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Briefs from the Systems Biology Community

Ingenuity Launches Analysis Services Business
Ingenuity Systems just launched Ingenuity Analysis Services, custom-tailored professional scientific services for scientists working with ‘omics’ data related to compound profiling, target identification, and mechanism of action studies. The new services are designed to meet the needs of research teams that require a rapid turnaround for a project, or who do not have the required resources internally. Examples of Ingenuity Analysis Services offerings include:  Analysis and interpretation of ‘omics’ datasets for compound profiling, lead identification and prioritization of therapeutic targets, and understanding disease mechanism of action and mechanism of toxicity.

“We are seeing an analysis outsourcing trend in the pharmaceutical and biotech industry because maintaining a fully trained and current analysis skill set in-house is not always the most efficient and effective way to get fast and high-quality analysis results,” said Sean Scott, SVP commercial operations, Ingenuity Systems, in a release.

Windber to Collaborate with GenoLogics
The Windber Research Institute will collaborate with GenoLogics to develop an integrated biomedical informatics software solution. Windber’s primary focus is improving patient care and quality of life by rapidly translating molecular and clinical research into action. “We decided to work with GenoLogics to deploy a biomedical informatics solution that will allow us to integrate both discovery and clinical data into a single system for a holistic view,” said Dr. Richard Mural, CSO at Windber. GenoLogics currently has a new product suite for Biomedical Informatics.

Harvard Debuts “little b” Language
Researchers from Harvard Medical School’s Systems Biology Department have developed a programming language, little b, that is customized for creating extensible models of biological systems. A paper describing little b will appear in the Royal Society journal Interface. Two of the project leaders, Jeremy Gunawardena and Aneil Mallavarapu, are both based at Harvard Medical School. For more on the motivation and design decisions behind the new language, see Ars Technica.

EU Law May Spur More Pediatric Simulations
The use of ‘virtual’ studies in children could soon become routine in drug development following the introduction of EU regulations requiring pediatric investigational studies for new medicines in development. Legislation was introduced to address the issue that over 50 percent of medicines currently used in children have not been officially tested in this age group.  Simcyp Limited, which provides modeling and simulation services to the pharmaceutical industry, has developed a Paediatric Simulator for evaluating medicines in virtual populations of babies, infants, and children. Traditionally, many medicines administered to children have been used ‘off-label,’ with doses determined by scaling back from doses used in adults. This results in increased risks of adverse effects.

Ariadne Inks Bayer CropScience Deal
Ariadne announced that Bayer CropScience AG has licensed its tool suite and database to supplement their plant stress reactions research. Bayer will use Pathway Studio for gene expression analysis of Plant and Fungi data. Separately, the company announced The Rat Genome Database at the Medical College of Wisconsin has published a rat signaling pathway diagram collection, created with Ariadne tools. The pathways were curated by RGD staff.

Galapagos Deposits Data with EMBL
The Wellcome Trust has awarded £4.7 million to EMBL’s European Bioinformatics Institute (EMBL-EBI) to support the transfer of a large collection of information on the properties and activities of drugs and a large set of drug-like small molecules from publicly listed company Galapagos NV to the public domain. It will be incorporated into the EMBL-EBI’s collection of open-access data resources for biomedical research and will be maintained by a newly established team of scientists at the EMBL-EBI. These data lie at the heart of translating information from the human genome into successful new drugs in the clinic. More information here.

Metabolon Works with UTHC Diabetes Researcher
Metabolon announced collaboration with Ralph A. DeFronzo, chief of the Diabetes Division, at the University of Texas Health Science Center (San Antonio.) “Our team has continuously sought key technologies that can best identify novel biomarkers relating to diabetes,” said DeFronzo. Metabolon will analyze samples from various studies conducted by Dr. DeFronzo’s team to discover and validate biochemical biomarkers reflective of insulin resistance and beta cell dysfunction. These markers will be used to help further develop Metabolon’s diagnostic tests in the area of insulin resistance, and how this relates to the risk of developing metabolic diseases such as diabetes. Separately, Metabolon reported that Pfizer’s Bioprocess R&D Group will use the company’s global biochemical profiling technology to conduct analysis of samples from bioreactor to help Pfizer to optimize bioprocesses and reduce manufacturing costs.

Cellumen Collaborates with NCTR
Cellumen will collaborate with the National Center for Toxicology Research (NCTR) to profile blinded samples of known liver toxicity compounds, including both failed and marketed drugs for the NCTR. The NCTR will incorporate the knowledge generated by Cellumen to develop a liver toxicity knowledge base. Cellumen will use the profiling data and compound safety data from the collaboration to further develop the diversity in the CellCiphr database and the types of cell panels, as well as to advance the classifier informatics tools. Cellumen provides cell-based assay solution combining tissue-specific cells, multiplexed functional biomarkers, advanced classifiers, and a compound reference library.

GSK Extends InforSense Agreement
InforSense reports GlaxoSmithKline (GSK) has extended its agreement to the InforSense platform and collaboration with the company. The InforSense system is currently leveraged by approximately 800 users across the organization. "GSK is one of our key customers and we are looking forward to continued work with them," said Jonathan Sheldon, CSO, InforSense. 

Tissue of Origin Test Gets FDA Nod
FDA has cleared Pathwork Diagnostics’ Tissue of Origin Test for use in determining the origin of uncertain tumors. The test analyzes a tumor’s gene expression pattern to help pinpoint the source of hard-to-identify tumors and is the first test of its kind to receive FDA clearance. Up to an estimated 200,000 newly diagnosed cancer patients annually in the U.S. may have a tumor for which the site of origin is uncertain after the initial diagnostic workup. The FDA’s clearance underscores the growing role that patients’ genomic information can play in helping physicians make better decisions.

The test measures the expression pattern of more than 1,500 genes and compares it to expression patterns of a panel of 15 known tumor types, representing 60 morphologies overall, to help determine the tumor’s origin. In the in vitro diagnostics clinical validation study submitted to the FDA, the test demonstrated 89 percent positive agreement (akin to sensitivity) with available diagnoses and 99 percent negative agreement (akin to specificity). The study consisted of 545 metastatic, poorly differentiated and undifferentiated tumors that had been identified as one of the 15 tumor types on the panel using existing methods.5 The test demonstrated an average 94 percent overall concordance across four laboratories in a cross-laboratory comparison study of 60 metastatic, poorly differentiated and undifferentiated tissue specimens.

CRI, Pharsight Strike an Alliance
Pharsight Corporation and CRI Worldwide, a provider of clinical research services, have formed an alliance to offer combined services, including trial design, simulation, execution, analysis and reporting. The alliance provides a broader solution to customers and addresses the growing need for drug development companies to improve the efficiency in their performance and analysis of clinical trials. "Our clients recognize the value of linking CRI's clinical trial execution capability with Pharsight's state-of-the-art design, analysis, and reporting expertise," said Ken King, CEO of CRI Worldwide.

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