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SNPbrowser, BioCluster Grid, BioBox, Sun N1 Grid Engine 6.0, Zv3 Zebrafish, caCORE 2.1.1, Isentris, ISIS

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Applied Biosystems has released an enhanced version of its SNPbrowser software, which now includes data on 20 million genotypes obtained from 160,000 SNPs typed on 180 individuals across four populations.

ABI said in a statement that the software is designed “to facilitate the ordering” of its “expanding collection of 1.8 million TaqMan SNP genotyping assays.”

The software is available for free at http://www.allsnps.com/snpbrowser.


The Sun Asia Pacific Science and Technology Center has released a new version of BioCluster Grid as part of the BioBox initiative at http://apstc.sun.com.sg/bioinformatics/biobox.php.

The BioCluster Grid is now integrated with Sun N1 Grid Engine 6.0 and has Redhat Linux binaries for the applications as well as Solaris.


The University of California, Santa Cruz, has released the Zv3 Zebrafish genome preliminary assembly (UCSC version danRer1) on the UCSC Genome Browser and Blat server. The assembly contains 1,459,115,486 base pairs in 58,339 supercontigs, with a sequence coverage of approximately 5.7X. UCSC plans to release the Zv4 version of the assembly in the Genome Browser in the fall.


The NCI Center for Bioinformatics has released caCORE 2.1.1, a maintenance release of the cancer informatics infrastructure, at http://ncicb.nci.nih.gov/core. NCIB said that the next major caCORE release is planned for the end of the calendar year.


MDL said it will be demonstrating its newly released Isentris n-tier discovery informatics platform at Drug Discovery Technology in Boston this week.

The platform is the successor to MDL’s ISIS integration platform for biological and chemical data, and offers an integration engine in combination with a workflow management solution, the company explained.

 

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.