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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

Booster Push

New data shows a decline in SARS-CoV-2 vaccine efficacy over time, which the New York Times says Pfizer is using to argue its case for a booster, even as the lower efficacy remains high.

With Help from Mr. Fluffington, PurrhD

Cats could make good study animals for genetic research, the University of Missouri's Leslie Lyons tells the Atlantic.

Man Charged With Threatening to Harm Fauci, Collins

The Hill reports that Thomas Patrick Connally, Jr., was charged with making threats against federal officials.

Nature Papers Present Approach to Find Natural Products, Method to ID Cancer Driver Mutations, More

In Nature this week: combination of cryogenic electron microscopy with genome mining helps uncover natural products, driver mutations in cancer, and more.