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Downloads & Upgrades: Genedata Biologics 2.0; TimeLogic's DeCypher J1; CytoSEED; BASE 3.0; RiceNet


Genedata has released version 2.0 of its Genedata Biologics data-management product for biologics R&D.

The new version features new protein-production modules, including molecule definition and cloning, expression, purification, analytics, and quality control. These modules may be used alone or with existing screening and engineering modules, the company said.

The release also includes improved features for molecule registration, sample management, in silico cloning, and analytics and quality control.

TimeLogic, a division of Active Motif, said that it plans to launch a new version of its DeCypher biocomputing platform that will accelerate Blast searches more than 400-fold.

The new version of the system, based on the same field programmable gate array technology that underlies other DeCypher products, is codenamed J1 and will be released early next year.

The company said the new system will offer "the equivalent performance of several thousand 3 GHz processor cores in a single 1U server.”

The bioinformatics group at Hope College has released version 1.1 of CytoSEED, a viewer for metabolic models generated by the Model SEED, an offshoot of the SEED genome annotation project.

CytoSEED is a plug-in for Cytoscape 2.8 that enables viewing, manipulating, and analyzing metabolic models created using the Model SEED. CytoSEED downloads the model data, reactions, and compounds and organizes the reactions into networks based on their corresponding KEGG pathway maps. The model data is then stored on the user's desktop.

Sweden's University of Lund has released BASE (BioArray Software Environment) 3.0, a free environment for microarray data analysis.

According to its developers, BASE 3.0 is a "major release." It now offers support for RNA-seq experiment, a subtype feature for classifying generic items, easier installation of plug-ins and extensions

The Department of Energy's Joint BioEnergy Institute has launched RiceNet, a genome-scale model for predicting the functions of rice genes and gene networks.

RiceNet is a probabilistic functional gene network for 41,203 Oryza sativa genes. Each interaction in RiceNet has an associated log-likelihood score that measures the probability of an interaction representing a true functional linkage between two genes.

The Scan

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A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.