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Entelos, ADA, Protein Data Bank, Insightful, CLC Bio, DNAStar, Ariadne Genomics, IDBS

ADA Expands Member Access to Entelos Realab ‘Virtual Mouse’ Platform
The American Diabetes Association and Entelos said this week that all ADA members now have free access to the Entelos Realab “virtual mouse” testing platform, which offers web access to the company’s computer model of type 1 diabetes.
ADA and Entelos began partnering a collaboration in 2006 to create an "in silico research facility" based on the company's type 1 diabetes PhysioLab platform, which represents the non-obese diabetic mouse [BioInform 06-16-06].
Entelos launched the web-based version of the platform via Realab last year [BioInform 05-25-07].
Researchers who wanted to access the technology initially had to apply through the ADA's peer-review grant process. Now, according to Richard Kahn, chief scientific and medical officer at the ADA, ADA health professional members can also access the online version for free.
“We believe that this will not only accelerate adoption of this innovative approach, it will also make a big impact on finding new therapies for type 1 diabetes,” Kahn said in a statement.
Researchers can use Realab to conduct simulations on drugs, drug combinations, dose levels, dosing regimens, therapeutic targets, and biological pathways and functions, Entelos said.
The company said it is also developing online Realab environments for rheumatoid arthritis, cardiovascular disease, and type 2 diabetes.

PDB Hits 50,000 Molecules, Anticipates Tripling by 2014
The Protein Data Bank said this week that the 50,000th molecular structure was deposited in the archive this month — a “significant milestone” for the 37-year-old resource.
PDB is managed by the worldwide Protein Data Bank consortium and is based at Rutgers University and the University of California, San Diego.
Initially launched in 1971 with seven structures at Brookhaven National Laboratory, the PDB now serves as the key repository for three-dimensional structures of large molecules and nucleic acids.
Today, the PDB archive receives around 25 new experimentally determined structures from scientists each day, according to a statement. More than 5 million files are downloaded from the PDB archive every month.
“We are estimating that the PDB will not only double but triple to 150,000 structures by 2014,” said Philip Bourne, associate director of the PDB and professor of pharmacology at the UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, in a statement.

Medical Prognosis Institute To Use Insightful’s S-Plus Software to Deploy R Code
Insightful said this week that Danish microarray services firm Medical Prognosis Institute has licensed its S-Plus 8 Enterprise Server platform for statistical data analysis and predictive analytics.
Medical Prognosis Institute will utilize S-Plus top deploy analytic models originally prototyped in R, the free open-source “dialect” of Insightful's S language, the company said.
"We selected S-Plus after a thorough review of applicable technologies, including R, which we have been using," said Steen Knudsen, chief scientific officer of Medical Prognosis Institute, in a statement.
Knudsen said that he was able to port the company’s R code into S-Plus in less than 20 hours.

CLC Bio to Develop Software for Potato Genome Study
CLC Bio said this week that it is partnering with several Danish research institutions to develop bioinformatics software for potato genomics research.
The project will include next-generation sequencing, digital gene expression, and bioinformatics technologies in order to learn more about how the potato could be engineered to satisfy food, energy, and chemical needs, the company said.
In addition to CLC Bio, the partnership includes the Institute of Food and Resource Economics and the Department of Plant Biology at Copenhagen University; Aarhus University; Aalborg University; Landbrugets Kartoffelfond; Andelskartoffelmelsfabrikken Vendsyssel; and Kartoffelmelscentralen.
The company said the project is centered on the potato because it produces twice the amount of energy per area as maize or wheat, “making it ideal for energy and food production.”
The project will analyze gene expression data for 40 growth conditions for 15 different cultivars.
CLC Bio said a number of new bioinformatics algorithms will be developed for the project and bundled into a comprehensive package that is based on CLC Bio’s workbench.

Prague Biotech Institutes License DNAStar's Software
Two research institutes in Prague, Czech Republic, will use DNAStar’s software for sequence analysis under a multi-site license agreement, the Madison, Wis.-based company said this week.
Under the agreement, two units of the Academy of Sciences of the Czech Republic will access the company’s Lasergene sequence analysis software for an unlimited number of users for a four-year period.
The agreement gives the Institute of Molecular Genetics and the Institute of Biotechnology access to the software, which offers a range of analysis tools for use in traditional and next-generation sequence analysis projects.
Financial terms of the agreements were not released.

Freiburg Researchers to Use Ariadne's Software, Databases
The Albert-Ludwigs University of Freiburg has licensed Ariadne Genomics’ software platform and databases for use in its mammalian, worm, and plant research programs, Ariadne said this week.
Under the license, Freiburg researchers will use Ariadne’s Pathway Studio, including MedScan, which extracts functional relationships from scientific texts.
The researchers also will use the ResNet Mammalian and Plant database, which includes information from PubMed and other journals about molecular interactions and holds around 1.5 million unique relationships.
Financial terms of the agreement were not released.

Boehringer Ingelheim to Use IDBS' Predictive Modeling Software
Boehringer Ingelheim researchers will use IDBS’ predictive modeling technology in its drug discovery research programs, IDBS said this week.
Pharmaceutical researchers at Boehringer Ingelheim’s Biberach an der Riss facility will use IDBS’ PredictionBase “to increase efficiency of the candidate identification process,” IDBS founder and CEO Neil Kipling said in a statement.
Guildford, UK-based IDBS said the scientists will use PredictionBase to build, deploy, and distribute predictive ADME quantitative structure-activity relationship models using existing data.
Financial terms of the agreement were not released.
In addition to its UK headquarters, IDBS has offices in California, New Jersey, and Massachusetts.

Filed under

The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.