NCBI Single Cell in the Cloud Codeathon—Project Proposals Due December 2

November 19, 2019

NCBI Codeathons: Bringing people with diverse backgrounds together to build tools for advanced analysis of biomedical data.

The New York Genome Center is hosting a National Center for Biotechnology Information (NCBI) Single Cell in the Cloud codeathon from January 15 – 17, 2020.

This codeathon will focus on single cell data, including RNA, DNA, and chromatin accessibility. Proposals for pipelines and analysis of SRA data, data interoperability, and the use of machine learning techniques in clustering are of particular interest. Proposals for tutorial pipelines and educational tools are also encouraged. Teams will have access to computational resources in the Cloud to turn ideas into working prototypes.   

You can choose to lead your project team, recommend someone, or request the assignment of a team lead. Providing a designated team lead increases the probability that the project will get selected for the codeathon.

Submit your project proposal by December 2.

To see a list of previous codeathon projects, visit the NCBI Codeathons website.


Children's Brain Tumor Tissue Consortium Dataset Now Available in the Proteomic Data Commons

November 14, 2019

National Cancer Institute Office of Cancer Clinical Proteomics Research Proteomic Data Commons Logo

The NCI Proteomic Data Commons (PDC) just released the proteomic dataset from the Children’s Brain Tumor Tissue Consortium (CBTTC).

The CBTTC and the Pacific Pediatric Neuro-Oncology Consortia (PNOC) are collaborative research consortia focused on identifying therapies for children with brain tumors. The consortia have contributed a Pediatric Brain Tumor Atlas (PBTA) dataset, a cohort of 991 brain tumor subject clinical data, with associated whole genome sequencing and RNAseq hosted by the Gabriella Miller Kids First Data Resource Center as part of the Gabriella Miller Kids First Pediatric Research Program (Kids First). Kids First is a Pan-NIH Common Fund program dedicated to the development of large-scale data resources to help researchers uncover new insights into the biology of childhood cancer and structural birth defects.

The Office of Cancer Clinical Proteomics Research (CPTAC) and CBTTC have collaborated to examine seven brain tumor subtypes in children to aid in the identification of therapies for pediatric patients. Data included in this release are proteomic and phosphoproteomic analyses of brain tumor samples included in the Kids First PBTA cohort and represent the first 199 patients analyzed, integrating the proteomic and genomic molecular characterization across seven pediatric and AYA (adolescent and young adult) histologies: Low Grade Glioma, High Grade Glioma, Ependymoma, Ganglioglioma, Craniopharyngioma, Atypical Teratoid Rhabdoid Tumor (ATRT), and Medulloblastoma. Mass Spectrometry raw data generation along with preliminary analyses were performed at the Thermo Fisher Scientific Center for Multiplexed Proteomics, Harvard Medical School, under the direction of Professor Steven Gygi. Samples were prepared using the streamline (SL)-TMT protocol and MS analysis was performed using the SPS-MS3 strategy developed in the Gygi lab. Additional data analyses from the CPTAC Common Data Analysis Pipeline and from the University of Michigan Proteomics and Integrative Bioinformatics Laboratory are also provided. All raw and processed genomic data, as well as pathology reports, radiology reports, MRIs, and histology slide images are accessible via the Kids First Data Resource Portal.


Comment on the NIH Policy for Data Management and Sharing and Supplemental Draft Guidance

November 14, 2019

Decorative image reading Data Sharing.

NIH is seeking public input on a trans-NIH data management and sharing policy proposal that further advances the Agency’s commitment to responsible data management and sharing. In 2018, the NIH Office of Science Policy released a request for information to gather input for a future draft policy aimed at replacing NIH’s existing Data Sharing Policy. The Draft NIH Policy for Data Management and Sharing and Supplemental DRAFT Guidance will be accepting comments until January 10, 2020. 

Review the guidance and submit your comment.


Apply to Join NCI's Center for Biomedical Informatics and Information Technology (CBIIT) Team as a Biomedical Imaging Informatics Specialist by November 13

November 4, 2019

NCI Center for Biomedical Informatics and Information Technology: Biomedical Imaging Informatics Specialist

Do you have experience advising and managing the development and implementation of biomedical imaging informatics solutions and technologies? If so, consider joining NCI's Center for Biomedical Informatics and Information Technology (CBIIT) as a Biomedical Imaging Informatics Specialist. This position will serve as the senior expert and recognized technical authority expert on biomedical informatics theory and practice.

This full-time appointment will develop computing solutions to realize a secure and user-friendly imaging informatics program, serve as a cancer research expert for biomedical informatics projects and as the Contracting Officer's Representative (COR) on CBIIT Imaging Informatics contracts. Must be able to apply knowledge of biomedical standards, protocols, and processes (BRIDG, HL7, DICOM) to foster collaboration, development, and implementation of biomedical informatics projects as they pertain to cancer imaging. Apply for this position by Wednesday, November 13.


The Center for Cancer Data Harmonization Kicks Off Efforts

October 18, 2019

illustration of the flow of data through the data commons.

The National Cancer Institute's (NCI) Center for Cancer Data Harmonization (CCDH) is kicking off a 3 ½ year-effort to make the volumes of data arising from cancer research more accessible, organized, and powerful. In line with Cancer Moonshot (sm) goals, CCDH will ultimately improve data sharing and data harmonization across NCI’s Cancer Research Data Commons (CRDC).

The Frederick National Laboratory for Cancer Research awarded the research contract on behalf of NCI to Oregon State University. Researchers from Oregon Health & Science University, the University of Chicago, Johns Hopkins University, and the University of North Carolina will team up to create and operate the CCDH.

The team will develop a “concierge service” for researchers needing help understanding how to leverage, incorporate, design, or use cancer data. The team’s work will be organized around five key areas: community development, data model harmonization, ontology and terminology ecosystem, tools and data quality, and program management.

Learn more about NCI’s CRDC and the data made accessible by the CCDH.


Brain Cancer Predictive Modeling and Biomarker Discovery Challenge

Brain Cancer Predictive Modeling and Biomarker Discovery Challenge Launches November 1

October 18, 2019

Clinical investigators at Georgetown University are seeking to advance precision medicine techniques for the prognosis and treatment of brain tumors through the identification of novel multi-omics biomarkers.

In support of this goal, precisionFDA, the Georgetown Lombardi Comprehensive Cancer Center, and the Innovation Center for Biomedical Informatics at Georgetown University Medical Center (Georgetown-ICBI) are launching the Brain Cancer Predictive Modeling and Biomarker Discovery Challenge on November 1, 2019. This challenge will ask participants to develop machine learning and/or artificial intelligence models to identify biomarkers and predict patient outcomes using clinical, DNA copy number, and gene expression data. Learn more about the challenge and pre-register.


ATOM Fellowship OpportunityATOM Fellowship Opportunity: Cancer Drug Discovery Data Scientist Positions Open

October 11, 2019

The Accelerating Therapeutics for Opportunities in Medicine (ATOM) Consortium is accepting applications for their Cancer Drug Discovery Data Scientist Fellowship program. This one-year appointment in computationally-driven cancer drug discovery is part of a unique public-private partnership and will begin in early 2020. Scientists with doctoral degrees and backgrounds in biomedical or computational disciplines interested in cross-disciplinary training and collaboration are encouraged to apply.

Two optional Virtual Information Sessions will be held on October 15 and October 28 to provide potential applicants with an opportunity to ask questions about the fellowship program and application process.

Application submissions will be considered as they are received. Apply now.

Headquartered in San Francisco, CA, the Accelerating Therapeutics for Opportunities in Medicine (ATOM) Consortium was formed with the goal of transforming drug discovery from a slow, sequential, and high-failure process into a rapid, integrated, and patient centric model. Founding members of ATOM are the University of California, San Francisco (UCSF), GlaxoSmithKline (GSK), Lawrence Livermore National Laboratory (LLNL, for the Department of Energy), and Frederick National Laboratory for Cancer Research (FNLCR, for the National Cancer Institute).


Susan Gregurick, Ph.D.Dr. Susan K. Gregurick Named Associate Director for Data Science and Director of the NIH Office of Data Science Strategy (ODSS)

September 18, 2019

The National Institutes of Health (NIH) announces Dr. Susan K. Gregurick as Associate Director for Data Science and Director of the NIH Office of Data Science Strategy (ODSS). Dr. Gregurick has served as the senior advisor to ODSS since November 2018, and brings substantial experience in computational biology, high performance computing, and bioinformatics to the new role.

Dr. Gregurick will help lead NIH efforts in coordinating and collaborating with appropriate government agencies, international funders, private organizations, and stakeholders engaged in scientific data generation, management, and analysis. As the ADDS, director of ODSS, and a co-chair of the trans-NIH Scientific Data Council, Dr. Gregurick is well positioned to lead the NIH Strategic Plan for Data Science.

Learn more from NIH leadership about Dr. Gregurick’s selection and experience now.


NCI ITCRNew Funding Opportunity for ITCR Education Resource

September 13, 2019

A new National Cancer Institute (NCI) Funding Opportunity Announcement (FOA) establishes an Informatics Technology for Cancer Research (ITCR) Education Resource to support educational activities that enhance the use and usability of ITCR informatics tools and other resources (UE5 Clinical Trial not allowed). Specifically, the awardee will provide short courses in: 

  • Cancer informatics for cancer researchers
  • Optimizing informatics tool usability and user support for informatics tool developers

The courses supporting education in cancer informatics should cover the variety of cancer research domains supported by ITCR tools and incorporate ITCR tools as exemplars for applying informatics methods. The courses in optimizing informatics tool usability and user support should focus on activities that target the needs of currently funded ITCR teams. View the funding opportunity now and submit your application by December 19, 2019.


SBIR National Cancer InstituteFunding Opportunities! SBIR Now Accepting Proposals for New Cloud-Based Analysis and De-Identification Solutions 

September 13, 2019

The National Cancer Institute (NCI) Small Business Innovation Research (SBIR) is now accepting proposals for two new contracts aimed at supporting data analysis and de-identification solutions for cancer research. Applications close Friday, October 23, 2019, at 5:00 p.m. EDT.

The NIH/NCI 407 Cloud-Based Software for the Cancer Research Data Commons (CRDC) contract seeks to provide support for development and implementation of innovative solutions for continued advancement and evolution of cloud-based informatics tools to integrate with the CRDC for broader user community engagement. This mechanism offers small businesses the opportunity to contribute solutions to address unmet challenges of big data analysis that are not currently provided by the existing tools in the CRDC by developing and extending tools and resources to integrate into the rapidly evolving CRDC. Learn more and submit your proposal.

The NIH/NCI 411 De-Identification Software Tools for Cancer Imaging Research contract aims to support development and sustainment of software tools and pipelines for image de-identification, especially for but not exclusive to CT patient datasets and images produced by whole slide imagers (WSI) for digital pathology applications. These tools will selectively remove PHI while retaining other metadata fields that help provide interoperability with other image formats and other data types, such as genomic data and proteomic data. Learn more and submit your proposal.


RSS email Data Science updatesNew RSS Feed Brings Data Science and Informatics Updates Right to Your Inbox

September 11, 2019

Last month, the National Cancer Institute’s Center for Biomedical Informatics and Information Technology (CBIIT) launched a new RSS feed featuring data science and informatics updates. The email goes out weekly, providing readers with upcoming events, news pieces, blogs, and more. Subscribe now to get important updates.


CPTAC PortalUpdated Data Portal Interface for the Clinical Proteomic Tumor Analysis Consortium

September 9, 2019

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) data portal now boasts a new interface. The update also has expanded the search criteria to select for datasets with corresponding images and genomic data. Visit the CPTAC data portal today.


Apply by September 13 to Join NCI's Center for Biomedical Informatics and Information Technology as Clinical BioinformaticianApply by September 13 to Join NCI's Center for Biomedical Informatics and Information Technology as a Clinical Bioinformatician

September 6, 2019

The National Cancer Institute’s (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) seeks a dynamic professional in support of NCI’s Intramural and Extramural Division programs. Apply for this position by Friday, September 13.

The Clinical Bioinformatician will participate in developing concepts and implementation plans for clinical and translational informatics, support relevant requests for information and solicitations, lead NCI project teams, and help translate research program needs into biomedical informatics solutions. The ideal candidate will have experience developing, planning, and implementing clinical and translational informatics solutions that support cancer research programs and initiatives.


Metadata Automation DREAM ChallengeAre You Up for the Challenge? Pre-Register for the Metadata Automation DREAM Challenge

September 3, 2019

The Metadata Automation DREAM Challenge provides an opportunity for developers, cancer informaticists, data scientists, and data engineers to develop a solution to automate metadata annotation. Using structured biomedical data files, challenge participants will develop solutions to automate annotation of metadata fields and values, using available research data annotations (e.g. caDSR) as well as established terminologies and ontologies (e.g. NCIt, LOINC, Mondo, ICD).

A cash prize will be awarded to first, second, and third place winners, and entries will inform future development of the NCI Cancer Research Data Commons (CRDC).

Pre-register and learn more about the Metadata Automation DREAM Challenge. 


Childhood Cancer Data InitiativeWatch the Videocast from the NCI Childhood Cancer Data Initiative Symposium

August 9, 2019

Cancer researchers, scientists, advocates, and stakeholders came together on July 29 – 31 at the National Cancer Institute’s Childhood Cancer Data Initiative (CCDI) Symposium to discuss opportunities to enhance data sharing and collection for progress in childhood, adolescent, and young adult (AYA) cancer research. If you couldn’t attend or wish to review one of the presentations, watch the archived videocast from each day of the event now.

Day 1: Monday, July 29, 5:00 p.m. - 7:30 p.m.

Day 2: Tuesday, July 30, 8:30 a.m. - 12:30 p.m.

Day 3: Wednesday, July 31, 8:30 a.m. - 12:00 p.m.


Scientific DiagramNew Publication Available: Value of Collaboration Among Multidomain Experts in Analysis of High-throughput Genomics Data

August 1, 2019

Dr. Daoud Meerzaman of the National Cancer Institute’s (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) and Dr. Barbara Dunn of NCI’s Division of Cancer Prevention recently published an article, Value of Collaboration Among Multidomain Experts in Analysis of High-throughput Genomics Data, in the Cancer Research Journal. The article offers insights into the challenges faced by non-geneticist healthcare providers when interpreting large-scale genomic data intended for clinical applications and proposes initiatives to address these communication and management hurdles. Read the article now.


Research Specialist Award R50Data Scientists: Apply for the NCI R50 Research Specialist Award by October 18

July 31, 2019 

The National Cancer Institute’s (NCI) R50 Research Specialist Award encourages the development of stable research career opportunities for exceptional scientists who want to pursue research within the context of an existing NCI-funded cancer research program, but not serve as independent investigators. These staff scientists working in research laboratories, core facilities, and data science centers, are vital to sustaining the biomedical research enterprise. The R50 Award is intended to provide salary support and sufficient autonomy so that individuals are not solely dependent on NCI grants held by others for career continuity. Submit your application by October 18, 2019.


Multiple Myeloma Research FoundationMultiple Myeloma Data Released in the NCI Genomic Data Commons

July 17, 2019 

Genomic and clinical data collected for nearly 1,000 cases of multiple myeloma by the Multiple Myeloma Research Foundation (MMRF) over eight years is now being shared with the cancer research community through the National Cancer Institute's (NCI) Genomic Data Commons. Read the guest blog by Dr. Louis M. Staudt, Director of the NCI Center for Cancer Genomics, for more information on what this newly available data means for informing cancer treatments.


Submit a Proposal to Build the Cancer Data Aggregator (CDA) by August 22

July 10, 2019

The functionality of the cancer data aggregator can be described as this: a user is currently on a data portal or application (for example one of the NCI Cloud resources from the Broad Institute, ISB, or Seven Bridges Genomics). That application will connect to the Cancer Data Aggregator through an API that allows users to query parameters for data sets. The aggregator then queries across the Cancer Research Data Commons (which will be secured by Auth/AuthZ authentication), NCI Data Coordinating Centers, and other NIH repositories, aggregating data that matches that query. The data will return to the aggregator to be transformed through a common data model. The aggregated data will then be displayed for the user on the portal or application where they initiated the query.

Frederick National Laboratory for Cancer Research is requesting proposals to develop a query engine called the Cancer Data Aggregator (CDA). The CDA will allow users to aggregate data via queries across the NCI Cancer Research Data Commons (CRDC) nodes, NCI Data Coordinating Center (DCC) repositories,  and other NIH data repositories.  

The CDA is a critical component of the National Cancer Data Ecosystem, a key recommendation from the Cancer Moonshot℠ Blue Ribbon Panel. Integrative cancer research is currently hampered by the fact that important datasets are stored in different repositories. The CDA will allow users to query across datatype-specific and program-specific repositories through a common data model, translating research and results into knowledge to inform cancer treatment and discovery.

Learn more about the CDA and submit your proposal by Thursday, August 22. 


NCI Childhood Cancer Data Initiative Invites Responses and Ideas to Enhance Data Sharing

June 24, 2019

Decorative image - Banner for CCDI Ideascale websiteCalling patients, parents, researchers, clinicians, advocates, data scientists, engineers, and developers! The NCI Childhood Cancer Data Initiative invites you and anyone with a bold idea to submit ideas to enhance data sharing for progress against childhood cancer by August 9th, 2019.

The ideas will help the National Cancer Institute develop recommendations on how to make the most of the federal investment to collect, analyze, and share data to address the burden of cancer in children, adolescents, and young adults.

Read and respond to the questions posed by the initiative.


Vivian Ota Wang, Ph.D.Dr. Vivian Ota Wang of the National Cancer Institute's Office of Data Sharing Recognized as Change Agent for Sexual and Gender Minority Community

June 7, 2019

The National Institutes of Health Office of Equity, Diversity, and Inclusion define change agents as visionaries and cultivators who act as a catalyst for change. Dr. Vivian Ota Wang of the National Cancer Institute’s Office of Data Sharing (ODS) has been recognized as a change agent for the Sexual and Gender Minority (SGM) community and named a 2019 Ally Leader Awardee. In her position as Deputy Director of ODS, Dr. Ota Wang focuses on data access and sharing by bringing together her expertise in race, sex, and gender issues, and experience in science policy and research participation protections. 

Read more about Vivian’s impact and the importance of change agents now. 


Tony Kerlavage, Ph.D.Dr. Tony Kerlavage Named Director of NCI’s Center for Biomedical Informatics and Information Technology (CBIIT)

May 22, 2019

The National Cancer Institute (NCI) announces Dr. Tony Kerlavage as Director of the Center for Biomedical Informatics and Information Technology (CBIIT). Tony has served as acting CBIIT director for two years and previously served as the Cancer Informatics Branch chief since 2012. Tony’s expertise and contributions to the cancer research community throughout his career make him a valuable addition to NCI leadership. 

Bookmark datascience.cancer.gov to stay up to date on current data science and informatics news, including insights from Dr. Kerlavage on data science at NCI, as CBIIT continues to support the NCI mission.


Amanda, a young cancer patient, and her mother Rosemary (left) at the NIH Clinical Center talking with a doctor from the NCI Pediatric Oncology Branch.NCI Invites Abstracts for Childhood Cancer Data Initiative (CCDI) Symposium

May 21, 2019

NCI invites submission of abstracts to be considered for poster presentations at the Childhood Cancer Data Initiative (CCDI) Symposium, July 29–31 in Washington, D.C. Areas of interest for poster submission include research, methodologies, and tooling with focus in any of the following categories:

  • Scientific and clinical research data needs in childhood and adolescent and young adult (AYA) cancers
  • Establishing meaningful datasets for clinical care and associated research progress
  • Building infrastructure to enable federation among disparate databases
  • Extracting knowledge from data
  • Developing adequate and equitable policies for shared data resources 

Learn more about submitting your abstract for consideration.


Cancer Data Science Pulse Blog header imageNew Name and Home for Cancer Data Science Blog and Seminar Series

May 21, 2019

The National Cancer Institute’s (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) is excited to introduce two new features to the datascience.cancer.gov website. CBIIT’s former informatics blog, renamed as the Cancer Data Science Pulse, provides insights on trends, policies, initiatives, and innovation in the data science and cancer research communities. In addition, the CBIIT Speaker Series has been updated to the Data Science Seminar Series, a bi-weekly talk where thought leaders and innovators within and outside of NCI can share their work, discuss trends, and stimulate collaboration.

Visit the news and events section to find new blog posts and upcoming seminar series talks.


Informatics Technology for Cancer Research Request for ApplicationITCR RFAs Available for Innovative, User-Friendly Informatics Tools 

April 3, 2019

Four funding opportunities are now available from the NCI Informatics Technology for Cancer Research (ITCR) program. Applicants should focus on innovative, research-driven, user-friendly informatics technology that spans the cancer research continuum. The requests for applications (RFAs), aimed at successive stages of informatics technology, are for algorithm development, prototyping and hardening, enhancement and dissemination, and sustainment. Letters of intent are due 30 days prior to the deadline.

Learn more about these funding opportunities.


BD-STEP Trains Tomorrow’s NeBD-STEP Big Data Training Programxt-Gen Big Data Scientists

March 19, 2019

The National Cancer Institute (NCI) and the Veterans Health Administration (VHA) of the Department of Veterans Affairs (VA) are recruiting postdoctoral fellows with backgrounds in physical sciences, advanced mathematics, or engineering for the Big Data Scientist Training Enhancement Program (BD-STEP). BD-STEP is a two-year fellowship that matches individuals who have experience with data modeling and computer programming, as well as interests in clinical, health services, and bioinformatics research, to VA medical centers where they will participate in collaborative training in research-focused environments. This opportunity prepares the next generation of healthcare data scientists who will be capable of using large clinical and research datasets to efficiently and effectively advance cancer research.

Learn more about this fellowship opportunity and program.


Funding GrantsNew NCI K99 Award for Early Stage Postdoctoral Researchers (K99/R00)

January 30, 2019

The Pathway to Independence Award for Outstanding Early Stage Postdoctoral Researchers (K99/R00) is a new NCI training award suited towards postdoctoral fellows pursuing careers in data science and cancer control science. Unlike other K awards offered by NCI, this Early K99 is designed for researchers who typically require a limited period of mentored training beyond their doctoral degrees. This award will help these researchers completed the necessary training and make a timely transition to independent faculty positions.

Read more about this award and how to apply.


hexagons holding icons meaning information overlayed over bright colors and numbers

NIH Releases New Strategic Plan for Data Science

June 2018

NIH released its first Strategic Plan for Data Science in an effort to support the storing, managing, standardizing, and publishing of data produced by biomedical research. This plan describes NIH’s overarching goals, strategic objectives, and implementation tactics for promoting the modernization of the NIH-funded biomedical data science ecosystem.

Read the strategic plan, and learn more about the mission of advancing data science at NIH.


Image for the American association for cancer research 2019, cancer research focus on computer resources

Freely Available Special Issue of the AACR Journal Cancer Research: NCI Funded Computer Resources

November 2017

The National Cancer Institute (NCI), in collaboration with the American Association for Cancer Research (AACR), launched a special open-access issue of the journal, Cancer Research, with a focus on NCI funded computer resources. This special issue features an editorial by Drs. Juli Klemm, Warren Kibbe, and John Quackenbush. The issue highlights NCI’s Informatics Technology for Cancer Research (ITCR) Program, Cloud Resources, and Genomic Data Commons. It includes papers on a range of topics such as computing tools, machine learning, and data analysis in biomedical science.

Check out this special online-only issue now to learn about these freely available computing tools and resources that you can incorporate into your work.

 

 

Cancer Data Science Pulse Blog

The Cancer Data Science Pulse blog provides insights on trends, policies, initiatives, and innovation in the data science and cancer research communities from professionals dedicated to building a national cancer data ecosystem that enables new discoveries and reduces the burden of cancer.

 

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