linkstream2 microblog

http://www.broadinstitute.org/oncotator
https://github.com/broadinstitute/oncotator

Useful listing of data sources, viz:

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Protein Annotations

Site-specific protein annotations from UniProt.
Druggable target data from DrugBank.
Functional impact predictions from PolyPhen-2.

Cancer Annotations

Observed cancer mutation frequency annotations from COSMIC.
Cancer gene and mutation annotations from the Cancer Gene Census. Significant amplification/deletion region annotations from Tumorscape and theTCGA Copy Number Portal.
Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia. Significantly mutated gene annotations aggregated from published MutSiganalyses. Cancer gene annotations from the Familial Cancer Database.
Human DNA Repair Gene annotations from Wood et al.

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Uses bamboo testing software
https://www.atlassian.com/software/bamboo

BLOG:
http://blog.pacificbiosciences.com/2013/12/data-release-human-mcf-7-transcriptome.html

DATASETS:
http://datasets.pacb.com.s3.amazonaws.com/2013/IsoSeqHumanMCF7Transcriptome/list.html

PanCancer.info has fantastic #viz of the progress & int’l effort in the Pan-#Cancer Analysis of Whole #Genomes (#PCAWG) project

Deadlines: 7/19,8/2,8/16
https://www.synapse.org/#!Synapse:syn312572

Contains information on analysis pipelines and datasets produced from Broad’s Firehose. Access to the protected pages requires an NCI login.

https://confluence.broadinstitute.org/display/GDAC/Home

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BioLayout Express3D has been specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not
exclusively, from biological data.
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www.biolayout.org

http://genome.cshlp.org/content/early/2013/01/02/gr.144600.112.abstract

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To demonstrate the promise of personalized genome analysis, the genome of HuRef was sequenced using the Life SOLiD™ platform. Nimbus Informatics performed the analytical work for this project and has made the resulting data available here, running entirely on the Amazon Cloud.
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http://huref.nimbusinformatics.com

http://bioinformatics.oxfordjournals.org/content/early/2013/12/12/bioinformatics.btt719.short

http://chronicle.com/article/Still-Hunting-Medical/143221/

Paul Basken
The Chronicle of Higher Education