GenomeSpace

GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer.

DISCOVAR

DISCOVAR is a variant caller and genome assembler that uses the latest low cost sequencing data. It can generate highly accurate variant calls for individual humans, or assemble genomes de novo.

Medulloblastoma Portal

A collection of recent publications aimed at identifying the drivers of medulloblastoma, such as mutations or chromosome alterations, which will enable development of more effective and and less toxic targeted therapies.

Project Achilles Data Portal

Project Achilles is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. The project uses a genome-wide shRNA library to silence individual genes and identify those genes that affect cell survival. Large-scale functional screening of cancer cell lines provides a complementary approach to those studies that aim to characterize the molecular alterations (mutations, copy number alterations, etc.) of primary tumors, such as The Cancer Genome Atlas.

Genome Data Analysis Center (GDAC)

On behalf of The Cancer Genome Atlas, the Broad Genome Data Analysis Center designs and operates scientific data and analysis pipelines which pump terabyte-scale genomic datasets through scores of quantitative algorithms, in the hope of accelerating the understanding of cancer.

Cancer Therapeutics Response Portal

The Cancer Therapeutics Response Portal enables analyses a genomic cancer cell-line profiling to identify more comprehensively relationships between genetic and lineage features of human cancer cell lines and small-molecule sensitivity.

Pilon

Pilon uses read alignment analysis to diagnose, report, and automatically improve genome assemblies, and it can also be used to make variant calls among similar haploid strains.

ATHLATES

HLA typing from exome capture sequencing.

Nozzle

Nozzle is an R package for generation of reports in high-throughput data analysis pipelines. Nozzle reports are implemented in HTML, JavaScript, and Cascading Style Sheets (CSS), but developers do not need any knowledge of these technologies to work with Nozzle. Instead they can use a simple R API to design and implement powerful reports with advanced features such as foldable sections, zoomable figures, sortable tables, and supplementary information.

Inflammatory finding

Paul Goldsmith, May 2nd, 2013

To convert food into energy, our bodies rely on a complex network of molecular pathways known broadly as metabolism. Along the path from food to energy, intermediate molecules emerge that form the starting materials for the next step. Traditionally, these intermediates were viewed simply as building blocks — essential for the process, but otherwise inert.

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