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DataScience@NIH The BioCreative VI workshop will take place in October 18-20, Bethesda, Maryland, at the Double Tree hotel (walking distance from the NIH main campus). This event consists of five challenges:
In addition, BioCreative VI will host a general session to provide an opportunity to discuss related work to BioCreative topics, including data set preparation, evaluation, biomedical information extraction. We are soliciting submission of your bioNLP/biocuration/text mining work in the form of a 2 page abstract (more information can be found in the links below). There is an opportunity to be selected for oral presentation during the general session. Keynote speakers are:
Planned panels are:
For more information, please visit: http://www.biocreative.org/ Registration for attendance: http://www.udel. Travel Funds are available for US participants for the amount up to $700 to participate in the BioCreative workshop. Women, under-represented minorities, students, and post-doctoral fellows are encouraged to apply. NIAID is offering an exciting fellowship opportunity in data science for recent graduates (past 5 years) who are interested in acquiring a unique training experience involving rotations throughout the Institute to either intramural or extramural programs engaged in data-intensive science. Please see the following link for more information: https://www. The BD2K KnowEng Center is about to release its platform for genomics data analysis. See a presentation by the co-director of the Center for a brief overview of the KnowEnG system from the user's perspective, while also touching upon some key features of the underlying technologies. "KnowEnG: Knowledge Network-guided analysis of genomics data on the Cloud" 9/20/2017, 11AM Central Time (12 PM ET). NCATS Funding Opportunity Aimed at Building Computational "Brain" Prototype to Mine Disparate Data NCATS announced it is seeking applications to develop reasoning tool prototypes for its Biomedical Data Translator (Translator) program. Through a unique funding mechanism, candidates must complete a series of computational tasks in the first part of a three-step application process to access the complete funding opportunity announcement (link is external) (FOA). The tasks, or "challenge," are designed to provide important background and insights for building a biomedical reasoning tool prototype. Through its Translator program, NCATS aims to develop a computational platform that brings together disconnected biomedical data types to reveal complex relationships that help scientists better understand disease behavior and biology, and develop treatment options. Through this latest FOA, NCATS intends to fund up to three awards of approximately $1 million each to create Translator reasoning tool prototypes. The tool, or "brain," will contain software algorithms needed to coordinate the different data sources and types to find relevant patterns and relationships among them and assemble the appropriate information to answer complex biomedical questions. NCATS supports Translator through its Cures Acceleration Network (CAN), which enables high-risk, high-reward research funding and includes Other Transaction authority (OTA). OTA allows NCATS to employ innovative methods to support applications outside the normal National Institutes of Health funding approaches. This Translator "challenge" process will help ensure applicants have the requisite technical and problem-solving skills to develop a reasoning tool in a relatively short period. By successfully completing each challenge task, the applicant gains access to the next part of the FOA, and ultimately, the instructions for submitting the required concept letter which is due on Sept. 22, 2017. Reminders You May Need DC DATACON: A focus on the applied tools, technologies, and methodologies that make data science work. Join the conversation! Data Community DC is proud to partner with George Washington University on Tuesday, October 3, 2017, to bring together nearly 1,000 stakeholders in the data community of the National Capital Region. Are you part of the data science community in the Mid-Atlantic Region? Commercial, government, academia, research, and nonprofit—come gather with your community and be a part of charting the path ahead. Join us to participate in a robust agenda of highly relevant speakers and presenters. DC DATACON seeks to inspire conversation as the Mid-Atlantic region lays the groundwork for the direction data science will take in years to come. At this inaugural DC DATACON, we aim to explore topics that focus on the things that we need to do to make sure our work as data scientists has a real, tangible impact including organization, design, and technology. We will drive conversations about getting data science out of the lab and into the enterprise so we can finally begin using data as a strategic asset. Looking into our special concentration of public and private sector organizations, this region is ripe with qualified people to engage in the dialogue. Come participate in discussions focused on the impact data science has on industries including intelligent transportation, unmanned aerial systems, cybersecurity, public policy, defense, and intelligence. https://www.ncsi.com/ The NIH Data Science Mentoring program is now accepting applications from NIH-affiliated individuals interested in participating in the program as either a mentor or a learner. Skills in the area broadly defined as data science, like programming in languages like R and Python, machine learning, and data visualization, are increasingly important in many areas of biomedical research. This program provides an opportunity for mentors with experience in these areas to help learners acquire the skills they need. We suggest mentors and learners meet for up to one hour every other week at a place and time convenient to both of them, but mentoring pairs can establish a mutually-agreed-upon approach that works best for them. There is no required ongoing commitment; either mentor or learner can opt out at any time. Mentors and learners will receive a guidelines document to help them make the most of the mentoring experience and the program committee welcomes questions and feedback. The program committee will make an effort to pair everyone who applies, but because we typically receive more applications from learners than from mentors, we cannot guarantee that we will be able to pair every learner with a mentor at this time. To sign up as either a mentor or a learner, please complete the form at https://goo.gl/forms/ The BD2K Training Coordinating Center has been creating and populating the Educational Resource Discovery Index (ERuDIte), a database of 10,000+ data science educational resources from collective BD2K activities and from around the web.
The bioCADDIE DDICC Core Team is pleased to announce the release of DataMed v3.0! DataMed is designed to be for data what PubMed has been for scientific literature. This version of the Data Discovery Index (DDI) prototype includes many additional datasets and reflects considerable user/stakeholder input. The user interface has also been updated to reflect this input.
Data Science Events: NIH Data Science Week 2017 The NIH Data Science week is a biannual series of talks and workshops focused on data science hosted by the Data Science and Bioinformatics Scientific Interest Groups. Thursday, September 21st 11 am–12 pm Speaker: Jake Lever from UBC–NLM Visitor Center - PubRunner: Keeping text mining up-to-date with the latest publications Biologists face a daunting challenge when trying to read all relevant scientific literature for their field. Text mining tools are designed to assist them by aiding search, summarizing the latest research and identifying important patterns in the literature. However, many published tools lay dormant, as code is not public and any results shared become out-of-date as new publications enter the field. Through the NCBI hackathons initiative, we have built PubRunner, a framework for managing download of the latest publications, execution of text mining tools, and sharing of the results. This effort aims to help research groups keep text mining tools alive and make text mining results even more valuable to the biology community. 3 pm–4 pm Speaker: Imran Haque from Freenome–NLM Lindberg Room, Bldg 38 - Embracing heterogeneity: statistical limitations and opportunities in early detection liquid biopsies The discovery of tumor-derived circulating cell-free DNA (ctDNA) in cancer patients has ignited interest and investment in developing blood-based assays to detect cancer at early, treatable stages. The existence of many analytical methods (dPCR, BEAMing, UMI-tagged high-depth NGS) to detect mutated tumor-derived material combined with increasing knowledge of the characteristics of tumor genomes has driven an empirical approach of "more is better" to translate assays developed on late-stage cancer patients to the early detection setting. However, there exists a lack of data and analysis on the feasibility of such a translation. In this presentation, Imran will analyze fundamental statistical challenges in liquid biopsy, including benign somatic heterogeneity, and quantitative limitations in the analysis of patient samples. He will further demonstrate that these limitations arise from upstream statistical assumptions about the nature of the problem and that relaxing these assumptions admits potential solutions of a different flavor: making use of modern machine learning to integrate both prior data as well as multi-analyte analysis on individual samples to address the fundamental challenges of liquid biopsy. Upon approval by presenters, materials or links will be available at https://www.slideshare.net/
Submissions: We welcome your input! Submissions must be received prior to 12:00 noon ET on Monday to be included in that same week's edition. If you are requesting attendance at an event by Federal employees, it is recommended that you submit your event information a minimum of one month in advance. To submit a news item, contact: Grace.Middleton@nih.gov. Follow DataScience@NIH on This service is provided to you at no charge by the Office of Communication and Public Liaison.
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Tuesday, September 19, 2017
DataScience@NIH Updates from the NIH Interim Associate Director for Data Science
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