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University of Wisconsin-Madison, Public Health Agency of Canada, DNAStar, Mitrionics, NIH, FDA, UCI, CODA Genomics, GenoLogics, Affymetrix, Bar Harbor BioTechnology, Amylin, Kelaroo, UW, Fred Hutchinson

Bioinformatics Training Program at UW-Madison Scoops $5.2M NLM Grant
The Computation and Informatics in Biology and Medicine Training Program at the University of Wisconsin-Madison has been awarded a $5.2 million grant from the National Library of Medicine to extend its training program for bioinformatics at UW-Madison for five years.
The 41 CIBM faculty span 15 different departments and five colleges at UW-Madison as well as several faculty at the Marshfield Clinic Research Foundation.
CIBM focuses on the development of bioinformatics algorithms to analyze molecular data, including genome sequences; proteins levels, interactions, and structures; and regulatory pathways. New tools for imaging, genetic analysis, and health delivery systems will result.
In its second five-year period, the CIBM Program is adding a translational molecules-to-bedside medicine component. In a collaboration with the Marshfield Clinic, CIBM trainees have the opportunity to develop algorithms to predict clinical parameters, such as disease susceptibility or treatment response, from combined molecular and clinical data.
The National Library of Medicine grant for training in biomedical informatics will fund 14 predoctoral and four postdoctoral traineeships at UW-Madison annually.. Since its start in 2002, the program has supported 35 individual predoctoral and 10 postdoctoral trainees.
Karen Nafzger, program administrator, told BioInform that because of the extended grant, “We have another five years to both recruit people and send them out for jobs.”

Public Health Agency of Canada Licenses DNAStar’s Lasergene
The Public Health Agency of Canada has signed a site license agreement for the use of DNAStar’s Lasergene sequence analysis software.
Under terms of the four-year site license, Lasergene can be used anywhere on the Winnipeg campus of PHAC.  
Lasergene is a suite of tools used primarily in the assembly and analysis of DNA and protein sequences for molecular biologists and geneticists. The software provides researchers with a variety of analysis tools that can be used with Sanger and next-gen sequence analysis projects, the company said. It runs natively on Windows, Mac PowerPC, and Mac Intel chips and is Microsoft Vista-compatible.

Mitrionics Opens US Offices in Silicon Valley, Seattle
Lund, Sweden-based FPGA developer Mitrionics has opened two new US offices: one in Los Gatos, Calif., and another in Seattle.
The company said the new offices are an important part of a planned global expansion and will allow it to be closer to partners and customers. 
Mitrion’s Virtual Processor and Mitrion Software Development Kit provide FPGA supercomputing power to a range of organizations because the tools ameliorate the need for circuit design skills, according to the company.

NIH, FDA License Simulations Plus Software
Simulations Plus, which provides software for pharmaceutical discovery and development, said that it has received orders for its software from the US Food and Drug Administration and the National Institutes of Health.
The FDA has ordered additional licenses for the company’s GastroPlus simulation software and has acquired new licenses for its DDDPlus in vitro dissolution software, Simulations Plus said.
Walt Woltosz, chairman and chief executive officer of Simulations Plus, said in a statement that the software will help the agency “apply the new biomedical science to medical product development” as part of its Critical Path initiative.
Separately, the company said the NIH had licensed its ClassPharmer software.

UCI and CODA Genomics to Jointly Re-engineer Yeast for Biofuel Production
Furthering the quest for “green” energy, scientists from UC Irvine and CODA Genomics are partnering on a $1.67 million research project aimed at turning a common strain of yeast used in the production of beer and bread into a producer of ethanol.
Researchers at UCI’s Institute for Genomics and Bioinformatics are using CODA Genomics’ gene-protein-production algorithms to tweak the genetic structure of Saccharomyces. The results could turn switchgrass, hemp, corn, wood and other natural materials into ethanol, turn switchgrass, hemp, corn, wood and other natural materials into ethanol, UCI said.
The collaboration began Sept. 1 and is funded by synthetic biology firm CODA Genomics and a UC Discovery Grant that provides matching funds for industry-university research partnerships.
The multidisciplinary research project involves UCI researchers in the schools of information and computer sciences, engineering and medicine, as well as researchers at CODA Genomics, which spun off in 2005 from UCI research.

GenoLogics' Geneus Achieves Affy GeneChip-compatible Status
GenoLogics, a developer of lab and data management life sciences software, has joined the Affymetrix GeneChip-compatible Applications Program, and its Geneus product has achieved GeneChip-compatible status with Affymetrix’s GeneChip microarray platform.
GenoLogics has integrated its Geneus solution, built for multiple genomics applications, with the Affymetrix GeneChip platforms, GeneChip Operating Software, and the new GeneChip Command Console Software.
Since mid-last year the GenoLogics team has been working closely with the Affymetrix development team to ensure integration between Geneus, a lab information management system, and the Affymetrix GeneChip microarray platform.

Bar Harbor BioTechnology Completes Series A Financing for Product Launch
Bar Harbor BioTechnology said this week that it has completed a “multimillion-dollar” Series A financing round in anticipation of its first product launch, scheduled for Oct. 1. The round was led by Borealis Ventures.
Further financial details were not disclosed.
The company develops gene expression products and software for scientists to perform real-time quantitative polymerase chain reactions.
The company is developing a suite of products that include bioanalysis software, qPCR arrays, and bioinformatics applications that it said will help scientists prepare, execute  and analyze gene expression experiments.

Amylin Expands Bioinformatics Collaboration with Kelaroo, Takes Equity Stake
Kelaroo, which develops and sells drug discovery software for bioinformatics and cheminformatics, has received an undisclosed equity investment from Amylin Pharmaceuticals as part of an extended bioinformatics research contract.
Details of the investment and the terms of the extended contract were not provided.
Amylin's PHINDER system for peptide hormone identification and optimization was developed using Kelaroo's SeqR sequence-profiling technology, which combines machine-learning methods and high-performance sequence analysis for genome-scale data mining and sequence optimization.

UW, Fred Hutchinson Secure $4.8M NHGRI Grant to Coordinate GWA Studies
The University of Washington and the Fred Hutchinson Cancer Research Center have pocketed $4.8 million from the National Human Genome Research Institute to coordinate a number of genome-wide association studies being conducted at research institutes across the country, the Hutch said this week.
Under the four-year program, UW and the Hutch will provide statistical and data-management support and services to research teams comparing genetic profiles of individuals with diseases to controls in order to identify the site of genes contributing to the disease.
"This is a first step in determining the genetic basis of disease and is necessary for the development of therapies and eventual cures," Lon Cardon, a UW biostatistics professor and co-director of the Computational Biology Program, said in a statement.
Cardon, who is also a member of the Human Biology Division at the Hutch, recently led statistical analysis efforts for whole-genome studies of diabetes, rheumatoid arthritis, and coronary heart disease conducted by the Wellcome Trust.
"The recent discovery of 21 new disease gene associations from the Wellcome Trust Case Control Consortium offers great hope for success from these new NHGRI studies," Cardon said.
UW and the Hutch said these studies will provide information about the “non-gene sequences that comprise 98 percent of the genome” and that “contain instructions for switching genes on or off, or control how DNA is packaged and replicated within a cell.” The researchers plan to find out if some of these functional elements of DNA sequences are implicated in disease.

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The Scan

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