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July 16, 2009 | Genedata Refreshes Web Site
A new look is intended to streamline navigation through the site ( Separately, the company announced a multi-year contract with Chugai Pharmaceutical, a leading Japanese research-based pharmaceutical company, for the use of the Genedata Expressionist system to streamline their internal R&D process.

“We are working with tens of thousands of GeneChip data sets. In the past, we were limited to normalizing small batches at a time. With Expressionist we can normalize the entire data set in one go,” said Mr. Junichi Muroya, member of the bioinformatics team at Chugai Pharmaceutical. Read release.

Linguamatics Extends AstraZeneca License
AstraZeneca, a customer of Linguamatics since 2003, has extended its license to the I2E semantic knowledge-discovery platform with a further multi-year deal. I2E provides flexible and scalable enterprise text mining within AstraZeneca's knowledge engineering strategy, and supports decision making at many points in the drug discovery process, including target selection, biomarker discovery and safety/toxicology. Financial details of the agreement were not disclosed.

"The early prediction of candidate drug efficacy and safety is paramount in any successful drug discovery campaign," said Ian Dix, Knowledge Engineering Capability Lead, Discovery Information, AstraZeneca. "I2E is being used for knowledge discovery to support better-informed scientific decision-making, impacting discovery performance and competitiveness." Read release.

Merrimack Initiates Enrollment in MM-111 Phase 1/2 Study
MM-111 is a bispecific antibody and Merrimack reports preclinical studies demonstrated the bispecific approach shows antitumor activity in a wide range of tumor types. The current Phase 1 / 2 study will evaluate the human safety and pharmacokinetics (PK) of MM-111, which is designed to target cancer cells that are characterized by overexpression or amplification of ErbB2 (also known as HER2). MM-111 is the first bispecific antibody binding two different receptors on the same cell to enter clinical development.

“MM-111 is a novel biologic with a unique approach to treating ErbB2 amplification in tumors,” said Ulrik B. Nielsen, PhD, Senior Vice President and Chief Scientific Officer at Merrimack. “We used a systems biology approach integrating computational modeling, experimentation and protein engineering to optimize this therapeutic to address the complex signaling dynamics between ErbB2 and ErbB3 and to exquisitely target cancer cells.”

MM-111 has two antibody arms; a targeting arm that binds to ErbB2 with high affinity and a therapeutic arm that binds to ErbB3 (also known as HER3). Read release.

Invitrogen Launches Resource for Cellular Technologies and Education
Invitrogen, part of Life Technologies Corporation, says its Cell Resource Center Web portal brings together educational resources and the latest technologies for advancing cellular research. This Web-based hub enables scientists to access the broadest range of products and scientific resources for cell biology from a single source.
The Cell Resource Center features a broad range of highly characterized primary cells, stem cells including embryonic stem cells, induced pluripotent stem cells, and reprogramming technologies, along with more than 200 validated assays for basic research, drug discovery and screening. As part of the rollout of this industry resource, Invitrogen is also launching a new comprehensive line of GIBCO rat neural cell products including neural stem cells, neurons and glial cells, marking the first cells within its industry-leading portfolio of neurobiology products. Read release.

DREAM4 Posts Final Challenge
The last challenge (Challenge 3, ) has been posted rounding out this year’s DREAM4 exercise. All of the challenges are online at The best performers in these challenges will be invited to present in the joint RECOMB Systems Biology/Regulatory Genomics/DREAM4 conference.

See for details on this conference. To learn more about the DREAM4 conference, please go to .To learn more about the DREAM project, please go to 

DREAM 4 Timeline
Oct 15, 2009 - Predictions Submission Deadline.
Nov 15, 2009 - Notifications to Predictors of their Scores and Ranks.
Dec 2-Dec 6, 2009 - RECOMB Systems Biology/Regulatory Genomics/DREAM4 conference. (The DREAM4 conference track is on Friday December 4th.)

BioSeek in EPA’s ToxCast Program
The Environmental Protection Agency (EPA) will use BioSeek’s BioMAP technology to profile the biological effects of compounds in a second phase of the agency’s ToxCast program. The new program expands upon a successful proof-of-concept phase begun in 2007, after which EPA and independent investigators compared the toxicity profiling data from a wide number of profiling technologies including BioMAP.

BioSeek will now generate BioMAP data on an additional set of chemicals selected by EPA in order to assess the potential impact of these compounds on the environment and human health.

Under the new Phase II task order, BioSeek is eligible to receive $1.74 million over the next year, and remains eligible to participate in both further downstream phases of the ToxCast program and its eventual implementation. The specific value of any future orders will depend on the volume of testing required during the contract period. The results from the ToxCast program will aid the EPA in prioritizing chemicals with the greatest potential health threat for additional, more detailed testing in a cost-effective, efficient manner. The five-year effort, divided into three phases of evaluation, was initiated and is managed by the EPA’s National Center for Computational Toxicology (NCCT). Read release.

Optimata to Collaborate with Teva
The collaboration agreement focuses on clinical development of drug candidates for solid tumor cancers. The agreement is intended to efficiently rescue and redirect the clinical development of discontinued drug candidates which have been shelved by their originators pharmaceutical companies, using Optimata’s bio-simulation technology known as the Optimata Virtual Patient. Optimata will receive upfront payments, development milestones and royalty payments; in a separate agreement, Teva has also made an undisclosed equity investment in Optimata.

Dr. Pini Orbach, COO of Optimata, stated in a release that, “Having Teva Pharmaceutical Industries Ltd. as a partner is clearly a transforming event in the history of our company. With this new collaboration we continue to fulfill Optimata’s goal of accelerating the oncology drug development process.” Read release.
This article first appeared in Bio-IT World’s Predictive Biomedicine newsletter. Click here for a free subscription.

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