The California Institute of Technology has released a database of predicted genetic interactions in C. elegans at http://tenaya.caltech.edu:8000/predict/. A paper describing the database and the computational methods developed to create it was recently published [Zhong W, Sternberg PW. Genome-wide prediction of C. elegans genetic interactions. Science. 2006 Mar 10;311(5766):1481-4]. The genetic interaction network includes 2,254 genes and 18,183 interactions.
3rd Millennium has released ARDAS (Array Repository and Data Analysis System) 2.0, a data-management and -analysis platform for microarray data. ARDAS includes a LIMS for managing the collection of data from two-color spotted arrays; an Analysis Information Management System (AIMS) that integrates a workflow engine with computational tools for the analysis of two-color and Affymetrix data; and a data warehouse for storing both raw and normalized data sets.
Agilent Technologies has released MassHunter Workstation, software for its new 6000 Series triple quadrupole and quadrupole time-of-flight LC/MS systems. The MassHunter Workstation software supports instrument control, data acquisition, qualitative and quantitative analysis, and reporting. Agilent also released a range of application-specific software to complement the MassHunter Workstation software, including MassHunter Profiling software for comparative expression analysis, MassHunter Bioconfirmation software for characterizing recombinant proteins or synthetic peptides, and an upgraded version of Spectrum Mill for high-throughput protein identification, characterization, and quantitation.
MIRA V2.5.4, a freely available sequence assembly program for genome and EST sequences, is available at http://chevreux.org/mira_downloads.html. Enhancements include a new routine for fast all-against-all overlap checking, which was added to handle sequencing reads from 454 data.
Inpharmatica has released a new version of its Admensa Interactive compound-optimization platform, which includes ADME Edition a range of validated ADME QSAR models for desktop installation, P450 Edition a set of quantum-based models that predict sites of P450 metabolism on chemical compounds, and Professional Edition which combines the ADME QSAR and P450 quantum models.
Nonlinear Dynamics has added SameSpots, a new spot-detection algorithm, to its TT900 S2S software for 2D gel analysis. The combined technologies "eliminate the problem of missing values within 2D gel image analysis data," according to the company.
Aureus Pharma has released AurWEB, a web portal that offers access to all of the company's AurScope databases and applications. AurWEB is available on a subscription basis and includes access to the company's GPCR, ion channel, kinase, ADME/drug-drug interactions, and hERG databases.
Gene Codes has released Sequencher 4.6. The latest version of the company's DNA sequencing analysis software includes a Variance Table for identifying SNPs and heterozygotes across large collections of sequences. Sequencher 4.6 also offers improved integration of GenBank features, which allows users to customize how features are imported and displayed on their sequences.
The National Center for Biotechnology Information has released a beta version of MINiML, a new data exchange format for microarray gene expression data, at http://www.ncbi.nlm.nih.gov/projects/geo/info/MINiML.html. MINiML (MIAME Notation in Markup Language) captures all components of the MIAME checklist, as well as any additional information that the submitter wants to provide, and uses XML Schema as syntax. NCBI's Gene Expression Omnibus (GEO) database supports both data submissions and data retrievals in MINiML, which is an XML version of SOFT (Simple Omnibus Format in Text), the data exchange format that GEO was using previously.
Massively Parallel Technologies has added Blast support for the complete UniGene library to its BioTech Virtual Power Center, available at http://www.mptbiotech.com.