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University of Florida, Ariadne, Johns Hopkins, GeneBio, Proxeon, TGen, BioDiscovery, caBIG, NCI, TNO, Linguamatics, Genedata, FDA

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University of Florida Renews Site License for Ariadne’s Pathway Studio
 
Ariadne announced this week that the University of Florida has renewed its site license for Pathway Studio, which researchers have been using for medical and agricultural-related gene expression and proteomics.
 
Pathway Studio helps scientists create visual interactive networks of biological relationships that are extracted from scientific literature and reference data sources.
 
The license is available to scientists at the University of Florida’s Interdisciplinary Center for Biotechnology Research Bioinformatics Core, which is equipped with a server farm and various types of open source and commercial software.
 
“We work on many of non-model organisms and create microarrays for them using 454 and Agilent technologies,” Li Liu, bioinformatics director at the ICBR Bioinformatics Core, said in a statement. “After mapping genes from these non-model organisms to model organisms, we use Pathway Studio to explore the gene networks.”
 

 
GeneBio and Proxeon to Integrate Phenyx and ProteinCenter
 
Geneva Bioinformatics and Proxeon have signed an integration and distribution agreement focused on GeneBio's Phenyx protein identification platform and Proxeon's ProteinCenter data interpretation software.
 
Under the terms of the deal, GeneBio's Phenyx will be integrated with Proxeon's ProteinCenter to make interpreting mass spectrometry data more efficient, for example through direct links from Phenyx identifications to ProteinCenter and specific Phenyx exports loaded into ProteinCenter.
 
ProteinCenter is based on a biologically annotated, protein sequence database derived from all major protein databases. It gives scientists one tool to filter data, group proteins, and perform statistical bioinformatics analysis on either single or combined proteomics search results. Users stand to benefit from having the possibility to interpret their data through one analytical tool, the companies said in a statement.  
 
Phenyx was developed in collaboration with the Swiss Institute of Bioinformatics to identify and characterize proteins and peptides from mass spectrometry data and is geared toward high-throughput MS data analysis.
 
The collaboration has a co-marketing aspect: ProteinCenter will be distributed through Proxeon and GeneBio’s sales channels, while GeneBio will continue as the supplier of Phenyx.
 
Financial terms of the deal were not disclosed.
 

 
TGen Spins Out Oncology Data Resource
 
Arizona’s Translational Genomics Research Institute said that it has spun out a new company that will offer a data resource for clinical oncologists to include genetic information discovered by TGen.
 
MedTrust Online, which is based in Scottsdale, will be a web-based resource that will serve as a “one-stop medical information resource” for oncologists, the company said.
 
The new company will offer information about potential drug therapies and a consultation service allowing doctors to discuss difficult cases with experts.
 
MedTrust said that cancer care provider South Texas Oncology and Hematology is helping to develop the MedTrust website, which is expected to launch in December.
 
MedTrust spun out of TGen Accelerator Management, which is aimed at translating TGen’s genetics research into medical treatments and services, TGen said.
 
MaryAnn Guerra, TGen’s chief business officer and president of TGen Accelerator, said in a statement this is the first informatics-focused business spinout for the non-profit institute, and it “marks a beginning in the effort to use the vast knowledge generated by TGen scientists for the commercial benefit of doctors and the general public.”
 
TGen said it signed a licensing and services agreement with MedTrust Online in early August that covered the use of TGen’s technologies and personnel.
 
Financial terms of the license agreement were not released.
 

 
Johns Hopkins To Use Nexus Expression for Gene Regulation Analysis
 
BioDiscovery said this week that Johns Hopkins Medical Institute has acquired a multi-seat license for Nexus Expression, a tool for microarray gene expression analysis that supports all array platforms including Affymetrix, Agilent, Illumina, Roche NimbleGen, and custom arrays
 
Nexus Expression “combines statistical rigor at the back end while allowing the user maximum flexibility at the front end allowing him/her to view any selected subset of genes in heat map form for all samples in a project with immediate data capture and annotation linkouts readily available at all stages of the analysis,” said Chris Cheadle, director of the Lowe Family Genomics Core at Johns Hopkins Bayview Medical Center, in a statement.
 
Nexus provides both functional annotation, enrichment analysis, and gene set analysis in real time and also allows the user to input custom lists of genes for advanced signature analysis. “We are encouraging our clients to consider the use of this tool for comprehensive microarray data mining," Cheadle said.
 
Financial terms of the license were not released.
 

 
NCI Names Three New caBIG Support Service Providers
 
The National Cancer Institute’s Cancer Biomedical Informatics Grid project this week named Semantic Bits, ScenPro, and Terrapin Systems as caBIG Support Service Providers, a designation that allows them to market their services as part of the caBIG Support Service Providers Program. 
 
The caBIG Support Service Providers are independent entities that meet specific criteria for performance of support services needed by the caBIG community, NCI said. 
 
There are four categories of support: Help Desk Support; Adaptation and Enhancement of caBIG-Compatible Software Applications; Deployment Support for caBIG Software Applications; and Documentation and Training Materials and Services. 
 
NCI added that it is currently accepting applications for additional caBIG Support Service Providers here.
 

 
TNO to Use Linguamatics Text-Mining Platform for Food Safety Alerting System
 
Linguamatics said this week that food safety firm TNO is using its I2E text-mining platform to help develop a food-safety alerting system for use by risk managers in industry and government agencies.
 
Fred van de Brug, project leader at TNO, said that by combining TNO’s knowledge of food safety issues with information mined from the scientific literature and news articles, “risk managers can gain early awareness and intelligence about possible risks to food production.”
 
Van de Brug added that TNO chose I2E “because of its flexibility and power to increase precision and recall of relevant information."
 
Financial terms of the agreement were not provided.
 

 
Genedata Extends Licensing Deal with FDA
 
Genedata said this week that it has extended its bioinformatics licensing deal with the US Food and Drug Administration’s National Center for Toxicological Research.
 
NCTR is using Genedata’s Expressionist biomarker discovery platform, which integrates transcriptomics, proteomics, and metabolomics data in a single enterprise software system. Genedata did not disclose the length or further terms of the agreement.
 
Weida Tong, director of the Center for Toxicoinformatics at FDA, said that the agency has used the Expressionist platform in a number of projects including Critical Path and the Liver Toxicity Knowledge Base project.

Filed under

The Scan

Booster for At-Risk

The New York Times reports that the US Food and Drug Administration has authorized a third dose of the Pfizer-BioNTech SARS-CoV-2 vaccine for people 65 and older or at increased risk.

Preprints OK to Mention Again

Nature News reports the Australian Research Council has changed its new policy and now allows preprints to be cited in grant applications.

Hundreds of Millions More to Share

The US plans to purchase and donate 500 million additional SARS-CoV-2 vaccine doses, according to the Washington Post.

Nature Papers Examine Molecular Program Differences Influencing Neural Cells, Population History of Polynesia

In Nature this week: changes in molecular program during embryonic development leads to different neural cell types, and more.