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Realab, RefSeq 23, Beacon Designer, FABLE 3.0, BioXM 2.4

The American Diabetes Association and Entelos have launched Realab, a simulation tool that offers web access to Entelos’ computer model of type 1 diabetes.
Researchers can use Realab to conduct simulations on drugs, drug combinations, dose levels, dosing regimens, therapeutic targets, biological pathways, and functions. Simulation results are available within 24 hours, Entelos said.
The ADA and Entelos collaborated to develop the Type 1 Diabetes PhysioLab platform, a computer model of the non-obese diabetic mouse, which underlies Realab for type 1 diabetes.

RefSeq 23 is available here from the NationalCenter for Biotechnology Information. RefSeq 23 includes 5,503,385 records from 3,648,590 proteins and sequences from 4,300 different organisms. The number of species represented in each release sub-directory includes 4,300 complete species, 77 fungi, 277 invertebrate, 1,115 microbial, 1,143 mitochondrion, 100 plant, 531 plastid, 82 protozoa, 215 mammalian, 555 other vertebrate, and 1849 viral.

Premier Biosoft has released Version 7 of Beacon Designer with support for Scorpions assays. The company claims that the software is the only product that supports all qPCR chemistries. Beacon Designer, a desktop tool for designing real-time PCR assays, has been bolstered to better perform under fast cycling conditions, making the technology a fit for applications such as viral load testing and pharmacogenomics, the company said. Beacon Designer designs oligos for SybR Green, TaqMan, LNA spiked TaqMan, MethylLight, molecular beacon, NASBA, and FRET assays.

FABLE (Fast Automated Biomedical Literature Extraction) version 3.0 is now available from the Children’s Hospital of Philadelphia here. Among its features, 3.0 includes a literature-enabled local mirror of the University of California, Santa Cruz, Genome Browser with a literature track called LitTrack that connects journal articles with genome locations of genes referenced in the articles. The new release also uses updated hardware for faster searches. FABLE performs gene-based extraction of information from Medline abstracts, including the identification of abstracts mentioning a human gene, the generation of lists of human genes associated sets of keywords, and the viewing of abstracts as an annotation track aligned to the human genome sequence assembly.

BioMax has released BioXM 2.4, a data-integration and data-management platform for high-throughput “-omics” research based on semantic technologies.
The framework now provides integrated text mining, combining biological and medical term dictionaries with a free-text querying facility, the company said.
BioXM 2.4 also includes support for web services, which allows organizations to more easily build their own applications on top of a BioXM server. The software now supports Mac OSX X as a client platform and Open Document formats for data exchange.
The updated BioXM framework also includes an optional text-mining module, which combines biological and medical term dictionaries with free-text querying capabilities.

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The Scan

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In Science this week: genome-wide association study ties variants to white matter stricture in the brain, and more.