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Briefs from the Systems Biology Community - April 16, 2008

Entelos Reports ’07 Results; Wins Diabetes Lab Patent
Entelos this week reported financial results for the full year, its second as a public company: “The net loss for the year ended 31 December 2007 was $132,000 (2006: net loss of $754,000) on revenue of $21.8 million (2006: $21.6 million). This resulted in net loss per share (basic) of $0.00 (2006: $0.02). Net loss is after investment in research and development (R&D), including new applications and therapeutic development. Investment in R&D for the full year 2007 was $6.1 million (2006: $6.7 million). At year end 2007 the Company had cash, investments and accounts receivable of $10.0 million (2006: $9.9 million). Management believes the Company will achieve its 2008 plans and stay in compliance with all of its debt covenants.” The full report is here.

Earlier in the month, the company reporting winning U.S. Patent No. 7,353,152 entitled "Method and Apparatus for Computer Modeling Diabetes". This technology forms the basis for the Entelos Metabolism PhysioLab platform which can simulate diabetic patients and drug effects and is used to select the most effective compounds, find the best doses, and support clinical trial design. This patent relates to the mathematical and computer modeling of multiple biological processes.

"This patent represents another milestone in Entelos' intellectual property strategy and strengthens the [its] position in the quantitative modeling of human biology generally and diabetes in particular," stated John Rigsbee, Entelos general counsel. Entelos now has 34 issued patents and 120 pending applications worldwide, says the company.

Separately, the American Diabetes Association (ADA) and Entelos, announced extending their in silico (computer simulation) diabetes research center capability and offering free access to Entelos’ Realab “virtual mice” testing platform to all ADA health professional members. Realab allows direct web access to Entelos’ computer model of type 1 diabetes, enabling scientists and clinicians to investigate the onset, progression, and treatment of diabetes. Realab currently has a virtual environment available for type 1 diabetes. Environments for rheumatoid arthritis, cardiovascular disease and type 2 diabetes are under development by Entelos. Details regarding Realab can be found at

Albert-Ludwigs University Licenses Ariadne Tools
Ariadne announced that the Albert-Ludwigs University of Freiburg has licensed its Pathway Studio Enterprise system with the ResNet database of molecular interactions extracted from the whole PubMed to support their mammalian, worm and plant research.

PerkinElmer Strikes Deal with Cerep
PerkinElmer signed a supply and co-marketing agreement to exclusively offer Cerep’s target screening and profiling services to its customers, and the companies will jointly promote PerkinElmer’s assay technologies and Cerep services to the drug discovery market. “This agreement represents the latest step in our strategy to build the most comprehensive offering in biochemical and cellular screening for drug discovery,” said Robert F. Friel, president and CEO, PerkinElmer.

David Haussler Honored by ISCB
The International Society for Computational Biology (ISCB) has awarded its Senior Scientist Accomplishment Award to David Haussler, professor of biomolecular engineering in the Baskin School of Engineering at UC Santa Cruz. Haussler will receive the award and deliver a keynote presentation at the 2008 International Conference on Intelligent Systems for Molecular Biology (ISMB) in Toronto in July. The ISMB is the largest conference on computational biology worldwide.

A Howard Hughes Medical Institute investigator, Haussler is director of the Center for Biomolecular Science and Engineering at UCSC and scientific codirector of the California Institute for Quantitative Biosciences (QB3). His research lies at the interface of mathematics, computer science, and molecular biology. He develops new statistical and algorithmic methods to explore the molecular evolution of the human genome, using cross-species comparative genomics to study gene structure, function, and regulation.

Haussler joined the UCSC faculty in 1986. A member of the National Academy of Sciences and the American Academy of Arts and Sciences, he is a fellow of the American Association for the Advancement of Science (AAAS) and the Association for the Advancement of Artificial Intelligence (AAAI). He has won a number of awards, including the 2006 Dickson Prize for Science from Carnegie Mellon University and the 2003 ACM/AAAI Allen Newell Award.

Screener 5.5 Debuts
Genedata released Genedata Screener 5.5, its new enterprise solution for high throughput and high content screening analysis. The company says users will benefit from the ability to integrate new fit models that are relevant for their particular workflows, such as the Morrison equation for Ki fitting, or new proprietary and public fit algorithms. In addition, the open and scalable architecture extends Screener’s applicability as enterprise screening analysis platform, from uHTS centers to therapeutic areas, and provides access to a wide range of information in corporate research and drug discovery systems.  

Compaq Founder Donates $18M to Caltech
The Benjamin M. Rosen Family Foundation of New York has donated $18 million to the California Institute of Technology to establish the Donna and Benjamin M. Rosen Bioengineering Center. The Rosen Center will advance both basic scientific exploration and development of engineering analysis and synthetic approaches. Innovations in these areas are resulting in rugged and inexpensive diagnostic devices, in new insights into the functioning of the heart, and in the engineering of molecular devices capable of recognizing and responding to disease processes in individual cells, said Caltech spokesperson Jill Perry.

Ben Rosen was founding chairman of Compaq Computer Corp. and a founding partner of Sevin Rosen Funds, a venture capital firm that has provided initial financing for more than 100 technology companies. Previously, he was vice president and senior electronics analyst at Morgan Stanley & Co., and before that he was an electronics engineer at Raytheon and Sperry Gyroscope. In 1992, Computerworld chose Rosen as one of 25 people in the computer industry "who changed the world." Rosen joined Caltech's board of trustees in 1986 and became chairman in 2001.

Simcyp 8.0 Handles More Formulations
Simcyp launched Version 8.0 of the Simcyp Population-based ADME Simulator, a platform for ADME modelling and simulation in virtual populations. The Simcyp Simulator allows preclinical data to be used to in drug development; informing the design of human studies and allowing ‘what if’ questions to be explored in the safety of a computer.

Among improvements, the Simcyp absorption model can now accommodate a variety of different drug formulations. Many factors which affect the subsequent bioavailability of a drug, including food intake, variability in pH and concentration-dependent effects of efflux transporters in the gut, and these can now also be simulated using Simcyp, according to the company

Novartis Completes Renal Biomarker CRADA
Novartis announced successful completion of a CRADA with the FDA as one of the first projects conducted under the FDA's Critical Path Initiative. The FDA-Novartis CRADA had two primary objectives: 1) To define a process for qualifying preclinical safety biomarkers for regulatory decision making; and 2) to test this pilot process by submitting kidney-related safety biomarkers identified and characterized through preclinical studies to the FDA for qualification.

Efforts conducted under the CRADA resulted in the publication of the first pilot framework for a preclinical regulatory biomarker qualification process. In addition, the preclinical data identified thus far have demonstrated evidence for the superiority of new renal biomarkers over the current standards used to assess renal injury in drug testing, namely serum creatinine and blood urea nitrogen (BUN), says Novartis. Further efforts will focus on the extended clinical qualification of biomarkers that could allow clinicians to detect kidney injury in patients earlier than current clinical practice allows.

The CRADA data, together with data generated by other partners in the PSTC has been submitted to FDA and the European Medicines Agency (EMEA) as part of a Voluntary Exploratory Data Submission (VXDS). The two regulators are now considering whether to approve use of these biomarker data in support of particular aspects of regulatory decision making. As a result of this data submission, FDA and EMEA have  utilized appropriate internal boards and worked to refine the process to qualify such preclinical safety biomarker data. Further joint evaluation of additional data under the auspices of the PSTC is expected to lead to additional submissions of peripheral biomarkers representing additional renal pathologies.

ISC Launches the Parallel Lounge Blog for HPC
Interactive Supercomputing launched a multi-author blog to provide scientists, engineers and analysts insights into how to solve problems faster with high performance computing (HPC). The Parallel Lounge blog aims to be an online resource for researchers seeking the latest in parallel programming approaches and HPC applications. The blog features regular contributions on a mix of real-world case studies of leading research institutions, YouTube video interviews, parallel programming constructs, and productivity in high performance computing. Recent topics have ranged from “Performance Tuning 101: Client-Server Communications and Vectorization” to trade-offs among approaches to accelerate Python and MATLAB applications.

Ingenuity Hits CRADA Milestone; Expands Pfizer Deal
Ingenuity Systems says it has achieved key milestones in the ongoing Cooperative Research and Development Agreement (CRADA) with the Food and Drug Administration, including the curation of new biomarker and toxicology content and the expansion of existing ontological classifications. Under the terms of the CRADA, Ingenuity Systems and the FDA will expand Ingenuity‘s content and software solutions to facilitate the research and regulatory review of biomarker, pharmacogenomic, and toxicogenomic data.

The collaboration directly relates to the FDA's need to develop better tools for the review of genomic data. Separately, Ingenuity Systems and Pfizer announced a new multi-year partnership that promotes enterprise-wide deployment of IPA. The two will also integrate IPA and content from the Ingenuity knowledge base with other informatics solutions used throughout Pfizer. "We have selected Ingenuity as a partner to support our vision to implement an integrated and enterprise-scale pathway solution,” said Giles Day, senior director of the Targets and Mechanisms Informatics Group, Pfizer. Ingenuity is also providing Pfizer with a suite of customized “capabilities" according to Ingenuity CEO Jake Leschly.

Takeda Joins the HRP Initiative
BG Medicine, a key organizer of the High-Risk Atherosclerotic Plaque Initiative, reports that Takeda Pharmaceutical has joined BG Medicine, Merck, AstraZeneca, and Philips as the newest member of the Initiative. The HRP Initiative is a pre-competitive industry collaboration that is focused on discovering and developing novel blood tests and imaging methods to find individuals with high-risk plaque disease before the occurrence of the first cardiovascular event.

Compugen Signs Agreement with Biosite
Compugen reported the discovery and experimental verification of CGEN-144, a novel variant of Troponin I biomarker, and the signing of a research and license option agreement with Biosite. Compugen also announced that a patent for this biomarker has been granted by the US Patent and Trademark Office. The novel Troponin I variant was one of a group of putative cancer and cardiovascular biomarkers previously predicted by Compugen’s immunoassay biomarker computational discovery platform. The molecule has subsequently been experimentally verified to be differentially expressed - as serum protein - in myocardial infarction patients compared to healthy individuals.

Under the recently signed agreement, Compugen will provide Biosite with all existing proprietary data related to the molecule and Biosite will develop and select antibodies that bind to CGEN-144 to determine assay sensitivity and specificity in various disease states and as an addition to the current commercial Troponin I test. The agreement also provides Biosite with an option to obtain worldwide royalty bearing commercialization rights for possible immunoassay diagnostic products based on this biomarker.

Lipomics Launches Biomarker Validation Effort
Lipomics Technologies is launching an effort to validate its proprietary biomarkers for fatty liver disease. Lipomics' proprietary lipid biomarkers proved effective in identifying patients with varying degrees of metabolic liver disorders in recent clinical trials. This new initiative will focus on accessing large clinical cohorts for validating its diagnostic products through the company's collaborative network. Lipomics will use its analytical and bioinformatic technology to validate the clinical utility of its biomarkers associated with various aspects of fatty liver disease.

“The current gold standard of diagnosis is invasive liver biopsy. Our diagnostics provide noninvasive blood-based tests that will empower doctors to detect liver disorders in their earliest stages and support management of patient care where liver disease is present. These safe and effective tests will open the door to a greatly improved standard of care for millions of patients,” says Steve Watkins, Ph.D., chief executive officer of Lipomics.

Scripps Joins MetaMiner Cardiac Consortium
The Scripps Translational Science Institute has joined the MetaMiner Cardiac Consortium, sponsored by pathway tool provider GeneGo. The goal of the Consortium is to build the first systems biology and pathway analysis platform for cardiovascular diseases in the world. The Consortium members will vote on deliverables that will include disease specific pathway maps and networks built by experts in the field. GeneGo will also develop relevant ontologies for cardiovascular diseases and drugs. The MetaMiner environment will also serve as a repository for OMICs and other experimental data. "We are very excited to have The Scripps Translational Science Institute, lead by Dr. Eric Topol, Director, as a member, the project," said Julie Bryant, GeneGo's VP of Business development.

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