Tools

Infrastructure is critical to scientific research, and here at cBio, we have a strong commitment to developing open source software and maintaining open-access data resources.

cBio has specifically developed tools and infrastructure in the following areas:

Highlighted Projects:

The cBio Cancer Genomics Data Portal provides direct download and visualization of large-scale cancer genomics data sets. It currently provides direct access to over 5,000 tumor samples in 20 cancer types.

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.

Together, the two projects enable cancer researchers to evaluate high-throughput cancer genomic data in the context of known biological pathways and interaction networks.


In the News:

The cBio Cancer Genomics Portal was recently profiled in both The Scientist and Cancer Discovery:

Combing the Cancer Genome: A guided tour through the main online resources for analyzing cancer genomics data. The Scientist, March, 2012.

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cerami et al., Cancer Discovery, 2012 May;2(5):401-4.

Meet the Team: Benjamin Gross

Benjamin Gross has been developing software at cBio for the past six years. With expertise in Java, databases, and software engineering, Benjamin has been a core developer for Cytoscape, Pathway Commons, and the cBio Cancer Genomics Portal. He is also the creator of cBio’s only (so far) iPhone application: BioGene.