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Genome Analyzer, ADMET Predictor 3.0, Reactome 25, MiMI, BioPuppy

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Genomatix Software has released Genomatix Genome Analyzer, or GGA, an integrated hardware/software solution for analyzing data from second-generation sequencers.
 
Genomatix said the system is designed for ChIP-seq and transcriptome studies. Results include clustered and classified enriched regions, transcription factor over-representation, and TF associations.
 
In addition, researchers can use the software to study genome-wide correlations with genomic features, as well as meta-analysis with genome-wide chromatin modification, methylation state, expression levels, or any data derived via next-generation sequencers, the company said.
 
GGA is driven by a browser-based interface. All database structures, scripts, and tools are accessible and can be tailored to the user’s needs, the company said.
 

 
Simulations Plus has released ADMET Predictor 3.0, which predicts the properties of molecules based on their structure. The upgrade includes 14 new predicted properties as well as new retrained models for the predictions. 
 
Among the new prediction tools are eight models for metabolic inhibition and five for intrinsic clearance that have been added to the software’s Enslein Metabolism Module. The initial Enslein Metabolism Module predicted metabolic rate of certain enzymes but not the potential for metabolic inhibition that can cause interactions with other drugs metabolized by the same enzymes, the company said.
 
The company has also added a new environmental toxicity prediction based on data originally generated by the US Environmental Protection Agency.
 
Another enhancement to ADMET Predictor is the addition of a graphics engine called Miner3D, which allows scientists to visualize multidimensional relationships among properties and descriptors.
 

 
Version 25 of the Reactome knowledgebase is accessible here.
 
New additions include an expanded and reorganized pathway module for biological oxidations, along with several new pathway topics: glutamate neurotransmitter release cycle, beta cell development, and integrin cell surface interactions. Pathway topics updated with new curated events include: apoptosis/regulatory reactions, metabolism of amino acids/ODC regulation, metabolism of vitamins, NGF signaling, and lipid metabolism/HDL synthesis.
 
In addition, a beta version of a new pathway visualization tool is available, along with a new search tool.
 

 
The University of Michigan has released an updated version of the MiMI plug-in for Cytoscape, whichprovides access to an integrated resource of molecular interaction data, literature links, and annotation. 
 

 
A beta version of BioPuppy 1.0 is available here.  
 
BioPuppy is a minimal Linux electronic workbench for bioinformatics and computational biology designed to meet the needs of beginners, according to its developers.
 
BioPuppy is available as a CD with ready-to-use bioinformatics tools, including the sequence analysis tools Sim-4, Genewise, Sigma, HMMer, ClustalW, and mafft; the structure prediction tools mfold and gibbs; the protein structure analysis tools Garlic and Rasmol; the phylogenetic analysis tools Fast DNA, Phylip, and Phylodraw; Modeller for protein modeling; MGL Tools for docking; and the Copasi systems biology tool.

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The Scan

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.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.