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BioCyc, Pathway Tools, UCSC Genome Browser, ProteinCenter 1.5, TissueView

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SRI International has released version 12.0 of the BioCyc databases and Pathway Tools software. New features include limited Macintosh support for Pathway Tools. Users can also now create accounts on the BioCyc website that will allow them to define preferences, such as default parameter settings for the Omics Viewers, and organism lists for use in comparative analysis operations.
 
In addition, all BioCyc databases, including MetaCyc, are now free for all users.
 
Further details are available here.
 

 
The University of California, Santa Cruz, Genome Bioinformatics Group has released a genome browser and blat server for the October 2007 draft assembly of the cow genome, Bos taurus. The assembly was produced by Baylor College of Medicine’s Human Genome Sequencing Center as Baylor release Btau_4.0.
 
The data is available via FTP here or the UCSC downloads page here.
 

 
Proxeon has released ProteinCenter 1.5, a software tool that is used after protein identification by “conventional search engines,” the company said. The software is based on a consolidated, annotated, protein sequence database derived from “all major protein databases” to support statistical analysis of search results.
 
New features include a map that shows the location of all the identified proteins within a cell, as well as new export formats that support comparison of data sets.
 

 
Applied Biosystems/MDS SCIEX has released TissueView, a software package for processing mass spectrometry imaging data to provide a “deeper understanding of how drugs and proteins are distributed within biological tissue,” the companies said. 
 
According to the partners, “existing commercially available tissue imaging software solutions are less efficient for processing, limited in visualization capabilities and more complex for researchers to use.”
 
TissueView has been “tailored” for mass spectrometry users, they said, and is able to rapidly display “the spatial location and intensity of compounds – both proteins and small molecules – in all tissue types.”

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The Scan

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Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.