Nov 06

We Face a New “Tragedy of the Commons.” The Remedy is Better Metadata.

Mark A. Musen, M.D., Ph.D.Mark A. Musen, M.D., Ph.D.

By Mark A. Musen, M.D., Ph.D. The data science community is awash with “FAIRness.” In the past few years, there has been an emerging consensus that scientific data should be archived in open repositories, and that the data should be Findable, Accessible, Interoperable, and Reusable.1 The campaign for FAIR data is particularly palpable at the …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/face-new-tragedy-commons-remedy-better-metadata/

Aug 30

Towards a Cancer Research Data Commons

Allen Dearry, Ph.D.Allen Dearry, Ph.D.

By Allen Dearry, Ph.D., Program Director I recently joined NCI to help support strategic data sharing and informatics projects within the Center for Biomedical Informatics and Information Technology (CBIIT). Having worked on information management at another Institute for five years and the trans-NIH Big Data to Knowledge (BD2K) initiative since its inception, this is an …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/towards-cancer-research-data-commons/

Mar 28

Precision Medicine Meets Imprecise Medicine

Michael N. Liebman, Ph.D.Michael N. Liebman, Ph.D.

By Michael N. Liebman, Ph.D., Managing Director, IPQ Analytics, Adjunct Professor, Pharmacology and Physiology, Drexel College of Medicine Biomedical research is evolving with an increasing emphasis on data science, e.g., data integration and storage, data privacy and security, data analytics and data representation, driven by the transformative technologies that have become the currency of genomics …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/precision-medicine-meets-imprecise-medicine/

Mar 07

Democratizing Access to CCG Data: Cancer Genomics Cloud Pilots

By Izumi Hinkson, Ph.D., NCI CBIIT Cancer Informatics Branch In recent years, genomics has been described as a big data science on par with the likes of Twitter, YouTube, and the scientific pursuit of understanding the universe1. These comparisons are certainly not exaggerations, especially considering that genomic data is generated at a rate of 1 zetta-bases …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/democratizing-access-ccg-data-cancer-genomics-cloud-pilots/

Feb 13

Imaging: A Key Component of a Cancer Data Ecosystem

    By Edward Helton, Ph.D., Government Sponsor, CBIIT Clinical Imaging Program, Robert Nordstrom, Ph.D., Branch Chief, Imaging Guided Intervention Branch, and Eve Shalley, Program Manager, NCI CBIIT Cancer Informatics Branch Precision medicine has quickly moved to the forefront of clinical research and practice, and is particularly pertinent to cancer since cancer is a disease of the …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/imaging-key-component-cancer-data-ecosystem/

Nov 29

Precision Medicine Inspires HPC

By Eric Stahlberg, Ph.D., Director, High Performance Computing Initiative, Data Science and Information Technology Program, Frederick National Laboratory for Cancer Research (FNLCR) The recent weeks have been momentous as the high-performance computing (HPC) community embraced the challenge of precision medicine.  The theme of this year’s leading international supercomputing conference, SC16,  was “HPC Matters” and it …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/precision-medicine-inspires-hpc/

Oct 31

The Real Value of an Atlas

Trey Ideker

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/

Sep 14

The Protein Data Bank and the Importance of Sustaining Primary Data Archives

                    By Helen M. Berman, Ph.D.*, Director Emerita, RCSB Protein Data Bank, and Stephen K. Burley, M.D., D.Phil.*+, Director, RCSB Protein Data Bank Scientific discovery involves collecting and analyzing data, and communicating new knowledge arising therefrom. What happens, though, when someone wants to repeat an experiment, or …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/protein-data-bank-importance-sustaining-primary-data-archives/

Aug 29

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

Anthony Kerlavage, Ph.D.Tony Kerlavage, Ph.D.

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/

Jul 20

Cancer Data and Computation in the Cloud: One Path to Affordable Genomics Research

Dr. Gad Getz

By Gad Getz, Ph.D., Broad Institute / MGH The cost of DNA sequencing has dropped more than one million-fold over the last decade, making it increasingly possible to discover the genetic basis of cancer and response to treatment. Three challenges, however, impede this goal: 1) Analysts lack the resources to download, store and compute on …

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Permanent link to this article: https://ncip.nci.nih.gov/blog/cancer-data-computation-cloud-one-path-affordable-genomics-research/