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Downloads and Upgrades: Sep 23, 2011

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This week, the Fox Chase Cancer Center announced that it has updated the Protein Common Interface Database, ProtCID, a repository of clusters of common interfaces observed in multiple crystal structures of homologous proteins.

Updates include improvements in how PFAM domains are assigned to structures in the Protein Data Bank; and Pymol script files for the interface superposition of a cluster are now included in the cluster interfaces' tar.gz files


Ingenuity has added new miRNA data to Ingenuity Pathway Analysis.

The company said it has included new experimentally validated miRNA-mRNA target interactions from miRecords, plus thousands of additional miRNA-mRNA interactions manually curated from additional peer-reviewed literature.

Ingenuity said the new content will improve the ability of IPA's miRNA target filter to help researchers prioritize miRNA target interactions.


Reactome 38 is available here.

The release includes new topics on grouping pathways for meiotic recombination; nodal signaling; signal transduction; and metabolism. Furthermore, a new Reactome tutorial has been published.


The GenePattern development team at the Broad Institute has released GenePattern Archive, or GParc.

According to the developers, GParc is a place to share modules and help grow the GenePattern community. Users can make GenePattern modules that they have created available to the bioinformatics community by creating an account and uploading modules to GParc.


The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.