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SRS 8.0, DNASIS GeneIndex, ENCODE portal, ORNL Genome Channel GrailExp, Progenesis 2D, Quantum 2.0

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Lion Bioscience has released SRS 8.0. The latest version of this integration platform offers web service capability; Java servlets; support for large sequence entries so that users can work with whole genomes in a single view; pre-defined queries and link views; and a quick search page that can be customized to show preferred queries.


MiraiBio said that it will launch version 3.5 of its DNASIS GeneIndex web-based data mining service on July 1. GeneIndex allows users to query more than 20 public and commercial biological databases using a single query search system. The system also retrieves sequence-related information from journal abstracts using weighted keywords and a proprietary search engine. Databases accessible through the system include Genbank/DDBJ/ EMBL, SAGEmap, UniGene, RefSeq, dbSNP, HomoloGene, TrEMBL, PubMed, KEGG, PDB, LocusLink, Swis-Prot, Prosite, and Pfam.


The University of California Santa Cruz genome bioinformatics group has released the ENCODE portal — a version of the UCSC Genome Browser tailored to the ENCODE (Encyclopedia of DNA Elements) project community. Resources include sequences for the current human assemblies (hg16, hg15, hg13, and hg12); sequences of the comparative species from ‘s Intramural Sequencing Center; tools for coordinate conversion between human assemblies; format de- scriptions for data submission; and contact information for help with submitting annotation data and analyses. Bulk downloads of the sequence and annotations are also available. The ENCODE portal is http://genome.ucsc.edu/encode.


Oak Ridge National Laboratory’s Life Sciences Division has released the ORNL Genome Channel GrailExp genes for NCBI human build 34.1 at http://compbio.ornl.gov/channel/index.html. The new version of the database was built with ORNL’s EXP6 gene-finding algorithm, which uses both ESTs and proteins for evidence of putative genes.


Nonlinear Dynamics has released a new version of its Progenesis 2D gel analysis software. The new release includes enhanced cross-stain analysis technology, which allows users to analyze multiplexed 2D gels. The software also includes INCA (Intelligent Noise Correction Algorithm), a proprietary algorithm developed to reduce image noise.


Quantum Pharmaceuticals has released Quantum 2.0, the latest version of its protein docking software. The company said it has improved the method of calculation of entropy loss for protein-ligand complexes and has also added a new model of the water environment along with electrostatic and Van der Waals energy contributions for flexible molecules.

Filed under

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.