As part of a series of NIH-wide initiatives to enhance rigor and reproducibility in research, we recently launched a Web page that will serve as a clearinghouse for NIH and NIH-funded training modules to enhance data reproducibility. Among other things, the site will house the products of grants we’ll be making over the next few months for training module development, piloting and dissemination.
Currently, the page hosts a series of four training modules developed by the NIH Office of the Director. These modules, which are being incorporated into NIH intramural program training activities, cover some of the important factors that contribute to rigor and reproducibility in the research endeavor, including blinding, selection of exclusion criteria and awareness of bias. The videos and accompanying discussion materials are not meant to provide specific instructions on how to conduct reproducible research, but rather to stimulate conversations among trainees as well as between trainees and their mentors. Graduate students, postdoctoral fellows and early stage investigators are the primary audiences for the training modules.
Also included on the page are links to previously recorded reproducibility workshops held here at NIH that detail the potentials and pitfalls of cutting-edge technologies in cell and structural biology.
Training is an important element of the NIGMS mission and a major focus of NIH’s overall efforts to enhance data reproducibility. In addition to the training modules we’ll be funding, we recently announced the availability of administrative supplements to our T32 training grants to support the development and implementation of curricular activities in this arena.
I hope you find the resources on this site useful, both now and as we add more in the future.
Cryogenic tanks filled with liquid nitrogen and millions of vials of frozen cells. Credit: Coriell Institute for Medical Research.
We have just funded a new, 5-year award to continue operation of the NIGMS Human Genetic Cell Repository, an important resource for the scientific community since 1972. The repository contains more than 11,300 human cell lines and 5,700 DNA samples derived from them. These high-quality, well-characterized and rigorously maintained resources, which you can order for a nominal fee, include:
- Specimens from individuals with inherited diseases, apparently healthy individuals and those of diverse geographic origins that are divided equally between those from males and those from females.
- A group of 39 induced pluripotent stem (iPS) cell lines that carry disease gene mutations or that are normal control iPS cell lines.
- An inherited disease collection that represents almost 900 disorders.
Last year, 1,500 scientists received more than 5,000 cell lines and 40,000 DNA samples. I encourage you to peruse the catalog and consider whether these specimens may be useful in your research program.
I 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.
I previously told you about the formation of two committees focused on Protein Structure Initiative (PSI) transition planning. These committees were charged with identifying high priorities for future NIGMS investments in structural biology and determining what unique resources and capabilities developed during the PSI should be preserved to address the needs of the scientific community. Dr. Leemor Joshua-Tor, one of the committee co-chairs, presented the groups’ report at the National Advisory General Medical Sciences Council meeting on January 23.
The committees’ recommendations for preserving PSI resources that the committees felt will be important for the community in the future include:
- Support for a modest number of protein expression resources to serve the needs of the community.
- Continued support for a materials repository similar to the one that has been supported through PSI.
- Possible continued support for a structural biology knowledgebase .
The committees identified these areas as high priorities for the future of structural biology:
- Continued support for synchrotron beamlines for crystallography.
- Support for modern cryo-EM resource centers.
- Continued support for NMR resources for structural biology.
- Support for the integration of structural biology methods.
- Support for collaborative, multi-investigator efforts in membrane protein and large macromolecular assembly structure determination.
We’re now developing plans for implementing the report’s recommendations.
The NIH Extramural Nexus blog has published posts on video resources that you may find helpful:
New Webinars Connect Applicants to NIH Peer Review Experts: The Center for Scientific Review is hosting webinars in early November to give R01, R15, SBIR/STTR and fellowship grant applicants and others useful insights into the submission and review processes. Register by October 28.
New Video Tutorials Can Help You Navigate eRA Commons: A 10-part series of short video tutorials walks you through the steps for submitting just-in-time information, a no-cost extension, a relinquishing statement and more. Watch the tutorials on the NIH Grants playlist on YouTube.
The National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL) closed earlier this week as a newer, more advanced facility, NSLS-II , began to come online.
Thousands of NIH researchers have used beamlines at NSLS over the last 30 years to collect data to characterize biological macromolecules including drug targets, ion pumps and enzymes. Because the beamlines for biological research at NSLS-II will not be available until 2016, other synchrotron facilities are temporarily expanding their capacity to address the beamline reduction.
Here are some sources that will help you identify and access beamlines at other U.S. synchrotrons:
If you have questions about NIH-funded synchrotron resources, please contact me or Ward Smith.
Earlier this year, I told you about the formation of two committees focused on Protein Structure Initiative (PSI) transition planning. These committees are charged with determining what unique resources and capabilities developed during the PSI should be preserved after the initiative ends and how this preservation should be done.
An important part of this process is getting input from the community, so we have just issued a request for information (RFI), NOT-GM-14-115, seeking comments about structural biology resources that have a high impact on the community, whether those resources have been supported through the PSI or by other means. We also want to hear what you think about the future of structural biology-related technology development, which has been an important feature of the PSI.
While the RFI invites comments on these specific topics, you should not feel limited to them—we welcome any comments that you feel are relevant.
To respond to the RFI, send an e-mail to email@example.com by May 23, 2014. When we compile the responses, we’ll remove any personal identifiers like names and e-mail addresses and only use de-identified comments.
If you have any questions about the RFI or the transition committees, please let me know.
Shortly after NIGMS Director Jon Lorsch announced plans to sunset the Protein Structure Initiative after the completion of the PSI:Biology phase in 2015, he commissioned two committees to determine what unique resources and capabilities developed during the PSI should be preserved and how that should be done. The committees, which are working together, held their first meetings in December and expect to present their recommendations within the year.
The external committee, which includes practitioners of structural biology and biomedical researchers who use structural biology data and resources in their work, will primarily focus on community needs. It also will suggest emerging challenges and opportunities in structural biology.
The internal committee, which is composed of NIH staff, will focus on how to implement the priorities identified by the external committee. The group includes a member from each NIGMS scientific division as well as several representatives from other NIH institutes who have experience managing structural biology and large, complex research programs.
The work of these committees will help define how we can provide continued access to important structural biology resources and identify new directions for technology development with potential for broad biomedical impact.
As Jon wrote in a Feedback Loop post about bolstering support for investigator-initiated research and as also reported in a Nature news article , the decision to sunset a large set-aside program that has received substantial investments, such as the PSI, should not be interpreted as a lack of support for team science. Multidisciplinary collaborations are likely to become increasingly important as we delve deeper into complex biological problems, and we will continue to sponsor team approaches to biomedical research. We also remain committed to supporting structural biology research through investigator-initiated grant mechanisms, innovative technology development and access to critical resources.
Our Biomedical Technology Research Resources (BTRRs)—until recently known as Biomedical Technology Research Centers—develop and disseminate cutting-edge technologies and methods that allow scientists nationwide to advance their projects beyond the levels that could be attained using commonly available laboratory resources.
If you’re a researcher who works collaboratively to create and integrate potentially transformative biomedical technologies and are interested in providing service and training to the scientific community, you may want to apply for a BTRR grant. The first step is to submit your concept in a pre-application. Feedback from its review can help you decide whether to submit a full application.
If you’re a biomedical researcher with a project in need of technology resources, you may be able to access them at an existing BTRR. The Biomedical Technology Resources Portal includes descriptions of the available resources , including those funded through NIH’s National Institute of Biomedical Imaging and Bioengineering, and instructions for accessing them .
Before granting use of its technologies (whether remotely or in-person), the BTRR will evaluate your research project for demonstrated need as well as the level of engagement and assistance that would be required of resource staff. It’s also possible that, if your project has potential for advancing a newly emerging technology, you’ll be able to collaborate with BTRR investigators as they develop it. This close collaboration benefits your research and also furthers innovation at the BTRR.
For more details about the BTRR program, please contact me or Doug Sheeley.
We’re hosting another Cell Day interactive Web chat on Friday, February 28, from 10 a.m. to 3 p.m. EST. During this time, members of the NIGMS scientific staff, including our director Jon Lorsch, will answer questions from students, teachers and the public about cell biology and research careers.
You can follow the chat live from the Cell Day Web site or read the transcript, which will be posted there shortly after the event. The site also includes registration information, the transcript from the 2012 event and classroom resources about the cell.
Please let people in your local schools and community know about Cell Day.
This event is just one example of the Institute’s commitment to encouraging and preparing future generations of scientists via formal research training and informal learning opportunities.