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IBM middleware, GeneDirector, FinchTV, Finch Sequencing Center, DNAsis Max, Prospect Pro, UCSC Genome Browser, Ensembl


As part of its industry-specific software effort [BioInform 12-08-03], IBM last week launched new middleware solutions for the life sciences domain: Corporate Information Asset Management, Investigator Recruitment and Trials Management, Clinical Genomics, Clinical Trials Management, and Annotations and Knowledge Sharing.

BioDiscovery has released version 2.6 of its GeneDirector enterprise microarray data management platform for spotted arrays and Affymetrix arrays. The new release is integrated with the Affymetrix GeneChip Operation System version 1.1 and includes a standardized data cleansing process.

Geospiza last week released the Finch Trace Viewer, FinchTV, a freely available software utility for viewing DNA sequencing chromatogram files. The utility is available at The company also said that it plans to release the Finch Sequencing Center for the Power Mac G5 in April, with pricing starting at $9,995.

MiraiBio said it plans to release version 2.5 of its DNAsis Max sequence analysis software in April. New customers can purchase version 2.0 of the software (free trial available at, and receive the upgrade to v2.5 at no additional charge, the company said.

Bioinformatics Solutions has released version 3 of its Prospect Pro protein structure prediction software. New features include a PyMol-based 3D alignment viewer that allows users to view and manipulate the sequence and structure of predicted proteins; an interactive batch command line; and an updated PDB template library.

The UCSC Genome Browser and Ensembl have both added data from the draft assembly of the chicken (Gallus domesticus) genome produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis. The genome has been sequenced to 6.63X coverage, and around 88 percent of the sequence has been anchored to chromosomes. Bulk downloads of the chicken sequence and annotations are available from the UCSC Genome Browser FTP server at Ensembl has posted a pre-annotated version of the genome at

The European Arabidopsis Stock Center has released an Arabidopsis thaliana Ensembl genome browser at The browser includes data from annotation centers other than the Ensembl pipeline gene build and uses two independent genome assemblies: one from the Institute for Genomic Research, and one from the Munich Information Center for Protein Sequences.


Filed under

The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.