Author: Susan Gregurick

Headshot of Susan Gregurick.

Before transferring to the NIH's Office of Data Science Strategy, Susan directed the NIGMS division that supports a range of research and training activities, including in the fields of computational biology, bioinformatics, mathematical and statistical biology, and biomedical technology development.

Posts by Susan Gregurick

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Request for Input on the Science Drivers Requiring Capable Exascale High-Performance Computing

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UPDATE: The response deadline has been extended to November 13.

On July 29, 2015, the White House issued an Executive Order establishing the National Strategic Computing Initiative as a government-wide effort to create a coordinated, cohesive, multi-agency strategy to maximize the benefits of High Performance Computing (HPC) for the United States. In support of this initiative, the Department of Energy, National Science Foundation and National Institutes of Health are seeking your input to identify scientific research that would benefit from a greatly enhanced new generation of HPC computing technologies and architectures. The request for information (RFI) asks for responses in scientific domains including the biomedical and physical sciences, mathematics, geosciences, energy sciences and engineering research.

We hope to hear from our research communities on topics that include:

    • Research challenges that would need the projected 100-fold increase in application performance.
    • Specific barriers in current HPC systems that limit scientific research.
    • Capabilities needed for the data-intensive sciences.
    • Additional barriers in such areas as training, workforce development or collaborative environments.

While this RFI invites comments on several specific topics, we would also welcome any comments that you feel are relevant to this initiative.

To respond to this RFI, send an email to NIGMS_exascale@nigms.nih.gov by October 16.

If you have any specific questions about the RFI, please let me know.

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Wanted: Genetics and Developmental Biology Division Director

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Search Committee Members:

William Gelbart, Harvard University

Susan Gregurick, National Institute of General Medical Sciences, Chair

Carole Heilman, National Institute of Allergy and Infectious Diseases

Pamela Oliver, Office of the Director, NIH

Alejandro Sánchez Alvarado, Stowers Institute for Medical Research

Jeffery Schloss, National Human Genome Research Institute

Belinda Seto, National Eye Institute

Dinah Singer, National Cancer Institute

Laura Stanek, Office of Human Resources, NIH

UPDATE: This vacancy announcement has been extended and will now be open for 90 days from April 13, 2015.

With the selection of Genetics and Developmental Biology (GDB) division director Judith Greenberg as NIGMS deputy director, the search is now open for an outstanding individual to serve as the GDB director.

GDB has supported many of the exciting fundamental discoveries that have led to deeper knowledge of how cells and organisms function as well as to new technologies and approaches. The division is organized into two branches, one focused on genetic mechanisms and one on developmental and cellular processes, and has 11 scientific staff members who serve as program officers.

While concentrating on general principles of genetics, gene expression and developmental biology, often using model organisms, research supported by GDB underpins studies on human health and disease. This position offers important opportunities to set scientific priorities, lead change and improve the research enterprise.

The division director reports to the NIGMS director and is a member of the NIGMS senior leadership team, which helps set policies and priorities for the Institute. There are also opportunities to participate in and advise on NIH-wide activities and collaborations with other federal agencies.

Candidates must have an M.D., Ph.D. or equivalent degree in a field relevant to the position. The ideal candidate will have considerable research experience demonstrating a strong understanding of genetics, gene expression, and/or developmental biology. In addition, candidates should possess recognized research management and leadership abilities. Broad knowledge of the fundamental mechanisms of inheritance, development and cell function is desired.

Continue reading “Wanted: Genetics and Developmental Biology Division Director”

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NIH Data Science Leader’s Vision of a Digital Enterprise for Biomedical Research

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Phil BourneI recently had the opportunity to talk to Phil Bourne, NIH’s associate director for data science, about some of the current Big Data to Knowledge (BD2K) initiative activities. I asked him how they tie together his vision of a digital enterprise for biomedical research and how they might benefit NIGMS grantees.

Phil explained that the goal of his office, commonly referred to as ADDS, is to achieve efficiencies in biomedical research, such as by making it easier for researchers to locate and manipulate data and software. “If we could just achieve a 5 percent improvement in efficiency in research that would be, in NIH budget dollars, more than $150 million a year that could be spent on funding more people and doing more research,” he said.

An active area that we at NIGMS are engaged in with ADDS is sustaining biomedical data resources, of which we support a fair number. As someone who previously set up databases and who now oversees them, I’m very passionate about this topic. A key question is how to sustain support of data resources in the current research budget environment. Led by Phil’s team, NIH has issued a request for information on sustaining biomedical data repositories that seeks input on every aspect of maintaining these resources. I encourage you to share your ideas by the March 18 response date.

Training is important in Phil’s vision for a digital enterprise, too. He told me of a number of recent training activities at NIH, including a “software carpentry” workshop for experimental researchers to learn how to use a wide variety of analysis tools. In a blog post about this and another event, the ADDS office asks for suggestions on other types of data science courses to offer. They want to provide workshops that train more experimentally versed scientists to work with big data and take those skills back to their labs. In addition, the ADDS office is planning to stand up a workforce development center to catalog classroom and online courses in the data sciences.

Another effort that’s in the works is creating a virtual space called the Commons where researchers can share, locate, utilize and cite datasets, software, standards definitions and documentation. Phil anticipates that the first components of the Commons will be available in 2016.

I’m really excited about Phil’s efforts and believe that they will help drive the “data quantum leap” I described in my first Feedback Loop blog post.

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Wanted: Biomedical Technology; Bioinformatics and Computational Biology Branch Chiefs

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We’re recruiting for two outstanding individuals to serve as branch chiefs within our Division of Biomedical Technology, Bioinformatics, and Computational Biology (BBCB), where they will oversee the scientific and administrative management of either the Biomedical Technology Branch or the Bioinformatics and Computational Biology Branch. In addition, they will be responsible for advising, directing and evaluating program activities for a portfolio of research grants in one of the branch areas.

The vacancy announcement, which includes detailed descriptions of the job requirements and application procedures, is scheduled to post this weekend on USAJOBS.gov and remain open for a short period. We’ll update this post early next week with a link to the announcement and the closing date. In preparing an application, Applying for Scientific Administration Jobs at NIGMS may offer other useful information.

Now is a particularly exciting time for the division. In previous posts, I’ve talked about our efforts in big data and open science. But these are just two areas of BBCB interest. The main focus of the Biomedical Technology Branch is supporting the research and development of new or improved instruments, methods and approaches that have broad application to biomedical research. The Bioinformatics and Computational Biology Branch is primarily focused on funding basic biomedical research that leads to an integrative understanding of biomedical systems, as well as funding research to create or maintain databases and to develop methods to manage, visualize and analyze data.

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Fostering Open Science

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Recently, I participated in a workshop on Open Science: Driving Forces and Practical Realities. The idea to make scientific research, data and information accessible to the public isn’t new and arguably has historical roots dating back to the late 1600s, when academic journal publishing began. But it’s particularly timely today in light of the rapid increase in the volume of data and the value it has to the public.

During the workshop, we explored the technical, financial, political and cultural forces that drive open science and how these forces impact information sharing, re-use, interoperability and the preservation of the scientific record. I also talked about NIH’s ongoing commitment to open science.

In 2003, NIH created a Data Sharing Policy, and, in 2008, it issued a Public Access Policy for publications. A Genomic Data Sharing Policy is currently in draft form. All of these documents communicate the need to ensure public access to the relevant biomedical data, information and publications that are a result of federally funded biomedical research.

In addition to establishing these guidelines, NIH funds projects that foster open science, including the RCSB Protein Data Bank , The Cancer Genome Atlas, The Cancer Imaging Archive , the Neuroimaging Informatics Tools and Resources Clearinghouse  and PhysioNet . NIH is also playing a role in crowdsourced projects, such as the systems biology-related Dialogue for Reverse Engineering Assessments and Methods challenges (no longer available), as well as projects to develop common languages for research, such as the Common Data Element Resource Portal. Another exciting NIH-funded initiative is the Medical Device “Plug and Play” Interoperability Program , which aims to create cost-effective and innovative third-party medical “apps” for clinical diagnosis, treatment, research and safety.

In preparing my presentation for the recent workshop, I recalled the day when I heard about the biomedical community taking a quantum leap forward into open science. It was the early spring of 1996, and I was eating lunch with my graduate student and postdoc colleagues. We were discussing the International Large-Scale Sequencing Meeting and the resulting “Bermuda principles” for the release of data generated by the Human Genome Project. We were particularly excited to learn that scientists associated with that project had unanimously agreed that all genomic sequencing data should be freely available and in the public domain prior to publication.

Nearly 20 years later, the move toward open science continues to offer a forum for scientists–from fields that range from astronomy and physics to medical and clinical research–to discuss policies and practical tools for collaboration. It also allows the community to come together and tackle the challenges and unique opportunities of sharing science in a truly collaborative way. I invite you all to join me in the discussion and in furthering progress in this important area.

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Enabling Science through Data (Big and Otherwise)

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NIH’s recent focus on data-intensive and data-driven biomedical research makes this an exciting time for me to be joining NIGMS and leading its Division of Biomedical Technology, Bioinformatics, and Computational Biology (BBCB).

New steps toward harnessing the power of data began well before my arrival and include the NIH Big Data to Knowledge (BD2K) initiative. The overarching aim of this initiative is to enable, by the end of this decade, a “quantum leap” in the ability of the biomedical and behavioral research enterprise to use the growing volume of complex data to produce important insights into biological systems. This is an ambitious goal that requires the collective engagement and expertise of NIH’s many institutes, centers, and offices, including NIGMS, as well as the scientific community.

My colleagues from across NIH have already come together to discuss future solutions that will benefit NIH and the research community as a whole. We recognize that no one-size-fits-all solution will emerge as the “data quantum leap.” Our hope is that by engaging academic, industrial and other biomedical stakeholders, we will impact the volume, variety, velocity, viability and ultimately value of the data that NIH invests in.

To jumpstart this activity, NIH recently issued a new funding opportunity announcement (FOA) for Centers of Excellence for Big Data Computing in the Biomedical Sciences. The purpose is to establish an interactive consortium of centers that will develop approaches, methods and software tools for the aggregation, integration, analysis and visualization of data across NIH-funded research areas. NIH also has issued a request for information on the development of analysis methods and software for big data; responses are due by September 6.

NIGMS and the BBCB staff were actively involved in crafting the new FOA and, more generally, have played a central role in the creation and organization of the BD2K initiative. We will continue to be active partners in this endeavor.

Big data is just one example of the division’s efforts. We foster research in a range of fields, including computational biology, bioinformatics, mathematical and statistical biology, and biomedical technology development. We also support programs that train people in many of these areas.

I’m so happy to be involved in shaping the division’s activities, and I look forward to working together with many of you to continue innovating basic biomedical research.