Category Archive: Bioinformatics

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: http://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: http://ncip.nci.nih.gov/blog/ncis-clinical-proteomic-tumor-analysis-consortium-releases-openly-accessible-data-set-primed-multi-omic-integration/

Sep 09

The Future of the Pathway Interaction Database (PID) — A Conversation with Dr. Daoud Meerzaman

The Pathway Interaction Database (PID) is a collection of biomolecular interactions and events involving signaling and regulatory pathways that have been curated from the peer-reviewed literature. Users are able to browse through biomolecular interactions, run computational analyses, or synthesize and combine interactions to establish novel pathways. Begun as a collaborative project between the National Cancer …

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Permanent link to this article: http://ncip.nci.nih.gov/blog/future-pathway-interaction-database-pid-conversation-dr-daoud-meerzaman/

Aug 28

Reducing Friction: An Update on the NCIP Open Development Initiative

I was fortunate enough to attend the Bioinformatics Open Source Conference (BOSC) this summer and heard a wonderful talk by Cameron Neylon on “The Role of Open Source and Open Thinking.”  In his talk, he presented a clever equation for calculating the probability of helping someone through an open source project: P (of helping someone) …

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Permanent link to this article: http://ncip.nci.nih.gov/blog/reducing-friction-an-update-on-the-ncip-open-development-initiative/

Jul 10

NCI Board of Scientific Advisors Approves NCI Cancer Genomics Cloud Concept

In a series of previous blog posts, Juli Klemm and I discussed the challenges associated with the growth of biomedical research data, and the results of an informal survey of computational limitations currently experienced by biomedical researchers. One possible solution to resolving these challenges is what we are calling a “cancer genomics cloud,” a computing …

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Permanent link to this article: http://ncip.nci.nih.gov/blog/nci-board-of-scientific-advisors-approves-nci-cancer-genomics-cloud-concept/

May 31

Input on Cancer Knowledge Clouds: Key Themes from the Community

    “We cannot solve our problems with the same thinking we used when we created them.” — Albert Einstein There is no shortage of reports describing the informatics challenges presented by the massive data volumes generated by today’s genomics technologies, particularly ultra high-throughput sequencing.  The facility with which these data can be generated has the …

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Permanent link to this article: http://ncip.nci.nih.gov/blog/input-on-cancer-knowledge-clouds-key-themes-from-the-community/

Apr 15

Computational Needs for Large-scale Data Analysis: Towards a Cancer Knowledge Cloud

Biology is increasingly joining the ranks of the data-intensive sciences through increased use of “-omics” technologies (next-generation sequencing, expression profiling, proteomics, methylation studies, etc.) and the large-scale use of a variety of imaging technologies in research. This is great for scientists and the patients who are going to benefit from the research, but it poses …

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Permanent link to this article: http://ncip.nci.nih.gov/blog/computational-needs-for-large-scale-data-analysis-towards-a-cancer-knowledge-cloud/

Oct 15

Cultivating Collaborations on Imaging Research and Informatics

Within the National Cancer Institute (NCI), there is new potential for an increasingly beneficial collaboration between the Cancer Imaging Program (CIP) in the Division of Cancer Treatment and Diagnosis (DCTD) and the Center for Biomedical Informatics and Information Technology (CBIIT) in the Office of the Director.  The Institute’s recent launch of the National Cancer Informatics …

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Permanent link to this article: http://ncip.nci.nih.gov/blog/cultivating-intramural-collaborations-on-imaging-research-and-informatics/

Aug 15

Ephemeral Images, Indelible Data: The Promises and Challenges of Digital Imaging as Applied to Pathology

  Those of us working in biomedical informatics are well aware that one of our omnipresent challenges is overcoming the disparity between our capacity to use high-throughput research technologies to produce huge quantities of data, which is now very high, and our practical ability to store, aggregate, analyze, and integrate the resulting mountains of heterogeneous …

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Permanent link to this article: http://ncip.nci.nih.gov/blog/ephemeral-images-indelible-data-the-promises-and-challenges-of-digital-imaging-as-applied-to-pathology/

Aug 03

Radiation Therapy Oncology Group (RTOG) Bioinformatics

Word Cloud for Ying Xiao imaging presentation

The NCI-supported Cooperative Groups conduct national- and international-scale multicenter clinical trials.  They face escalating computational challenges as the amount of clinical trials data generated by a multiplicity of research technologies and clinical observations continues to expand. As part of our ongoing Speaker Series, we recently invited Dr. Ying Xiao to discuss informatics initiatives being undertaken …

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Permanent link to this article: http://ncip.nci.nih.gov/blog/radiation-therapy-oncology-group-rtog-bioinformatics/

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