversely, pharma seems to be shying away from the label but actually adopting many of its approaches. We may be seeing the maturing of SB approaches as they become more accepted and incorporated directly into therapeutic groups rather than acting as quasi service centers.

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

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 

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...


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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.
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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.
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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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