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Progeniq, IBM, University of Edinburgh, DuPont, GenBank, Definiens, Microsoft, IDBS

Progeniq Raises Financing from Singapore Investment Firm
Progeniq, a Singapore-based developer of reconfigurable accelerated computing technology with a focus on the life science market, said this week that it has raised an undisclosed amount of pre-series A financing from BAF Spectrum, a Singapore-based investment firm.
Spring Seeds Capital, the financing arm of Singapore’s national agency for enterprise development, also participated in the round.
The company said that the investment will support its Progeniq’s entry into a number of high-performance computing application markets “with a primary focus on life sciences and CGI animations.”
Sanjeev Shah, executive director at BAF Spectrum, will take a seat on Progeniq’s board of directors, while William Klippgen, another executive director at BAF Spectrum, will join the company’s advisory board.
Progeniq said that it plans to open a sales and support office in Palo Alto, Calif., this month, and that this will be “closely followed” with a regional sales office in Bangalore, India.
Progeniq was launched in 2005 and markets the BioBoost line of accelerated bioinformatics products.

IBM, U of Edinburgh Partner on Simulation-Based HIV Drug Discovery
The University of Edinburgh and IBM's TJ Watson Research Center said this week that they have begun a five-year joint research project that will use computational simulations to design drugs that will inhibit infection by human immunodeficiency virus.
The project will use IBM's Blue Gene supercomputer, combined with experimental methods, to design inhibitors for the surface protein of the virus that is responsible for allowing the virus' genetic material to enter the human cell.
The partners plan to simultaneously design multiple inhibitors that will prevent the virus from mutating, and thereby evade drug therapy as it does with single inhibitors.
"Our early results are promising, showing that we can use computers to simulate which molecules can stop the HIV virus from infecting humans, which drug makers could then use to more rapidly develop those drugs," said Jason Crain of the University of Edinburgh's School of Physics.

DuPont Donates Corn Fungus Genome Data to GenBank
DuPont said this week that it is depositing in GenBank the genomic sequence information about a fungal pathogen that affects corn plants.
DuPont’s Pioneer Hi-Bred business is releasing sequences of Colletotrichum graminicola. The fungus causes anthracnose leaf blight and stalk rot, which reduces corn yield worldwide due to premature death and weakened stalk strength.
Making this information publicly available will help researchers complete the genomic sequence of the pathogen, which could help to speed up disease-resistance studies, the company said.
DuPont said Pioneer already is selling anthracnose-resistant corn hybrids in Latin America, and it plans to incorporate an anthracnose-resistant gene into hybrids that could grow in the Northern Hemisphere.
"Defining and donating the gene sequences of C. graminicola will accelerate the scientific community's study of this important corn pathogen, creating knowledge that universities and, ultimately companies, can use to protect corn yields around the world," William Niebur, VP of crop genetics research and development at DuPont, said in a statement.
The US Department of Agriculture’s Cooperative State Research, Education, and Extension Service currently is mapping and sequencing a different strain of the pathogen through a collaboration with the Broad Institute.

Munich Research Center Deploys Definiens Image Analysis Software
Definiens said this week that researchers at Germany’s Helmholtz Zentrum München, formerly called the German National Research Center for Environment and Health, are using its Enterprise Image Intelligence Suite to automate image analysis.
Axel Walch of the Helmholtz Zentrum’s Institute of Pathology said that the use of the software has helped the researchers reduce the amount of time required to process its data from three months to “a few days.”
Financial terms of the agreement were not disclosed.

Microsoft Funds 5 Life Science Projects Under Award Program
Microsoft External Research this week awarded a total of $1 million to 10 research projects, including five in the life sciences, that it considers “breakthrough research.”
The projects were funded under Microsoft’s A. Richard Newton Breakthrough Research Award, which the company created last year to honor the late A. Richard Newton, former dean and professor of the College of Engineering at the University of California, Berkeley, and a longtime member of Microsoft Research’s technical advisory board. Newton died in January 2007.
The 10 winning proposals were selected by a panel of subject-matter experts from more than 89 proposals, Microsoft said. The proposals were evaluated “on the basis of potential impact and the academic researchers’ qualifications to perform the proposed research.”
Awardees in the life science arena include:
  • Stephen Kosslyn of Harvard University, who proposes to build a computer model to understand the effects of brain injury;
  • Shaofan Li of the University of California, Berkeley, who plans to simulate the ability of stem cells to sense their environment and adapt their development to it — a process called mechanotransduction;
  • Vladimir Cherkassky of the University of Minnesota, who proposes to improve data-mining applications that involve sparse and heterogeneous data, with particular applications in the biomedical research field;
  • Eric Klavins of the University of Washington, who proposes to implement a new algorithm for building stochastic models to help characterize genetically engineered systems in bacteria;
  • and Yuan Qi of Purdue University, who plans to develop computational and statistical tools to construct joint network models for transcriptional regulation and metabolic pathways from heterogeneous data sources, and utilize the integrated network models to predict target phenotypes for use in engineering biofuel crops with low amounts of lignin.

IDBS Reports Double-Digit Revenue Growth for 2007
UK-based data-management software provider IDBS this week said that it posted “double-digit revenue growth and profitability” for 2007 “despite increasingly challenging market conditions.”
The privately held firm did not provide details on its revenues for the year, but said in a statement that revenues have increased by “almost 50 percent” since 2005, “on the back of major developments to core product lines such as the ActivityBase Suite.”
The company said that it is also seeing revenue growth from existing customers who have adopted new products such as its E-WorkBook Suite.

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The Scan

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Sentence Appealed

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Genome Biology Papers on COVID-19 Effector Genes, Virtual ChIP-seq, scDART

In Genome Biology this week: proposed COVID-19 effector genes, method to predict transcription factor binding patterns, and more.