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Biological Modeling, Blue Gene, NCBI, Jubilant, Cancer Informatics Journal, Bioinformatics Center, Partek Pro, Ocimum Biosolutions, Strand Genomics


Agencies Earmark $15M for Multi-Scale Biological Modeling Projects

The National Science Foundation and three other federal funding agencies have issued a joint program solicitation entitled, “Interagency Opportunities in Multi-Scale Modeling in Biomedical, Biological, and Behavioral Systems.”

The solicitation is intended to “promote the development and dissemination of tools to enhance computational modeling of biological, biomedical, and behavioral sciences at multiple scales ranging from the molecular to population,” according to an NSF statement. While “major biology oriented modeling activities are now supported at most federal agencies,” the proposal said, “for the most part, these efforts have focused at a single level/scale, e.g., genomic/proteomic, cellular, tissue, organ, organ system, whole body, behavior, and population. Less is being done to develop the tools, techniques, algorithms, and mathematical theory needed to integrate the continuum from the micro- to the macro-scale in a seamless fashion.”

Multiple agencies are providing research funding for the solicitation, including NSF, NIH, NASA, and DOE.

Around 20 awards are expected under the program, and no eligibility limitations have been specified. Award sizes are expected to range from $100,000 to $500,000 in total costs per year, with durations up to three years.

Required letters of intent are due September 22, and proposals are due November 9.

Further information is available at

Mayo Clinic to Use Blue Gene for Molecular Modeling

IBM and the Mayo Clinic said that they have extended a collaboration that began in 2001 to provide Mayo with access to IBM’s Blue Gene supercomputer.

Mayo will be the first medical institution to use Blue Gene, and will have “on demand” access to the system for molecular modeling.

IBM and Mayo Clinic said that under their collaboration so far, they have integrated 4.4 million patient records into a unified system based on a standard technology platform.

NCBI to Host ‘Powerscripting’ Course

The National Center for Biotechnology Information will host “NCBI PowerScripting,” a three-day course including lectures and computer workshops on effectively using the NCBI E-utilities within scripts to automate search and retrieval operations across the entire suite of 23 Entrez databases.

The course will be held Oct. 20-22, 2004 at the Lister Hill Center at the NIH campus in Bethesda, Md. It is intended for bioinformatics specialists who are interested in accessing NCBI data in an automated fashion. A working knowledge of NCBI resources and the Perl scripting language is required.

The course is free but an application is required. Space is limited to 20 participants.

Further information and an application are available at eutils/course.html.

Jubilant Integrates Content with OmniViz Pathway Software…

OmniViz and Jubilant Biosys have entered into a collaboration under which content from Jubilant’s PathArt database of manually curated pathways will be deployed within the OmniViz Pathway Enterprise (OPE) visualization software.

OPE is a pathway display, drawing, and analysis package, supporting enterprise-wide sharing and searching. It uses a biological object model for semantic integration of data, OmniViz said. “OPE is designed so that data from all relevant sources can be loaded. Adding the Jubilant Biosys PathArt content to the list is part of our continuing effort to make all the sources important to our customers available,” Jeffrey Saffer, president of OmniViz, said in a statement.

PathArt includes more than 900 signaling and metabolic pathways and more than 20 curated disease pathways, covering cancer, Alzheimer’s disease, arthritis, multiple sclerosis, asthma, arthrosclerosis, HIV, rheumatoid arthritis, and diabetes.

…and with FDA’s ArrayTrack Software

Jubilant said separately that it has integrated PathArt with the Food and Drug Administration’s microarray analysis package ArrayTrack.

“The integration will allow users of ArrayTrack to use the built-in plug-in to dynamically map the results of their analysis within ArrayTrack onto the pathways in PathArt,” said Sreenivas Devidas, vice president of business development and strategy at Jubilant, in a statement.

ArrayTrack is freely available at

Open Access Cancer Informatics Journal to Launch

Open access publisher Libertas Academica is preparing to launch a new journal, Cancer Informatics. James Lyons-Weiler, an assistant professor at the Center for Oncology Informatics at the University of Pittsburgh Cancer Institute, is editor-in-chief of the new journal, and 16 scientists have been selected for the journal’s editorial board.

Lyons-Weiler told BioInform that a “spate of papers” are in review now, and will be posted online as soon as the review process is complete. The journal is looking for sponsors to support publication costs — a model that deviates slightly from other open access journals that are supported by author fees. Lyons-Weiler said that the University of Pittsburgh is also working to set up a $1.5 million endowment to support the journal.

Lyons-Weiler noted that there is a “danger of a proliferation of informatics journals,” but said that Cancer Informatics has defined a “specialized niche” by focusing on informatics methods that will specifically advance cancer research. The target readership includes bioinformaticists as well as clinicians “who wouldn’t otherwise read a bioinformatics journal,” he said.

Further information and a call for papers are available at

NMSU to Create Bioinformatics Center with $4.5M NSF Grant

New Mexico State University said it has received a five-year, $4.5 million grant from the National Science Foundation to establish a new bioinformatics center.

Desh Ranjan, head of the department of computer science at NMSU, said in a statement that the university plans to offer a master’s degree program in bioinformatics in “about two years” and eventually a PhD program.

The new center will draw together researchers from the departments of computer science, biology and biochemistry, and agronomy and horticulture. In addition to Ranjan, who will serve as director of the center, associated faculty include Brook Milligan, associate professor of biology; Mary O’Connell, professor of agronomy and horticulture; Jing He, assistant professor of computer science; and Enrico Pontelli, associate professor of computer science.

Canadian Science Center DNA Core to Use Partek Pro Software

Partek said that it has licensed its Partek Pro statistical analysis software to the DNA Core Facility at the Canadian Science Center for Human and Animal Health.

The center plans to use the software for analyzing gene expression data.

Financial terms of the agreement were not provided.

Scottish Bioinformatics Research Network Secures £2.4M in Funding

The Scottish Bioinformatics Research Network, a consortium of Scottish universities and research institutes led by the University of Dundee, said last week that it has been awarded £2.4 million ($4.4 million) by the Scottish Higher Education Funding Council, the Scottish Executive Environment and Rural Affairs Department, and Scottish Enterprise.

The cash will be provided over four years, and is to be used to help “provide the necessary infrastructure to improve bioinformatics research in Scotland,” according to an SBRN statement.

The network includes the Universities of Dundee, Edinburgh, and Glasgow, the Scottish Crop Research Institute, Biomathematics and Statistics Scotland, and the Scottish Bioinformatics Forum — a “virtual” organization of researchers and bioinformatics customers in Scotland.

In addition to the £2.4 million from the Scottish agencies, the three universities have each contributed £420,000 of their own funds to the network.

Bioniche, University of Ottawa License Ocimum’s Genowiz…

Ocimum Biosolutions said that it has licensed its Genowiz microarray analysis software to the Bioniche Therapeutics Research Center of Bioniche Life Sciences Inc and to the University of Ottawa.

Financial details of the deals were not disclosed.

…While Four Groups License Genchek

Ocimum said separately that it licensed its Genchek sequence analysis software to the University of Washington, the University of Virginia, Alcorn State University, and Acuity Pharmaceuticals.

Ocimum CEO Anuradha Acharya said that Genchek is the company’s first and “most mature” product. The software integrates public and proprietary data in an integral database system that can be used to access, store, organize, and retrieve DNA, RNA, and protein sequences in an environment that also offers editing, management, and annotation of sequences.

Financial details of the deals were not disclosed.

Strand Partners with MediBic

Strand Genomics said it is partnering with Japanese pharmacogenomics firm MediBic to provide bioinformatics and data mining solutions in Japan.

MediBic and Strand will jointly develop products and technologies, and offer consulting and customization services, in the areas of genomics, proteomics, clinical studies, predictive ADME-tox, and other pharmaceutical R&D areas.

“One of MediBic’s [goals] has been to strengthen its informatics and pharmacogenomics capabilities through key strategic partnerships,” Yasuhiro Hashimoto, president and CEO of MediBic, said in a statement. “This partnership provides us with the platform to offer an integrated discovery and development system.”

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The Scan

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