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

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Commentary: 2008 Midpoint: SB Business Seems Stronger 
Briefs from the Systems Biology Community 

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Briefs from the Systems Biology Community

Merrimack Raises $60 Million
Merrimack Pharmaceuticals has raised $60 million in a Series F private equity financing. Proceeds from the financing will be used to advance Merrimack's proprietary pipeline of biologic therapies targeting autoimmune disease and cancer. The company's lead product, MM-093, is currently in a Phase 2 study in rheumatoid arthritis and a pilot study in patients with autoimmune uveitis. Results from the two studies are expected later this year. MM-121, the company's second product and the industry's first Network Biology derived therapeutic, is expected to enter Phase 1 trials later this year. The company is also advancing a set of innovative, antibody therapies targeting solid tumors through pre-clinical studies and plans to file an IND on its third product in early 2009. Read release.

GenoLogics Releases Proteus 4.0
GenoLogics announced the new release and general availability of Proteus 4.0, its lab and scientific data management system for proteomics. Proteus' new adaptive reporting framework is said to allow customers to integrate data from different sources and enhance their scientific data analysis. "One of the enhancements we are looking forward to using with Proteus 4.0 is the integration to ProteinPilot," says Bruce Stanley, scientific director of the Penn State Milton S. Hershey Medical Center's Proteomics and Mass Spectrometry Core. "The updated LabLink web interface will allow us to better share quantitative proteomic results with our researchers as we focus on collaborations in translational research." Separately, Genologics announced a partnership with GenVault Corporation for its biospecimen data management system, BioVault.

GeneGo Works on Cancer Pathway DB and Analysis Tools
GeneGo made three announcements recently. It reports that KineMed has licensed MetaCore for application to its ongoing multi-center Phase II prognostic study of chronic lymphocytic leukemia (CLL). KineMed's kinetic biomarker of CLL flux as a predictor of disease course is intended to stratify indolent (simmering) versus aggressive disease. "Building cancer-specific pathway analysis software and databases is a key focus area for GeneGo this year," says Julie Bryant, VP business development. Separately, GeneGo reported Merck has extended its global enterprise agreement. This agreement provides Merck with access to GeneGo's content through MetaBase which includes access to MetaCore and MetaDrug content and GeneGo's internal database of disease biomarkers.

The company also announced that it has been awarded a Phase I SBIR grant from the National Cancer Institute for development of a platform for functional data analysis in cancer. GeneGo will collaborate with investigators at Dana-Farber Cancer Institute, Boston, on the project. The system, MetaMiner (Oncology), will combine pathway and network analysis tools, act as an OMICS data repository, and have advanced statistical tools based on functional descriptors.

Ingenuity Signs Borhringer Deal, Releases IPA 6.3
Ingenuity Systems inked a four-year agreement with Boehringer Ingelheim for Ingenuity Pathway Analysis (IPA). The agreement provides global access for Boehringer Ingelheim research scientists to access to IPA. Separately, Ingenuity announced the release of IPA 6.3, the newest version of its pathway analysis and life sciences knowledge software. IPA now supports Affymetrix GeneChip Exon Arrays and several new animal and plant species. Currently, IPA supports a variety of different research platforms, including gene expression, proteomics, SNPs, genotyping, and RNAi. Now with the support of Affymetrix GeneChip Exon Arrays, researchers using this system can use IPA for further analysis and interpretation of the gene expression data. IPA will provide a rapid assessment of the signaling and metabolic pathways, molecular networks, and biological processes most significantly perturbed in the dataset being examined.

Pfizer Licenses Ariadne Tools
Ariadne announced that Pfizer purchased a multi-site license for Pathway Studio Enterprise. Pfizer is going to use it to assemble reference networks of biological interactions from internal and public data sources for interpretation of experimental results throughout its research facilities. Pathway Studio Enterprise includes functionality to import and analyze microarray and proteomics data, and includes the Ariadne ResNet database, a collection of interaction data retrieved by MedScan technology from PubMed and open-text journals.

Pfizer also purchased a copy of Prolexys Human Interaction Database, a proprietary high-confidence source of human protein interactions built by Prolexys using Y2H technology and repackaged for Pathway Studio. "Pathway Studio provides Pfizer researchers with easy access to publicly available scientific information, and a way to integrate our proprietary data along with third-party high-confidence data such as the Human Interaction Database from Prolexys. We can also integrate Pathway Studio with in-house tools to assemble targeted data sets for research in specific disease, biomarker, and drug related topics," said Giles Day, senior director, target and mechanism informatics, at Pfizer. Read release. 

Merck Serono to Work with BioSeek
BioSeek will collaborate with Merck Serono to assess potential drug candidates, says the company. BioSeek will apply its cell-based BioMAP systems to evaluate small-molecule compounds and proteins across multiple therapeutic areas in support of target differentiation, lead selection, and nomination of candidates for preclinical development at Merck Serono. Financial details were not disclosed. Read release.

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Compugen Announces 10 Novel Targets
Compugen says it has discovered more than 10 novel targets of antibody therapy for various types of solid and hematopoietic cancer. The newly identified targets were initially predicted and selected in silico utilizing the company's Monoclonal Antibody Therapeutic Targets Platform and subsequently were experimentally validated, reports Compugen. Further experimental validation of the therapeutic potential has been initiated for five of these targets. All of the new targets are membrane-bound molecules that have been shown to display differential RNA expression in various tumor vs. healthy samples. In addition, a number of them are splice variant molecules, the existence of which had initially been predicted by the Compugen's LEADS platform. This class of molecules would be difficult to find using traditional discovery methodologies.
partners." Read release. 

ISB, TGen and Hutchinson to Work on Luxembourg Project
Three biomedical science leaders from the U.S. have been tapped by the government of Luxembourg for a collaboration to establish a bioscience center of excellence in the heart of the European Union. The initiative will include formation of a centralized biobank/tissue repository, two major projects to further research in the field of molecular biology, and a project to demonstrate the effectiveness of new diagnostics tests for earlier detection and treatment of lung cancer.

U.S. organizations involved in the collaboration are: The Partnership for Personalized Medicine (PPM) led by Dr. Leland H. Hartwell, director and Nobel winner (physiology or medicine in 2001) and president of the Fred Hutchinson Cancer Research Center; The Institute for Systems Biology (ISB), also in Seattle, led by Dr. Leroy Hood, president of ISB and co-founder of Amgen; and Arizona's Translational Genomics Research Institute (TGen), led by Dr. Jeffrey Trent, president and scientific director of TGen and former scientific director at the National Human Genome Research Institute. Luxembourg is investing more than $200 million in the initiative. Read release. 

BioBase Joins InforSense Partner Network
BioBase, a provider of biological databases, applications and services, announced a partnership with InforSense which will offer mutual customers the ability to access BioBase Knowledge Library products, including Transfac, Transpath, and Proteome within the InforSense workflow analytics platform. "This partnership presents our shared customers with a very exciting opportunity. Through the InforSense platform , it will now be easier than ever to integrate high quality BioBase data content and tools into their heterogeneous and complex infrastructure, and thus add value to their daily scientific work," says Frank Schacherer, EVP, BioBase. Read full release. Separately, InforSense has announced the appointment of David Bennett as EVP of worldwide sales.

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Metabolon Adds Another Patent
Metabolon was awarded a patent which expands the domain of previously issued patents to include multiple disease states related to nervous systems disorders including amyotrophic lateral sclerosis (ALS), Alzheimer's disease, Parkinson's disease, Huntington's disease, depression, and schizophrenia. "Metabolon has assembled the most substantial IP portfolio in the metabolomics and small-molecule diagnostics industries," said John Ryals, chief executive at Metabolon. "We have strategically built an IP estate comprised of trademarks, copyrights and patents, including broad metabolomics methods, data analysis and biomarker patents, and focused product patents that protect critical points along our value chain." Read more. Separately, the company announced the availability of mView, a data-rich biochemical profiling service for scientists in academic and government institutions.

MIT Graduates First Class of Bio Engineering Majors
When Alice MacDonald arrived at MIT four years ago, the biological engineering major did not exist. This spring, MacDonald and 22 other adventuresome MIT students will become the institute's first graduates from the new biological engineering program.
MIT has had a Ph.D. program in biological engineering (BE) for 10 years, but the undergraduate degree program was approved just three years ago, making it the first new major course of study at MIT in 39 years. Read article.

Pfizer Obtains Good Results with Simcyp Simulator
Scientists at Pfizer Global Research and Development used the Simcyp Simulator to successfully predict the extent of drug-drug interactions for maraviroc, which is used in combination with other medications in the treatment of HIV. The results of the research by Hyland et al. will appear in British Journal of Clinical Pharmacology. The group used the Simcyp Simulator, together with in vitro data, to predict in vivo outcomes. The results of this 'virtual' study were then compared with observed clinical data. The simulations were found to be in good agreement with the clinical results. The paper is entitled 'Maraviroc: in vitro assessment of drug-drug interaction potential'. For a link to the abstract and full text options please click here.

GSK Licenses Oncomine Enterprise
Compendia Bioscience signed a two-year licensing agreement with GlaxoSmithKline for Oncomine Enterprise Edition, a value-added product extension Compendia's flagship product, Oncomine, which is a growing compendium of nearly 26,000 gene expression and DNA copy number profiles collected and curated from the literature and other public sources. These data are coupled with analysis functions and a web application for data mining and visualization. Oncomine Concepts Map, licensed to commercial users as part of the Oncomine Enterprise Edition, uses gene sets as a common language to compare and link disparate biological concepts, allowing researchers to discover and explore new biology based on signatures related to drugs and/or disease pathways.



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) -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 - Application Analyst
MSKCC Genomics Core seeks an Application Analyst to configure UNIX and Windows systems, maintain LIMS server and install analysis software. Requires a Master�s degree, UNIX experience, and knowledge of a language besides PERL beyond the beginning level. Email or #015563. EOE/AA

Memorial Sloan-Kettering Cancer Center - Bioinformatics Engineer MSKCC Bioinformatics Core in Manhattan seeks Bioinformatics Engineer. Design and develop bioinformatics
processing and analysis pipelines for traditional and next-gen sequence data. Consult with, train, and analyze data for researchers. Master's degree and 5 years experience in Bioinformatics software development, sequence assembly, SQL, Perl, Python. Email or #015415. EOE/AA

Memorial Sloan-Kettering Cancer Center - Linux Systems Administrator - MSKCC Bioinformatics Core in Manhattan seeks Linux Systems Administrator. Install, configure and update OS, databases, software. 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. Email or #015429. EOE/AA

Paradigm-Sales/Business Development � IT Solutions and Services
Paradigm ( is a global IT services and solutions provider. Paradigm has over 1000 employees and is the recipient INC. 500 and D&T Fast 50 consistently.  Paradigm is looking for SALES / BUSINESS DEVELOPMENT PEOPLE.  Experience: 2-3 years Direct sales experience in Software Solutions or Services including Application development or support and preferably selling to Pharmaceutical, CROs or Health care industries. Location:Columbia, MD,Contact:  Erin Lowman,, 410-872-1008 x 100

More Life Science Jobs ~ Add a Job Listing



Computing Short Courses at MIT - June / July - Cambridge, MA 

DIA 44th Annual Meeting, June 22-26, Boston,MA 

5th Annual Meeting on the NCI�s cancer Biomedical Informatics Grid�CaBIG�initiative (Annual Meeting)S -June 23-25, 2008, Washington,DC

2nd Label-Free Protein Array- Latest Advances in Analysis of Macromolecular Interactions,July 3-4th 2008 -Paris- France

Barnett Educational Services, 2008 Schedule

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

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2008 Midpoint: SB Business Seems Stronger
By John Russell

At the start of 2008 it looked like the speed bumps slowing the pharmaceutical industry would also hobble many systems biology (SB) technology providers. Instead, the stumbling (and downsizing) by major biopharma companies seems to be stirring a small boomlet for a few SB companies.

At least three SB companies -- Entelos, Genstruct, and BioSeek -- say their business is up. This is from conversations last week during or shortly after Cambridge Healthtech Institute's Beyond Genome Conference in San Francisco. One of these companies is even deemphasizing its internal research programs. Not long ago the rush to 'products' was seen as the necessary cure to lagging demand for R&D collaboration services and the only realistic way to scale business up. The latter still may be true, but demand for business for several SB companies does seem improved right now. Read more.


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 

SGI's Meeting Today�s Computational Needs for Science
The quest to better understand disease mechanisms and find new treatments is driven by new laboratory technologies and ever-more sophisticated modeling and simulation efforts. As such, life sciences R&D investigations increasingly are relying on more powerful computing resources. The challenge is how to accommodate the broad mix of applications.
Addressing this issue, this paper produced by the Bio-IT World Custom Publishing Group discusses a new SGI Hybrid Computing Environment approach. It optimally uses shared memory systems, multi-processor clusters, and FPGAs to accelerate computational workflows. Download This Free Paper 

SGI's Supercharging Proteomics Discovery
The deeper study of proteins and their interactions can reveal scientific information once considered nearly untouchable to scientists and researchers. Today, unprecedented advancements in computing power are enabling the creation of mounds of proteomic based data along with the accompanying bottlenecks data can create.  Rather than just �simplify the experiment� to fit the computational resources an alternative is now available with the SGI Proteomics Appliance. This complimentary white paper, produced by the Bio-IT World Custom Publishing Group, looks at ways to use the Proteomic Appliance to handle the most intensive proteomics computing tasks facing science today. Download This Free Paper

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.


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

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