Category Archive: genomics

Oct 31

The Real Value of an Atlas

By Trey Ideker, Ph.D., Director, San Diego Center for Systems Biology, University of California San Diego, Department of Medicine These days there seems to be a lot of talk about atlases for cancer. Most of us are familiar with The Cancer Genome Atlas (TCGA), the long-running effort which, over the past decade, sequenced genomes from …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/real-value-atlas/

Aug 29

Cancer Genomics Cloud Pilots DREAM Challenge — Leveraging the Wisdom of the Crowd

By Tony Kerlavage, Ph.D., NCI CBIIT, Cancer Informatics Branch In recent years, Challenges have become a popular way to engage and motivate the research and innovation communities to solve difficult problems. Challenges are open competitions where communities are presented with specific and often difficult problems to solve. Participants are given guidelines and test data, and …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/cancer-genomics-cloud-pilots-dream-challenge-leveraging-wisdom-crowd/

Jun 14

Learn more about the Genomic Data Commons

NCI has launched the Genomic Data Commons (GDC), a system that will promote sharing of genomic and clinical data between researchers and facilitate precision medicine in oncology. The GDC was created to centralize, standardize, and broaden access to data from NCI programs such as The Cancer Genome Atlas (TCGA) and its pediatric equivalent, Therapeutically Applicable …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/genomic-data-commons-launched/

May 11

Collaborating Against Cancer: Inter-Agency Pilots

“We are on the cusp of breakthroughs that will save lives, benefit all of humanity. But we have to work together.” Vice President Joe Biden’s words at the American Association for Cancer Research conference resonate as a clear call to action. When we collaborate and share our expertise, the cancer informatics community can bring a …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/collaborating-cancer-inter-agency-pilots/

May 06

Usable, Collaborative, Reproducible, and Extensible: Four Key Tenets of Cloud Computing

The Seven Bridges Cancer Genomics Cloud (CGC) is one of three pilot systems funded by the National Cancer Institute with the aim of co-localizing massive genomics datasets, like The Cancer Genomics Atlas (TCGA), alongside secure and scalable computational resources for analysis. TCGA comprises multidimensional matched tumor-normal data from over 11,000 patients and 33 cancer types. …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/usable-collaborative-reproducible-extensible-four-key-tenets-cloud-computing/

Mar 15

NCI Data Catalog: Your One-Stop List for NCI Data

If you aren’t aware of the NCI Data Catalog, you should check it out! The NCI Data Catalog is a consolidated listing of the publicly available data collections produced by NCI initiatives, including The Cancer Genome Atlas (TCGA), The Cancer Imaging Archive (TCIA) and Surveillance, Epidemiology, and End Results (SEER) database. The catalog has been …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/your-one-stop-list-for-nci-datasets/

Feb 29

Informatics Community Crucial to the Cancer Moonshot

There has been a lot of press in the past couple of months about the “Cancer Moonshot,” first mentioned by Vice President Joe Biden in October 2015, and gaining steam recently with the President’s State of the Union address and an initial recommendation of $1 billion of funding. The White House released a Fact Sheet …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/title-informatics-community-a-crucial-component-of-cancer-moonshot/

Jan 06

FY 2017: NCI Looks to the Clouds

As the FY 2017 Annual Plan and Budget Proposal describes, some of the key components of the infrastructure and programs that comprise the National Cancer Program include: 69 NCI-designated Cancer Centers across the country, NCI’s National Clinical Trials Network, NCI Community Oncology Research Program, and the NCI-supported programs that are training today’s cancer research workforce and the workforce of the …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/1817-2/

Jan 27

Winning an HPN-DREAM8 Challenge: Competition and Collaboration Supporting Open Scientific Research and Development

While working with big genomics data can be very challenging, it can also be fun. And when your team wins a competition, it’s positively exhilarating, as our NCIP Computational Genomics Research Group discovered while participating in the 8th annual set of challenges posed by The Dialogue on Reverse Engineering Assessment and Methods (DREAM) project. DREAM …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/winning-hpn-dream8-challenge-competition-collaboration-supporting-open-scientific-research-development/

Sep 27

NCI’s CPTAC Releases an Openly Accessible Data Set Primed for Multi-omic Integration

On September 4, 2013, NCI’s Clinical Proteomics Tumor Analysis Consortium (CPTAC) publicly released proteomic data produced from colorectal tumor samples previously analyzed as part of The Cancer Genome Atlas (TCGA) initiative.  This is the first release of proteomic tumor data designed to complement genomic data from the same tumors. Since its launch in 2006, the …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/ncis-clinical-proteomic-tumor-analysis-consortium-releases-openly-accessible-data-set-primed-multi-omic-integration/