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SoftGenetics, GulfStream Bioinformatics, NCBI, Tripos, Pubreminer, Thermo Electron, and more ...


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SoftGenetics has released Mutation Surveyor 3.0. The new version of the company's mutation identification software includes raw data processing to correct for "poor early sequence mobility issues observed with the latest capillary sequencing systems and KB Basecaller from applied BioSystems," the company said. The software also includes an automated methylation detection application; enhanced het-indel detection algorithms, quantification of heterozygote and methylation, and intelligent base call editing.

GulfStream Bioinformatics has released BIGR 5.0, a new version of the biosample management system that was originally developed to manage the biobanking operations of Ardais [BioInform 05-05-06].The new version includes improved process and workflow control, clinical data annotation, and collaborative data management.

The National Center for Biotechnology Information has upgraded several of its resources. Blast results can now be shown using a new "TreeView" dendrogram, which clusters hits on the basis of the Blast using one of two methods, fast minimal evolution or neighbor joining. The NCBI Blast page is at: NCBI has also added its annotation of Mouse Genome Build 36.1 to the Map Viewer at, and has released RefSeq 17 at This release includes genomic, transcript, and protein data available as of May 1, and includes 2,631,538 proteins and sequences from 3,497 different organisms.

Tripos has released Benchware 3D Explorer 2.2, a new version of its 3D chemical information software that was formerly marketed as Lithium. The software now supports visualization of pharmacophore models and 3D molecular queries, and offers expanded representation of chemical structures and molecular interactions. In addition, Benchware 3D Explorer's VBA scripting environment is now included as a standard feature in the application. A free evaluation copy is available at

Pubreminer, a web-based tool for mining PubMed, is available from the University of Amsterdam at Pubreminer enables text-based query building and presents its results in frequency tables of journals, authors, and words, which can be included or excluded in an iterative fashion in order to refine the search.

Thermo Electron has released MetWorks, a software product for metabolite identification. MetWorks uses an extensive fragmentation library to compare sample and control files and elucidate the structure of compounds.

Varian has released Quick Access, a product that enables users of its MS Workstation software to direct operator workflows and manage multiple systems from a single computer. A single MS "administrator" can use the system to set up methods and monitor analyses for dozens of users, the company said. The company is accepting orders for Quick Access now with delivery scheduled to begin in July.

Premier Biosoft has released AlleleID 3. The software package for designing pathogen identification assays for both qPCR and microarrays now includes support for TaqMan Minor Groove Binding probes.

FlyMine 5.0, an integrated database of genomic, expression and protein data from Drosophila, Anopheles, and C. elegans, is available at New features include genome annotation for D. pseudoobscura and A. mellifera.

PDS Pathology Data Systems has added a hosted licensing model for customers who wish to access its software via the Internet. Hosted services are available for PathData, the company's system for preclinical pathology; ToxData, a system for toxicology and clinical pathology; and ReproData, a new system for reproductive toxicology and teratology.


People in the News

Genome Canada has appointed Michael Morgan as chief scientific officer. Morgan was formerly chief executive officer of the Wellcome Trust Genome Campus. He joined the Wellcome Trust in 1983 and was responsible for the development of several initiatives, including the International Human Genome Sequencing Project, the Mouse Sequencing Project, the UK Synchrotron, DIAMOND, the SNP Consortium, and the Structural Genomics Consortium.

David Sankaran is resigning as senior vice president and chief financial officer of Accelrys. He will continue in his role and assist the company with the search for a new CFO until Aug. 31. In an 8-K filing with the US Securities and Exchange Commission, Accelrys said that it will pay Sankaran $112,500, and "may" pay a discretionary bonus of up to $37,500.

The Society for Biomolecular Sciences has awarded its 2006 Accomplishment Award to Robert Pearlman, a member of the faculty of the College of Pharmacy at the University of Texas at Austin. SBS recognized Pearlman for his development of the DiverseSolutions software for assessing chemical compound collections. Pearlman founded Optive Research in 2003, which was acquired by Tripos in 2005.

The SBS Accomplishment Award consists of $1,000, recognition in the Journal of Biomolecular Screening, and a plaque. It is presented annually to an SBS member who has distinguished himself or herself "in advancing the art and science of drug discovery." The award presentation will take place during the Annual SBS Conference & Exhibition in Seattle, Wash., Sept. 17-21, 2006s.

Filed under

The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.