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MetaCore 3.0, PathwayExpert, Cell Component Ontology, Pathway Builder 2.0, ADMET Predictor, Merlin 1.0.0, Biopython 1.41, Ensembl 35, Migration Agent, Entrez Gene, and more


Downloads & Upgrades

GeneGo has released MetaCore 3.0. The new version allows scientists to build combined signaling/metabolic networks from gene-expression, proteomics, metabolomics, high-content screening, siRNA, and other types of experimental data. MetaCore 3.0 also includes a parser for visualizing metabolomics data in the context of pathways, and adds an enterprise-wide data-management and user-access system.

Ariadne Genomics said that it plans to launch PathwayExpert, an enterprise-class software platform for pathway analysis, later this year. PathwayExpert will allow scientists to analyze microarray and proteomics data, create and share custom pathways for diseases, drug targets, and biomarkers, and mine the scientific literature. The new platform will add to Ariadne's PathwayAssist desktop product and PathwayStudio client-server platform. Ariadne said that several companies have agreed to beta-test the new platform. Further details on the beta-test program are available at

The MetaCyc project has released a Cell Component Ontology at The CCO was developed to provide a controlled vocabulary of terms for annotating the subcellular locations of enzymes and compartments involved in transport reactions in the MetaCyc biochemical pathway database and contains 160 terms, many adopted from GO. The ontology can be downloaded in either OWL format or Ocelot format.

Protein Lounge has released Pathway Builder 2.0, a software tool for drawing signal transduction pathways. Pathway items such as membranes, protein/receptor shapes, and organelles are pre-made so users can select the items and arrange the pathway. A demo is available at

Simulations Plus has released a new hERG toxicity prediction model that extends the capabilities of its ADMET Predictor software into potential cardiac toxicity. The new model adds to six existing toxicity predictions that are currently in ADMET Predictor. The hERG (human Ether-a-go-go Related Gene) encodes potassium channels, which are responsible for the normal repolarization of the cardiac action potential.

The University of Michigan has released Merlin 1.0.0 at The release includes maximum likelihood allele frequencies estimation, parametric analysis with liability classes, an improved random number generator, and haplotype frequency estimates for long clusters of markers.

Biopython 1.41 is available at The release includes a Bio.MEME module, updates to the Blast parser, a new BLAT parser, updates in Bio.PDB, and improved user-friendliness in Bio.Seq.

Ensembl 35 is available at The release includes genome data for opossum (Monodelphis domestica), as well as minor updates for chimp, human, mouse, chicken, bee, and worm.

Thermo Electron has launched Migration Agent, a professional services and software offering to help customers migrate from an existing laboratory information management system to a Thermo LIMS. Migration Agent includes services staff and an ETL (extract, transform, and load) tool to migrate data to the new system in a six-step process.

The National Center for Biotechnology Information has added interaction data from EcoCyc and HPRD to Entrez Gene. The data are available for browsing as well as for bulk transfer by ftp. Interaction data are provided within the ASN.1 file for each Entrez gene record, as well as a tab-delimited extraction. The interaction data in tab-delimited format are reported in the GeneRIF subdirectory of Gene's ftp site at

Sage-N Research and the Institute for Systems Biology have partnered to release ISB's Trans-Proteomic Pipeline analysis platform as part of Sage-N Research's Sorcerer appliance. The Sorcerer appliance can be plugged into any network to deliver high- resolution, high-throughput data analysis through an easy-to-use web interface, the company said. With the integration of TPP, users can identify, characterize, and quantify proteins in complex mixtures using any vendor's LC-MS/MS data.

The National Cancer Institute has released BRB-ArrayTools v3.3, a stable release, at Version 3.3.0 includes a number of bug fixes and improvements over the beta version.

CARUS IT, a high-performance computing provider based in Norderstedt, Germany, has released an off-the-shelf supercomputer preconfigured for plug-and-play bioinformatics applications. The system was developed in collaboration with Linux cluster provider Emplics and has a starting price of €40,000 ($47,000). The company showcased the system at the recent Biotechnica trade show in Hannover.


People in the News

Spotfire has hired Christian Marcazzo as senior director of life sciences marketing. Prior to joining Spotfire, Marcazzo served as vice president of business development at InforSense, and worked in business development at Lion Bioscience.

Chris Larsen has moved from director of new products at Cognia to the position of senior scientist at Vecna Technologies, where he is working with the Northup Grumman NIAID Bioinformatics Resource Center [BioInform 10-24-05].

Edward Helton, chief strategist of regulatory and biomedical affairs at SAS, has been chosen as chair-elect of the board of directors for the Clinical Data Interchange Standards Consortium. Helton has been a member of the CDISC board of directors since 2003, and will serve as chair-elect for 2006 before becoming chairman in January 2007. He will replace outgoing CDISC chairman Stephen Ruberg, director of clinical data technology and services for Eli Lilly. Before joining SAS, Helton was an associate professor and senior clinical study director in the Neuroclinical Trials Center at the University of Virginia School of Medicine. He also served as vice president of regulatory affairs for Quintiles.

Filed under

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.