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Downloads and Upgrades: Feb 25, 2011

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This week, the Galaxy team at Penn State University launched new tool wrappers for several next-generation sequencing tools and assembly packages.

The wrappers, available here, support Velvet, ABySS, Phrap, CARPET, Newbler, AGILE, Mimulus2, FastQC, and LUCY and are available in the Galaxy Tool Shed.


Simulations Plus has released version 5.5 of its ADMET Predictor software.

The release has several improvements: a new metabolite module with 10 new models for sites of metabolism; an expanded toxicity module with nine new models, extending the total number to more than 30; an expanded Enslein metabolism module; and enhanced graphics presentations for visualization of new calculated properties among other features.


Genedata has released Genedata Biologics, a software package for managing and analyzing data for biologics research and development.

Among its features, Genedata Biologics documents and manages activities such as antibody screening (including phage display or hybridoma), cloning, molecular biology, protein expression and purification, analytics, and cell line development. In addition, the system supports data and material handovers among different departments and external service providers.

Furthermore, the company said that the software's Oracle-based database enables consistent storage and referencing of relevant biomaterials such as antibody clones, vectors, and cell lines; incorporates protein and nucleotide sequence information and assay and analytics readouts; and includes modules for screening, protein engineering and optimization, and protein production.


The National Center for Integrative Biomedical Informatics at the University of Michigan has launched version 3.1 of the MiMI plugin for Cytoscape.

The new plugin integrates with other NCIBI tools to provide literature information, document summarization, and pathway matching. It also retrieves molecular interactions from the Michigan Molecular Interactions, or MiMI, database and displays the interaction network with Cytoscape. The MiMi database gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1.


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.