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GenBank 152.0, STN AnaVist 1.1, COPASI, DogBox Online, caAdapter 1.2, BASE, Ensembl, Jamie Cuticchia, James Golden

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The National Center for Biotechnology Information has released GenBank 152.0 at ftp://ftp.ncbi.nih.gov/. The release contains 59,750,386,305 base pairs and 54,584,635 entries. Uncompressed, the 152.0 flat files require about 207 GB for the sequence files only. The ASN.1 version requires around 180 GB.


The Chemical Abstracts Service and FIZ Karlsruhe have released STN AnaVist 1.1, an analysis and visualization software package for the CAplus database and the patent databases USPATFULL and PCTFULL.


The Virginia Bioinformatics Institute has posted COPASI Release Candidate 1 (Build 17), a biochemical modeling software package, at http://www.copasi.org. COPASI is the successor to VBI's Gepasi modeling software and runs on Linux, Windows, OS X, and Solaris. COPASI is free for non-commercial use, and will be published as open source at the time of its full release. Features include stochastic time course simulation, deterministic time course simulation, steady-state analysis, metabolic control analysis, elementary mode analysis, mass conservation analysis, parameter estimation from experimental data, and more. The software imports and exports SBML.


Unleashed Informatics has launched DogBox Online, a free and open access version of the company's DogBox data warehouse product, at http://dogboxonline.unleashedinformatics.com. DogBox Online includes UnleashedNews, a service that provides more than 450 science and technology news feeds from 23 channels that are updated hourly.


The National Cancer Institute's Center for Bioinformatics has released caAdapter 1.2, an architecture that offers tools to support HL7 v3 message generation, at http://ncicb.nci.nih.gov/download. The caAdapter system includes the Core Engine, which provides a Java-based API to HL7, and the Mapping Tool, a GUI-based front-end application for mapping clinical data to HL7 version 3 specifications.


BASE (BioArray Software Environment) 2.0RC1, a rewrite of BASE 1.2 in Java, is available at http://base.thep.lu.se/base2 .


Ensembl has released the first low-coverage (2X) assembly of the rabbit (Oryctolagus cuniculus) genome, currently being sequenced by the Broad Institute, at http://pre.ensembl.org/rabbit/.

 

People in the News

Jamie Cuticchia has been named director of the Duke Bioinformatics Group, a new collaboration between the Duke Institute for Genome Sciences & Policy and the Duke Comprehensive Cancer Center. The new group will collaborate on the statistical design and analysis of cancer research involving genomic, proteomic, or similar data. Cuticchia most recently served as director of bioinformatics at RTI International. Prior to that, he held professorships at the Johns Hopkins University School of Medicine and the University of Toronto Faculty of Medicine. Cuticchia also founded the Ontario Center for Genomic Computing.


IO Informatics has formed a science advisory board. Members include: James Golden, chief technology officer of SAIC's Life Sciences Office; Sangtae Kim, professor of mechanical engineering and chemical engineering at Purdue University; Kelvin Lee, professor of molecular and cell biology in the School of Chemical and Biomolecular Engineering at Cornell University; Stuart Marson, the founder of MDL; and Robert Stevenson, founder and principal of the Abacus Group.

Filed under

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.