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Kenneth Coleman, Paula Jasper, Chuck Albright, Daniel Atkins, Nicola Day, TargetSeq Resequencing System, Y-Bio Cluster, SynaBlast, PathwayStudio 4.0., Lasergene 7, Sofia KnowledgeScan, Sorcerer Online


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Applied Biosystems has launched its TargetSeq Resequencing System, a new software system for high-throughput directed or medical sequencing designed for use with the company's 3730 and 3730xl DNA Analyzers. TargetSeq includes a software module for the sequencing of individual gene exons or other small DNA fragments. ABI said that the system can produce 200 to 400 base pair sequencing reads in 20 minutes or less, which increases the daily production capacity of the 3730 series instruments to more than 2.8 megabases or 6,912 samples per day. TargetSeq also includes a new version of the company's KB Basecaller software that is optimized for heterozygote/mixed base detection and includes added flexibility for de novo and directed sequencing applications.

Terra Soft Solutions has launched the Y-Bio Cluster, a pre-configured 8-node Xserve bioinformatics cluster. The default configuration of the Y-Bio cluster includes XRack Pro 2 mobile cluster housing; a dual 2.0 GHz G5 Xserve head node with 4 GB RAM and 1 TB storage; theY-HPC 64-bit OS and Cluster Construction/Management Suite; and the Y-Bio bioinformatics suite, which includes NCBI Blast, EMBOSS, Glimmer, ClustalW, HMMER, Wise, and Fasta.

Synamatix has released SynaBlast, a sequence similarity search tool that is freely available via the company's online bioinformatics applications platform, MGRC (My Genomics Resource Center), at SynaBlast is based on the company's SynaSearch application and is built upon the SynaBase structured-network-pattern database platform. According the company, SynaBlast is useful for identifying shorter functional domains, which Blast often misses.

Ariadne Genomics has released PathwayStudio 4.0. The new version of its pathway analysis software (formerly called PathwayAssist) includes new tools for microarray data analysis and pathway dynamics simulation, as well as more than 1,000 reconstructed pathways. PathwayStudio 4.0 also includes new tools for building relevance networks from gene expression data, Ariadne's MedScan Reader biomedical literature browser, and ResNet Core, a database of 50,000 validated facts. The software is fully backwards compatible with previous versions called PathwayAssist, the company said.

DNAStar has released Lasergene 7. The sequence analysis software package now includes automated virtual cloning, enhanced SNP discovery, and primer walking and bootstrapping.

BioWisdom has launched Sofia KnowledgeScan, a service based on the company's Sofia Intelligence Platform that provides information to support healthcare-related decision making. The service analyzes available data "to tease out intelligence that is relevant to specific commercially sensitive medical issues such as unexpected side-effects or toxicities," the company said in a statement.

Sage-N Research has launched Sorcerer Online, a web-based service for high-throughput protein identification. The service is targeted to proteomics researchers who need faster searches, but are not ready to install the FPGA-based Sorcerer appliance in their laboratory. Version 1.0 of Sorcerer Online offers searches of up to 10,000 MS-MS spectra against a variety of databases with options for mass settings and other parameters. It supports searches in Sequest format, as well as the PeptideProphet and ProteinProphet tools from the Institute of Systems Biology. Free trials are available at

The BioPAX (Biological Pathways Exchange) workgroup has released BioPAX Level 2 v1.0 at The release supports representation of metabolic pathways, molecular interaction databases, and "some aspects" of signal transduction, such as protein post-translational modifications, according to an announcement from the workgroup. Subsequent levels will support signaling pathways, gene regulatory, and genetic interaction networks.

Johns Hopkins University has released GeneDesign, a program for automating the design of artificial pieces of DNA, at The software includes six modules that can be used individually or in series to automate the tasks required to design and manipulate synthetic DNA sequences.

The European Bioinformatics Institute has released BioMart 0.4 at The new version of the query-oriented data management system allows users to federate BioMart databases over port 80 and supports restricted data access so that different users can see different parts of the data according to their privileges.

The International Tandem Repeat Consortium has launched MicroSat DB, a database of human microsatellites, at The ITRC said that its goal is to characterize hundreds of thousands of tandem repeats in diverse organisms, release this data into the database, and to integrate the information into existing genome databases.


People in the News

Kenneth Coleman has been elected non-executive chairman of Accelrys' board of directors. Coleman has served as a director since May 2003 and has been the company's independent lead director since May 2004. In a filing with the US Securities and Exchange Commission, Accelrys disclosed that the board approved an increase in Coleman's annual retainer from $75,000 to $100,000. The board also approved an increase in the annual retainers payable to the other independent members of the board from $25,000 to $30,000.

Geospiza said last week that Paula Jasper has joined the company as senior account executive, and Chuck Albright has been hired as director of product technology. Jasper was most recently director of technical sales and business development at Proligo. Prior to that, she was Western regional sales manager for the Codelink microarray product line in Motorola's Life Sciences Division. She has also worked for Agilent Technologies, IGEN International, and Pharmacia Biotech. Albright is a former Boeing executive, manager, and engineer.

The National Science Foundation has tapped Daniel Atkins to head its newly created Office of Cyberinfrastructure. Atkins is a professor in the School of Information and in the Department of Electrical and Computer Engineering at the University of Michigan, Ann Arbor. He will join NSF on June 5 as director of the OCI, which has a fiscal year 2006 budget of $127 million. NSF said that President Bush's budget request for OCI in FY 2007 calls for $182.4 million — an increase of 43.5 percent. Created in June 2005, OCI makes "competitive, merit-reviewed awards for leading-edge, IT-based infrastructure increasingly essential to science and engineering leadership in the 21st century," NSF said.

BioWisdom has hired Nicola Day as a healthcare analyst. She will work in the company's Healthcare Intelligence Services group to provide unbiased analysis of drug development issues to the pharmaceutical industry as part of BioWisdom's newly launched Sofia KnowledgeScan offering (see downloads and upgrades, above). Day joins BioWisdom from GlaxoSmithKline where she was involved in the management of a number of drug-development programs.

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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.