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caCORE, BASE, GeneLinker Gold and Platinum, Discovery Studio Gene Atlas, Reactome, SIMS-Express, E-Cell

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Version 2.1 of caCORE is now available from the National Cancer Institute Center for Bioinformatics at http://ncicb.nci.nih.gov/core. Enhancements include an improved common data element (CDE) curation tool, a form-builder application for creating CDE-compliant data collection forms, better correspondence between the APIs and the UML models, and improved interfaces to vocabulary services.


BASE (BioArray Software Environment) 1.2.11 is available from Sweden’s University of Lund at http://base.thep.lu.se/?m=download. The release includes a job queue system that allows users to define how many jobs may run at the same time and how much RAM they may use.


Predictive Patterns Software has released GeneLinker Gold and Platinum 4.5 for gene expression and proteomics analysis. The new versions include new statistical analysis methods such as Bonferroni-corrected p-values and false discovery rate calculations, as well as a feature that allows users to export data to Ariadne Genomics’ PathwayAssist.


Accelrys has released Discovery Studio Gene Atlas 2.1, a patch to DS GeneAtlas 2.0 that provides additional Linux server support (RedHat 7.2, 8.0 and AS 2.1) and incorporates several bug fixes. Further information is available at http://www.accelrys.com/dstudio/ds_modeling/ds_geneatlas.html.


Reactome, a curated database of biological processes in humans, is available from Cold Spring Harbor Laboratory and the European Bioinformatics Institute at http://www.reactome.org/. Reactome supersedes an earlier project called the Genome Knowledgebase and includes all the information from the previous effort.


Scimagix has launched SIMS-Express, an image-management solution for departmental or workgroup use. The product is a ready-to-install version of the company’s SIMS (Scientific Image Management System) platform.


Version 3.1.102 of E-Cell is available at http://ecell.sourceforge.net/download.html. Improvements include a model editor with pathway view, the ability to import SBML Level 2 documents, and “fairly stable” support for differential-algebraic equations.

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The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.