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cBioPortal goes Open Source

May 04, 2015 | By Ward Weistra

cBioportalThe cBioPortal for Cancer Genomics is a well known, and well loved, interface for interactive analysis of cancer data. It has been developed, maintained and is also heavily used by the Memorial Sloan Kettering Cancer Center in New York.

The public portal allows you to view the data from 89 cancer studies, including all studies from The Cancer Genome Atlas in both their published and online provided format. It combines this data with intuitive custom visualizations like an interactive study overview, the OncoPrint and the MutationMap.

One of the important 'simplifications' cBioPortal applies to allow for these multi-omics visualisations it to map most data types back to the gene level. This proves to be a very insightful approach, allowing for straightforward data integration.

Hosting the portal on your own server is also a possibility for those who want to view their own non-public datasets in the tool. Until recently the code was only freely available to academics and the license asked for making all loaded datasets available to the cBioPortal when they were made public. However, only last week the people from MSKCC delighted us with the announcement that they will go fully open source:

https://twitter.com/cbioportal/status/590495814772006912

At The Hyve we are proud to have been able to help Niki Schultz and his team in the considerations for and implications of making research software available as open source. MSKCC chose the GNU Affero GPL license for the cBioPortal code. This license makes sure that anyone commercially providing a version of the application as a standalone application or via the web, has to make any improvements to the source code available for the community to build on. The source code is now available on the Github page of cBioPortal.

With this important decision we are also happy to announce that we will be adding cBioPortal to the suite of open source bioinformatics tools around which we already provide our services. A connector between tranSMART and cBioPortal, which was developed by our partner the Netherlands Cancer Institute in the CTMM TraIT project, is also available. If you have data you would like to visualize in a user friendly interface highly insightful for, but not limited to, Oncology researchers and physicians, please contact us to see how we can help you.