Enabling Science through Data (Big and Otherwise)

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.

Funding Opportunities: Bridges to the Baccalaureate; Common Fund Awards; Legacy Community-Wide Scientific Resources; Research Centers in Injury and Peri-Operative Sciences

You may be interested in these recent funding opportunity announcements (FOAs):

Bridges to Baccalaureate Program (R25)
(PAR-13-333)

Purpose: Promote partnerships/consortia between community colleges or other 2-year post-secondary educational institutions granting the associate degree and colleges or universities that offer the baccalaureate degree, with the goal of increasing the pool of community college students from underrepresented backgrounds who pursue research careers in the biomedical and behavioral sciences and who will be available to participate in NIH-funded research
Application due dates: October 18, 2013; September 25, 2014; September 25, 2015
NIGMS contact: Michelle R.J. Hamlet, 301-594-3900

NIH Director’s Pioneer Award Program (DP1)
(RFA-RM-13-006)

Purpose: Support exceptionally creative individual scientists at any career stage who propose pioneering, and possibly transforming, approaches to major challenges that have the potential for unusually high impact on a broad area of biomedical or behavioral research
Application due dates: October 18, 2013; October 10, 2014; October 9, 2015
NIH contact: Ravi Basavappa, 301-435-7204

NIH Director’s New Innovator Award Program (DP2)
(RFA-RM-13-007)

Purpose: Support exceptionally creative early stage investigators who propose bold and highly innovative new research approaches that have the potential for major impact on broad, important problems in biomedical and behavioral research
Application due dates: October 25, 2013; October, 17, 2014; October 16, 2015
NIH contact: Ravi Basavappa, 301-435-7204

Limited Pilot for NIGMS Legacy Community-Wide Scientific Resources (R24)
(PAR-13-324)

Purpose: Maintain existing NIGMS research resources that demonstrate a high value to a community of NIGMS-supported researchers and that are no longer eligible for support under their original initiatives
Letter of intent due date: 30 days before the application due date
Application due dates: October 15, 2013; October 15, 2014; October 15, 2015
NIGMS contact: Mary Ann Wu, 301-435-0787

Research Centers in Injury and Peri-Operative Sciences (P50)
(PAR-13-291)

Purpose: Improve understanding at all levels of the biological processes invoked after traumatic or burn injury, or in critically ill patients, including pertinent aspects of wound healing; and foster translational research, bringing basic scientific observations and principles into the clinical arena and using clinical observations to generate or validate mechanistic hypotheses
Letter of intent due date: 6 weeks before the standard due date
Application due date: Standard dates apply
NIGMS contact: Scott Somers, 301-594-3827

Advancing Emergency Care Research

I’m the director of the newly created NIH Office of Emergency Care Research (OECR), which is housed in NIGMS. For the past 11 years, I was an emergency medicine physician and clinical researcher. So you might be wondering why I’m writing a post for a blog primarily read by thousands of basic scientists. Don’t stop reading, though, because OECR and NIGMS-funded research have more in common than you might think. Let’s take a quick look at one area where basic and emergency medicine research interests converge—sepsis.

NIGMS supports both fundamental studies and clinical research on sepsis, including the PRoCESS (Protocolized Care for Early Septic Shock) clinical trial. This study is designed to determine if early intervention with rigorous, standardized care in sepsis and septic shock can improve clinical outcomes. It’s an astonishingly important effort to address a disease that often presents to the emergency department and that has a mortality rate of about 30 percent. Should the study demonstrate improved outcomes, it will change the care of some 750,000 Americans who develop sepsis each year.

In addition to sepsis, NIGMS funds research in other areas relevant to emergency medicine, including trauma, burn injury, wound healing, and anesthesia.

I’m committed to helping all parts of NIH improve outcomes for patients in need of emergency treatment, and stepping into the OECR position is allowing me to focus on the national challenges that face emergency medicine research. Toward this end, OECR has four objectives:

  • To develop and refine NIH’s existing research portfolios in emergency care;
  • To coordinate research projects that involve multiple NIH components;
  • To create ways to fund new research that impacts patients with time-sensitive medical conditions; and
  • To promote the training of the next generation of emergency care researchers.

It’s a big mission for a small office, but we are fortunate to have many energetic partners across NIGMS, NIH and the broader community.

Whether you’re a basic scientist or a clinician, the ultimate goals are the same, so I welcome your interest in and input on OECR activities.

Additional Reviewer Scoring Guidance for Overall Impact Scores on Research Applications

NIH has posted additional scoring guidance for reviewers to consider when determining overall impact scores for grant applications. Here are answers to some key questions about this new guidance.

Why provide more guidelines?

Scientific review officers and program directors noticed that reviewers have tended to arrive at overall impact scores by comparing the number of weaknesses and strengths in an application, rather than balancing the importance of the weaknesses and strengths. In addition, there was significant compression of overall impact scores around the perceived funding range. Both practices made it more difficult to gauge reviewer assessments.

What’s changed?

The additional guidance chart simplifies and clarifies the way in which reviewers should evaluate the overall impact of an application. In particular, it encourages reviewers to focus on the importance of the research problem and the likelihood that the project will succeed. The chart emphasizes a balanced assessment of the review criteria and the use of the entire scoring range. The general Scoring System and Procedure also includes a new, simplified scoring guidance chart for assigning individual criterion scores.

When will this change occur?

Some Center for Scientific Review (CSR) study sections used the new guidelines in application reviews for May 2013 advisory council meetings. So that these applications would not be disadvantaged by the deviation from the impact score distribution of previous review cycles used for percentiling, CSR recalculated the percentile base. The vast majority of study sections and special emphasis panels are using the new scoring guidance with the reviews for fall 2013 advisory council meetings.

Note: New scoring guidelines are also available for fellowships, career awards and institutional training grants.

Looking Forward

Having been a fan of Jeremy Berg’s Feedback Loop posts, it’s a great pleasure to be writing one myself. I am very excited to be at NIGMS, and I am honored to have the chance to lead this extraordinary institute.

Over the past year, whenever I asked anyone familiar with NIGMS what the best thing about it was, they all said the same thing: the people who work there. My own observations have been completely consistent with these assessments. The staff at NIGMS is an exceptional group, deeply committed to ensuring that the biomedical and behavioral research enterprise thrives. No one embodies this commitment better than Judith Greenberg, who has done an outstanding job over the past 2 years steering the Institute through challenging times. I hope you will join me in thanking her for everything she has done.

A key part of Jeremy’s legacy at NIGMS was increasing communication between the Institute and the scientific community. I intend to stay on this course, using the Feedback Loop as well as other mechanisms to catalyze discussions. I encourage you to join in these conversations and to suggest specific questions that you’d like to see us address.

I also intend to push forward the data collection and analysis efforts begun by Jeremy, both to help inform our discussions with the scientific community and to guide our policy decisions.

Among my first orders of business are to conduct a thorough analysis of NIGMS’ grant portfolio and to begin developing a new strategic plan for the Institute. The overall goal of these synergistic undertakings is to ensure that we are investing the taxpayers’ money in the most efficient and effective way possible. Science and society both evolve rapidly, and the structures and strategies that worked well in the past are not necessarily optimal for the future. We will be thinking broadly, using data to inform our analyses, and we will be seeking your ideas and innovations.

This would also be a good time for the scientific community to engage in a parallel process of introspection, examining topics ranging from how the research enterprise is organized to how the impact of scientists’ work is assessed and recognized through peer review and other mechanisms. The process could happen both at a local level—within your own institutions—and at a national one, perhaps led by the relevant scientific and academic societies.

I will always be happy to hear your thoughts and suggestions, either through this blog or directly at jon.lorsch@nih.gov. I am looking forward to working with you!

FAQs on Public Access Policy Compliance and Publication Reporting in Progress Reports

Following on from my earlier post, Progress Reports and the Public Access Policy, I’d like to share answers to a few of the questions program directors/principal investigators (PDs/PIs) have asked about compliance procedures.

I didn’t submit my paper to PubMed Central until recently and my progress report is due. They tell me it may take 6 weeks to complete the process. What should I do?

Respond promptly when the NIH Manuscript Submission System (NIHMS) requests that you approve the version to be posted so your PMCID can be issued as quickly as possible. Also, check with your sponsored projects or research administration office about procedures during a possible gap in funding.

The public access policy requires papers to be submitted to the NIHMS upon acceptance for publication. Because so many PDs/PIs are still catching up on submitting their publications, PubMed Central processing times are much longer than the usual 2 weeks. As NIH announced in February, noncompeting continuation awards will not be made until publications arising from that grant are in compliance with the NIH Public Access Policy.

The law mandating the Public Access compliance requirement is based on the use of grant funds for published research. When in doubt about publication-grant associations, contact your NIH program official (PO).

Should I report ALL my grant’s publications in my annual progress report?

No. Just report the publications arising from this grant’s funding during the single grant year you’re reporting.

Even if they have only recently been added to your NCBI My Bibliography, don’t include publications from previous grant years. You should still make sure the earlier publications have PMCIDs, because it’s the law and a legal term and condition of your NIH award. In addition, you’ll need PMCIDs for competing renewal applications and NIH biosketches.

I inadvertently assigned a publication to my RPPR that describes work not funded by the grant being reported. What can I do?

If you realize this BEFORE the RPPR (or PHS 2590) is submitted to NIH by your sponsored projects or research administration office, you can remove the link in the My Bibliography Award View display by unchecking the box. (Yet another reason to run the Public Access Compliance report early: Making corrections is easy!)

A lock icon Lock icon indicates that a publication-grant connection has already been recorded. A yellow lock means the paper was linked to the award in the NIHMS. To undo this association, you’ll need to contact the NIHMS Help Desk. A gray lock means the paper has already been officially reported to NIH as arising from the award. To undo that association, you’ll have to officially amend the report that triggered the lock. Please contact the NIH PO for the grant. If your PO approves the correction, ask him or her to e-mail PublicAccess@mail.nih.gov to execute the change.

I thought the journal’s publisher would submit my paper for me. Why is the citation marked “noncompliant”?

The NIH Public Access Web site describes the four submission methods (A, B, C and D) and lists for each method what the publisher will do, what an author must do and what a designee can help with. Different publishers, and even different journals from the same publisher, follow different practices. The key is for you and any other authors to understand which method you and your publisher have agreed to. Perhaps the most common issues are:

  • An author expects a Method B publisher to complete the entire compliance process without having made a specific arrangement with the publisher.
  • An author (or designee) submits the final, peer-reviewed manuscript directly to the NIHMS (Method C) or a Method D publisher submits the manuscript, but one of the authors does not follow through to:
    • Authorize the NIHMS to process the manuscript to PMC format (a quick return e-mail), and
    • Approve the formatted version to be posted on PubMed Central.

All authors should agree on who will do the various steps. And it’s a good idea to have a back-up plan.

My paper was published as an open access article. Why do I need a PMCID?

Journals and publishers are free to change their access policies at any time or to remove papers that have been posted. NIH is required by law to assure that papers describing work funded by our grants are and remain available to the public through PubMed Central.

What if I have other questions?

Contact your PO, e-mail PublicAccess@mail.nih.gov and/or visit the NIH Public Access Policy Web site.

Encouraging the Use of Individual Development Plans

Strategic Plan for Biomedical and Behavioral Research TrainingMany of the themes in our strategic plan for research training have been echoed by the Biomedical Workforce Working Group of the Advisory Committee to the Director, NIH. Among these is the use of individual development plans (IDPs) to facilitate career development discussions and planning between mentees and mentors. I’m delighted to share some progress on this front.

A recent NIH Guide notice encourages institutions to:

  • Develop an institutional policy requiring an IDP for every graduate student and postdoctoral scientist supported by any NIH grant, and

For more details, read this blog post from NIH’s Sally Rockey.

The Blueprint for Implementation of our training strategic plan provides links to resources for developing IDPs, including AAAS’s myIDP Exit icon Web site. Another source of useful tips is a presentation on “Facilitating Career Development through Individual Development Plans” Exit icon given by Philip Clifford of the Medical College of Wisconsin at our recent Training, Workforce Development, and Diversity Program Directors’ meeting.

IDPs are a valuable tool to help graduate students and postdocs identify their career goals and what they need to accomplish to achieve those goals. They are one part of the changing conversations about preparing trainees for the broader landscape of exciting biomedical careers.

Funding Opportunities: Research and Academic Career Development Awards; International Cooperative Biodiversity Groups; Program Project Grants; Instrument Development for Biomedical Applications

You may be interested in these recent funding opportunity announcements (FOAs):

Institutional Research and Academic Career Development Awards (IRACDA) (K12)
(PAR-13-290)

Purpose: Develop a diverse group of highly trained biomedical and behavioral scientists through support of a traditional mentored postdoctoral research experience at a research-intensive institution combined with an opportunity to develop academic skills, including teaching, through workshops and mentored teaching assignments at a partner institution
Application due dates: October 2, 2013; September 24, 2014; September 24, 2015
NIGMS contact: Shiva P. Singh, 301-594-3900

Limited Competition: International Cooperative Biodiversity Groups (U19)
(RFA-TW-13-001)

Purpose: Address the interdependence of natural products exploration for potential applications in health, with investments in research capacity that support sustainable use of these resources, the knowledge to conserve them, and equitable partnership frameworks among research organizations in the United States and low- and middle-income countries
Letter of intent due date: October 20, 2013
Application due date: November 20, 2013
NIGMS contact: Barbara Gerratana, 301-594-3827

Support of NIGMS Program Project Grants (P01)
(PAR-13-280)

Purpose: Conduct research that aims to solve a significant biological question within the NIGMS mission through collaborations with outstanding scientists working on different aspects of a similar problem
Application due date: Standard dates apply
NIGMS contacts:
Cell Biology and Biophysics, Catherine Lewis, 301-594-0828
Genetics and Developmental Biology, Judith H. Greenberg, 301-594-0943
Pharmacology, Physiology and Biological Chemistry, Michael Rogers, 301-594-3827
Biotechnology, Bioinformatics and Computational Biology, Susan Gregurick, 301-451-6446

Instrument Development for Biomedical Applications (R21)
(RFA-GM-14-014)

Purpose: Develop new or improved instrumentation with broad applicability to biomedical research
Application due date: October 10, 2013
NIGMS contact: Fred K. Friedman, 301-435-0775

Chemical Biology Career Workshop Builds Model for Similar Efforts

CBI Career Development Conference Program CoverAn action recommended in our strategic plan for biomedical and behavioral research training and by a working group of the Advisory Committee to the Director, NIH, is providing graduate students with a greater awareness of their career options. An inaugural career development conference that we co-sponsored and that was recently highlighted in a Chemical & Engineering News article Exit icon may lead to the development of a sustainable workshop model to inform graduate students about and help them prepare for a range of scientific careers.

Organized by the directors of chemistry-biology interface graduate training programs at 10 Midwestern institutions, the
3-day event Exit icon took place in June on the University of Illinois at Urbana-Champaign campus. It brought together nearly 100 graduate students and 30 career mentors with jobs in academia, government and the private sector, including in nontraditional areas such as consulting, patent law and communicating science to the public.

A significant portion of the meeting consisted of structured discussion and presentations organized around different job opportunities. The meeting also included activities that let students improve their communication skills by explaining their research clearly and concisely to various audiences. Other career sessions focused on entrepreneurship and acquiring a postdoctoral position.

Early in the group discussions, students considering careers outside academia shared their concerns about the job market and about whether their graduate research training might potentially narrow their employment opportunities.  By the end of the meeting, however, most had the sense that their graduate training would actually open up new opportunities.  The group discussions also enhanced the mentors’ knowledge of various career paths and raised their awareness of the students’ career development needs.

A formal evaluation of the meeting’s usefulness and effectiveness is under way, and the organizers are experimenting with a variety of novel approaches to ensure sustainability for the conference by rotating venues, sharing organizational responsibilities and developing consistent sponsorships.

Susan Gregurick Joins NIGMS as Director of Biocomputing and Technology Division

Photo of Susan Gregurick, Ph.D.I’m pleased to introduce you to Susan Gregurick, the new director of our Division of Biomedical Technology, Bioinformatics, and Computational Biology (BBCB).

This is a particularly exciting time for the division, which funds research and training that join biology with the computer sciences, engineering, mathematics and physics. Its activities include supporting research centers in biomedical technology and systems biology as well as computational models of the spread of infectious diseases and the potential effects of interventions. The division also leads the NIH Biomedical Information Science and Technology Initiative and collaborates with the National Science Foundation to support programs in mathematical biology.

A leader in computational biology and bioinformatics with experience in government and academia, Dr. Gregurick brings the expertise and vision needed to help shape this relatively new division and advance its mission. Please join me in welcoming her to NIGMS.