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Ariadne, GeneGo, NIEHS, Mitrionics, Biodesign Institute, SmartGene, CSHL, OpenEye, Cornell University, Gene Network Sciences

Five Japanese Pharmaceutical Companies License Ariadne Pathway Studio Enterprise
Ariadne, which offers analysis and pathway-searching/molecular-interaction software, said this week that five Japanese pharmaceutical companies have licensed its Pathway Studio Enterprise, formerly known as Pathway Expert, as a primary tool for microarray, proteomics, and other experimental data analysis.
Ariadne said that sold the licenses through its distribution partner World Fusion, which has been marketing its products in Japan since 2004.
Ariadne did not name the five pharmaceutical companies that have licensed its software.  
Pathway Studio Enterprise includes an enterprise-class MedScan module, which enables databases to be updated daily, if necessary, through PubMed and online full-text journals. Targeted custom databases for specific research can be created in one to two days, the company said.

GeneGo Awarded Phase II Toxicogenomics Grant By NIEHS
GeneGo this week announced the receipt of a $750,000 Phase II Small Business Innovation Research grant from National Institute of Environmental Health Sciences for the development of functional descriptors for gene expression response to drugs and toxins.
The company plans to include the descriptors as part of its MetaTox toxicogenomics product line.

Mitrionics Secures $6M in VC Funding to Expand International
Operations and Product Development
Mitrionics, developer of the Mitrion Software Acceleration Platform software, has closed $6 million of venture capital funding from lead investor Grande Ventures as well as Creandum and Teknoinvest.
Mitrionics will use the funding to bolster its presence in the field programmable gate array-based accelerated computing market, expand its international sales and support operations, and increase its research and development efforts. 
The company claims that its accelerated applications can increase the speed of Blast and other applications up to 20 times or greater over traditional processors.

SFAz Awards Biodesign Institute $376K for Informatics, Genetic Imaging Technology
The Biodesign Institute at Arizona State University has received two research awards totaling $376,000 from the Science Foundation of Arizona to expand a bioinformatics database and to develop its genetic imaging technology.
Sudhir Kumar of the Biodesign Center for Evolutionary Functional Genomics received $142,000 to develop a database called the TimeTree, which is “a relational database of life on Earth that is easy to use for researchers, the public and K-12 students,” the institute said.
Neal Woodbury, director of the Biodesign Center for BioOptical Nanotechnology, received $234,000 to develop nanoscale techniques and imaging technologies to study gene regulatory networks of interest to biomedical research, the institute said.
Biodesign Institute spokesman Joe Caspermeyer said in an e-mail to BioInform’s sister publication GenomeWeb News that the institute is currently “ramping up our capabilities” in personalized medicine and bioinformatics, as well as other areas including convergence biology, public health and the environment.

SmartGene and SARL join Biotracer Consortium
SmartGene has signed a contract to develop a data analysis and management system dedicated to the typing of Campylobacter species as part of an EU project called Biotracer.
SmartGene specializes in the development and maintenance of databases for genetic information.
Biotracer will use the company’s Integrated Database Network System, which is designed for web-analysis and management of genetic data.
The Biotracer consortium will use multi-locus sequence typing method to survey the spread of Campylobacter infections.
SmartGene is collaborating with the Peter Kuhnert at the Institute for Veterinary Bacteriology of the University of Bern, Switzerland, as well as several dozen public and private partners from two dozen countries.

CSHL Gets $1.3M to Manage Data for NHGRI's ModENCODE Project
The National Human Genome Research Institute has awarded $1.3 million to Cold Spring Harbor Laboratory to coordinate the data that will come from its recently launched modEncode project, CSHL said Tuesday.
CSHR researcher Lincoln Stein will lead the data-coordination project.
On Monday, NHGRI said that it had awarded a total of $57 million to 10 research facilities under the modENCODE project, which aims to identify functional elements in the genomes of the model organisms Drosophila melanogaster and Caenorhabditis elegans.
The data from the modENCODE initiative is expected to be useful for genomic studies for humans and other organisms.
The CSHL data-coordination center will collaborate with computer scientists in the UK and in California to integrate the genomic data into a centralized database and combine it with public information from other sources.
The information then will be publicly available online.
Stein said in a statement that the project will "open an unprecedented window to how the elements of the genome influence the development of roundworms and fruit flies and how they respond to the environment." 

OpenEye to Integrate Scientific Software Apps with Altair Engineering’s PBS Pro
Altair Engineering recently announced a partnership with OpenEye Scientific Software to fuse several of OpenEye’s applications with Altair’s PBS Professional grid-management software.
OpenEye offers molecular modeling and cheminformatics software to the pharma industry. Its FRED software is a protein-ligand docking program that scores possible positions of each ligand in an active site. Another offering, Omega, is a general-purpose conformer-generation program tailored for use with large libraries used in computer-aided drug design.
Bill Nitzberg, CTO for Altair’s PBS GridWorks business unit, said that pharmaceutical and biotech firms are starting to realize that grid computing “can be an important source of competitive advantage in drug development and research.”

Cornell University and Gene Network Sciences Awarded Army Bioremediation Grant
The US Army has funneled grant money into the hands of Cornell University and Gene Network Services for a project entitled “Systems Biology of Dehalococcoides: Using Network Inference Modeling to Integrate Omics Datasets Under Varied Conditions.”
The funds will be used to build computational models of the bacteria Dehalococcoides.
Cornell’s Ruth Richardson, Stephen Zinder, James Gosset, along with GNS lead investigator Bruce Church, will spearhead the joint Cornell-GNS team.
Richardson’s team will experiment on generating gene expression, proteomics, and other molecular-level data from the bacteria, subjecting it to various conditions.
Colin Hill, CEO of Gene Network Sciences, said in a statement that the company’s technology contributes an “ability to rapidly integrate diverse data types to create casual and quantitative biological models.”

Filed under

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.