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

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Genstruct Adapts for Today's Challenges 
MIT Launches Interdisciplinary Cancer Center 
Briefs from the Systems Biology Community

Genstruct: Patience, Persistence, and Payoff
By John Russell

Finding the right business model for systems biology (SB) technology providers has been challenging -- that's hardly a new theme in biotech. Most SB pioneers were founded as platform providers, but soon encountered difficulties growing their sales sufficiently to increase valuations. Genstruct, a pioneer in using computational approaches to infer mechanistic hypotheses from large experimental data sets, is no exception.
Many reasonable-sounding explanations are offered for the community’s lack of traction: 1) the technologies weren’t (aren’t) really ready; 2) not enough biology was (is) known for predictive technologies to work very well; 3) desperate pharma jilted platforms for compounds; 4) collaborators wouldn’t share meaningful IP; 5) personnel shuffling inside pharma has made maintaining influence problematic, etc.
Keith EllistonGenstruct CEO Keith Elliston is familiar with the list and hardly agrees with all of them (try bringing up #2!). He is, however, a realist. What’s important is what will work. Genstruct’s bread and butter is hypothesis generation. In the past, most engagements lasted 2-to-4 months — Genstruct has done 30 or so such projects — and contrary to Elliston’s original expectations, none grew into a deep, long-term collaboration or produced the kind of glittering IP that excites the financial world. Read more.

MIT Launches Interdisciplinary Cancer Center
By Allison Proffitt

The David H. Koch Institute for Integrative Cancer Research at MIT (Massachusetts Institute of Technology) opened this month in Cambridge. The Koch Institute will replace the previous MIT Center for Cancer Research, an NCI-designated basic research center since 1974. The institute brings together cancer scientists and cancer engineers, said Tyler Jacks, David H. Koch Professor of Biology, and founding director of the Koch Institute. Read more.
BRIEFS from the Systems Biology Community

Applying Systems Biology meeting
CHI's tenth annual Applying Systems Biology meeting, June 9-11, 2008, in San Francisco, will bring together leaders from around the world to present case studies about how Systems Biology is being 'applied' to achieve real-world solutions for battling critical targets, and improving drug discovery and development. This year the meeting is featuring a comprehensive focus on "Collaboration" including international projects for modeling the immune system.  Along with data and project results, experts will address logistical issues in an interactive panel discussion addressing collaborating across areas of expertise, lingo and national borders. The second half - "Abstraction" -- will look at the tools and technology that support this new age of science.  During "Abstraction," the meeting will explore the journey from wet lab to dry lab in light of technological breakthroughs, including an indepth session focused on Gene Therapy.

Pathway Analysis Primer
Looking for a primer on pathway construction and theory? Check out Getting Started in Biological Pathway Construction and Analysis, by Ganesh A. Viswanathan and colleagues, in PLOS Computational Biology, last month. This brief overview discusses data-driven and knowledge-driven approaches and looks at few of the common tools available to help.

GeneGo Adds Mac and Linux Support
Pathway analysis tool and database provider GeneGo announced Mac and Linux support support for its portfolio of products (MetaCore, MetaLink, MapEditor and MetaRodent). "Mac-compatibility is good news for our industrial and academic users," said Julie Bryant, GeneGo's VP of Business development. "The Mac/Safari user base is a significant and growing sector for GeneGo so we wanted to make sure we made our software and databases compatible for the IT environment." GeneGo will support latest updates of Tiger and Leopard Mac OS, and Firefox 2. Separately, GeneGo reported GlaxoSmithKline extended and expanded its licensing agreement with GeneGo.

IPA 6.0 Contains Enhanced Graphics Tool
Ingenuity Systems launched IPA 6 last week, the newest version of its pathway analysis and life sciences knowledge software. IPA 6 features Path Designer, a tool within IPA that enables researchers to turn their networks and pathways into publication-quality pathway graphics with color, customized text and fonts, biological icons, organelles, and custom backgrounds. Ingenuity says researchers can now finish the entire workflow - from data analysis to data sharing and publication - within IPA. Separately, Ingenuity announced GSK extended its license to IPA and expanded it to become enterprise-wide.

Faster Digital Breast Tomosynthesis
Researchers at the Northeastern University Computer Architecture Research Lab (NUCAR) and the National Science Foundation's (NSF) Center for Subsurface Sensing and Imaging Systems (CenSSIS) are teaming with Massachusetts General Hospital (MGH) on a promising new breast cancer detection technology that improves breast cancer screening accuracy. The team is applying supercomputing technology to a 30-year-old imaging modality called tomosynthesis, which until now has been relegated to research labs due to its massive and expensive computational requirements.

Called Digital Breast Tomosynthesis (DBT), the system creates a 3D image of the breast using a series of x-ray projections collected during a 20-second, 40-degree sweep. It makes cancer lesions easier to detect among dense breast tissue by creating a stack of 1mm spaced high-resolution slices that can be displayed individually, or assembled into a 3D view that can be rendered for more careful examination. DBT also reduces the amount of breast compression required by traditional mammography, which can deter women from getting an annual screening.

NUCAR scientists addressed the computational hurdle by creating a DBT reconstruction application on their desktop PCs using MATLAB, and then running the code on an affordable Linux parallel cluster using Star-P software from Interactive Supercomputing, Inc. (ISC). Reconstructing DBT used to take many hours and now can be completed in just a few minutes. General Electric is developing a commercial DBT device that should be generally available in 2009. The Northeastern team has been supported by a NSF Small Business Technology Transfer (STTR) project with ISC, the NSF's CenSSIS, and by Mass General Hospital.

GeneChip Compatibility Expanded
Genedata's Expressionist platform added GeneChip-compatible status for Exon expression with the Affymetrix GeneChip microarray platform. Genedata Expressionist is a modular enterprise system for biomarker discovery. It represents a single-point-of-access for experimental, proprietary and public data, including sample information, raw and pre-processed transcriptomics, proteomics, metabolomics and lab chemistry data, analysis results, reports and documentation.

P&G Licenses AutoPilot
Pharsight reported that Procter & Gamble purchased floating licenses of WinNonlin AutoPilot to use in conjunction with their licenses of WinNonlin. WinNonlin AutoPilot is configurable software that pre-clinical and clinical research scientists can use to automate common or repetitive tasks during clinical pharmacokinetic (PK) analysis and to create report ready tables and graphs.

Upgraded Platform from Metabolon 
Metabolon launched its third generation metabolomics platform which enables greater speed and resolution for the discovery of biochemical markers from numerous chemical classes, says the company. The new platform is based on three separate analytical systems: An ultra-high pressure liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) system with positive ion MS/MS, a second UHPLC-MS/MS system with negative ion MS/MS and a gas chromatography-mass spectrometry (GC-MS) system. The three systems together provide analysis of the broadest range of biochemicals in complex samples such as plasma and urine.

Wyeth Seeks SB Director
Wyeth is seeking a Director, Systems Biology Technologies & Analytics. "The successful candidate will be coordinate the development and application of high-content "omics" technologies and analysis within Wyeth's Systems Biology program. With 10+ years experience post-PhD in molecular identification technologies, he/she will have direct experience in proteomics as well as metabolomics and/or lipidomics. Applicants will be required to demonstrate a record of innovation and strategic planning in these fields, and will have a record of publications and presentations that place themselves as a leader in these areas. The successful candidate will be responsible for planning "omics" studies across multiple therapeutic areas, ensuring their timely completion, and working closely with statisticians, bioinformaticians, and principal investigators to convert platform data into decision-enabling knowledge for drug discovery."



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: LSCDD

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: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: LSCDD 

Agilent Technologies-Asia Pacific - Job Requisition: 2021927
Job Title :   Application Engineer and Implementation Specialist for Lab Informatics Platform
Location(s) :  Bangalore, India.  Project management: small to large scale implementations, including integration/ validation of Agilent’s software platform.  Manage assigned customer account relationship, customer satisfaction and education of future Agilent plans.  On time and on budget implementation, focus Pharma, Petro and Chemical markets.  Qualifications:  BS/’MS Degree in Computer Engineering, or other related discipline or equivalent. Apply 

Agilent Technologies-Asia Pacific - Job Requisition:2021658, Job Title : Product Specialist – Laboratory Informatics Location(s) :  Bangalore, India.  Proactively understand customer needs and identify solutions to actively create business opportunities.  Manage a complex, enterprise solution sale with long sales cycle.  Develop approaches to achieve quota strategies.  Lead coordinated projects across organizations.  Solve complex broad range of problems.  Qualifications:  BS/MS Degree in Sciences, Engineering, Computer or equivalent plus 5 to 8 years work experience.Apply 

GNS Biotech - Computational Scientist, Discovery Biology 
Candidate will reverse engineer models from large coherent data sets.  In addition, 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.

More Life Science Jobs ~ Add a Job Listing 



IIR - 12th Annual EDC & Beyond, April 14-16, 2008, Las Vegas, NV

InforSense Translational Research Symposium, May 2,2008, Boston, MA 

BioInformatics Asia 2008, April 14-17, Singapore,

The Post-Approval Summit  May 14-15, 2008, The Conference Center, Harvard Medical School, Boston, MA 

The 1st Symposium on Protein Tomography -- May 1, 2008, Boston, MA

The First International Workshop on Label-free biosensing  April  8-9, 2008,  Enschede,The Netherlands 

Med-e-Tel, The International Educational and Networking Forum for eHealth, Telemedicine and Health ICT, 16-18 April in Luxembourg. 

TEPR 2008 -- May 17-21, 2008 Ft. Lauderdale,FL 

Laboratory Informatics -- March 25-April 3, 2008, San Francisco CA.

Lean Six Sigma for Pharmaceutical, Biotech, and Medical Device Excellence -- February 25-27, 2008, Philadelphia, PA.

Best Practices Awards Program -- April 29, 2008, Boston, MA 

MIT Professional Institute – 2008 Short Courses, Cambridge,MA 

GOT Summit: Getting Optimized Tools for Diagnostics - May 19-21, 2008, Boston,MA

Health 3.0 Summit, May 4-7, 2008, Las Vegas, NV

The World Congress Leadership Summit on Consumer Connectivity, May 6th, Boston, MA 

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

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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 


NuGenesis SDMS: Improving Data Accessibility 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.

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


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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.

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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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