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Compugen, National Science Foundation, BioTeam, MandrakeSoft, NTT Software, Riken Genomic Sciences Center, Weizmann Institute, Ensembl


Compugen has released version 3.0 of its Z3 2D-gel analysis system. The new version includes, among other features, clustering capabilities, which enable researchers to better understand protein pathways for drug discovery and development.

The National Science Foundation has released its NMI-R2 (National Middleware Initiative Release 2.0) suite of grid middleware. The package, which includes the GRIDS (Grid Research Integration Deployment and Support) software suite and NMI-EDIT (Enterprise and Desktop Integration Technologies) components, integrates key software packages, standards, and best practices for science, engineering, and education, and is freely available at

A version of HMMER 2.2 that has been enhanced to run on Apple’s Altivec vector co-processor is available from bioinformatics consulting firm BioTeam. The company wrote a binary Mac OS X installer for the enhanced version, developed by Stanford’s Erik Lindahl. Source code and installer are available at and, respectively.

Paris-based Linux distributor MandrakeSoft has released a new Linux clustering package named CLIC. Released under the GPL, the current package, available at, contains everything needed to quickly deploy a ready-to-run cluster, according to the company. Future releases, expected throughout 2003, will offer specialized administration, control and monitoring tools for the clustering solution, support for Itanium 2, and specialized tools for development in a parallel environment.

Tokyo’s NTT Software has released a series of bioinformatics products called VisualBio. The software, co-developed by NTT Software and the Riken Genomic Sciences Center, visualizes gene sequence information using four components: annotation, clustering, microarray display, and expression analysis. Pricing starts at $16,129. Further information is available at: en/index.html.

GeneCards version 2.26 is now available from the Weizmann Institute at: cards/index.html. The new release contains 44,738 entries with 3,385 new cards for novel genes predicted by Ensembl.

Filed under

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.