FASEB comments on an RFI from NIGMS, highlighting the importance of core scientists in the modernization of biomedical graduate education and the growing role of core science in both graduate education and as a viable career path

In response to a Request for Information (RFI) from the National Institute on General Medical Sciences (NIGMS) regarding Strategies for Modernizing Biomedical Graduate Education, FASEB submitted the following comments. The RFI presented six topics on which NIGMS sought input from stakeholders, with responses on each topic limited to 500 words. FASEB’s comments were submitted electronically via web form on August 5, 2016. The ABRF membership should note Topic #3, highlighting the importance of core scientists in the modernization of biomedical graduate education and the growing role of core science in both graduate education and as a viable career path.

Topic 1: Current strengths, weaknesses, and challenges in graduate biomedical education.

The Federation of American Societies for Experimental Biology (FASEB) has focused on three challenges in graduate biomedical education in the United States (U.S.) deserving of attention and discussion. First, technology is evolving and new scientific knowledge is being acquired faster than at any time in the past. Although this has proven a boon for scientific discoveries, one consequence is a paucity of expert educators in areas in which today’s trainees should be receiving instruction. Many programs, for instance, don’t offer training in the utility and use of technologies and concepts in the statistics and big data elements like databases, bioinformatics, modeling, imaging, and many of the “-omics” (e.g., metabolomics, proteomics, and microbiomics) fields. As research becomes more interdisciplinary and relies more heavily on the generation and analysis of large amounts of data, it is increasingly important that trainees acquire strong working knowledge in one or more of these emerging fields in order to successfully write grants, form collaborations, and prepare manuscripts for publication.

Second, curricula across graduate programs can differ dramatically. Some variation can be attributed to programmatic focus, whether interdisciplinary or discipline-specific, but there are basic tenets of biomedical research—experimental design and use of statistics, to name but a few—that should be addressed regardless of program type. Expectations and assessments of predoctoral students also vary considerably; the formats and intensity of qualifying exams, dissertation research proposals, and defense of dissertations, as well as dissertation committee composition and involvement, differ almost on a program-by-program basis. Levels of trainee independence and career development opportunities represent other areas in which graduate training differ. Although FASEB understands the importance of providing individual programs latitude to tailor their requirements to fit their focus and students’ needs, establishing basic principles and guidelines for core competencies in biomedical graduate education would help ensure consistency and quality across the educational spectrum.

Third, economic and institutional realities present numerous challenges to producing the next generation of responsible, successful researchers. Increased competition for federal grant dollars and decreased funding for state institutions have forced advisors to spend more time writing grants and less time supervising their trainees. Also, the recent classification of postdocs as non-exempt from overtime rules under the Fair Labor Standards Act, and NIH’s declaration that no supplemental funds will be provided to help with salary adjustments, will further strain laboratory and institutional budgets and could negatively impact graduate students’ productivity and prospects. Increasing pressure to publish rapidly—seen as necessary both to secure funding and maintain job security—may create an environment in which the normal prominence given to quality control and training can be de- emphasized. The push by both funding agencies and institutions to limit students’ time in training, although well-intentioned, can conflict with overall quality of supervision and increased expectations regarding career exposure, ethics training, and the rigorous conduct of research.

Topic 2: Changes that could enhance graduate education to ensure that scientists of tomorrow have the skills, abilities, and knowledge they need to advance biomedical research as efficiently and effectively as possible.

FASEB recommends focusing efforts on two aspects of the graduate educational process to ensure the effectiveness of tomorrow’s biomedical researchers: 1) modernization of course content to better reflect scientific and technological advances, and 2) examination of instructional methods to improve student comprehension and retention of key concepts and skills that will foster success in the biomedical sciences and related careers.

Major advances in life sciences such as deciphering the microbiome or precision medicine are the products of both new technologies and collaborative efforts across multiple disciplines. Keeping abreast of the most significant current scientific and technological developments is essential in order to update curricula to insure that they impart critical knowledge and emphasize important skills. FASEB suggests that “new” skills and disciplines such as data management, computational biology/bioinformatics and modeling, team work and leadership, and science communication be included in modern curricula. Data management skills include knowing how and where to store and backup data to ensure current and future accessibility, an issue that is of increasing necessity with the proliferation of databases and new requirements by many journals and funding agencies that data be publicly available. The importance of thorough, up-to-date lab notebooks—whether electronic or paper—should also be (re)emphasized in any course or module on data management. Students today also need to know how computational biology can augment and improve their projects, as well as how to choose the best software/programs to accomplish their goals. Training accomplished, effective scientists should include instruction in team participation, collaboration, and competence-based leadership, as well as management skills that include time and personnel management, conflict resolution, and delegation of responsibilities. Finally, students need to understand that science communication goes beyond writing manuscripts and includes the ability to present and explain research to a wide variety of audiences: others in their field, scientists in different fields, granting organizations, public relations offices and the press, and the general public. Throughout their training, students should be provided instruction and given opportunities to develop and put their knowledge and skills in communication to practical use.

Just as course content needs to be retooled to better reflect changes in scientific knowledge, technological advances, and evolving methodologies, so too does the way in which that content is imparted to trainees. Research has shown that active learning techniques (e.g., flipped classrooms, interactive lectures, problem-based learning) can increase both understanding and retention. Moreover, these methods more closely mirror how scientific problems are addressed in the real world than the traditional lecture format does. Experiments employing alternative learning methods are under way in some biomedical graduate programs; it would be helpful if these programs published analyses of best practices and effectiveness—and better still if all such analyses were compiled in a central repository— so that others interested in pursuing these strategies would have access to such valuable resources.

Topic 3: The major barriers to achieving these changes and potential strategies to overcome those barriers.

An obvious barrier to modernizing course content is that graduate programs often lack the expert personnel and/or resources needed to train students in the most current technologies (e.g., CRISPR/Cas9) and fields (e.g., bioinformatics). Core laboratories and shared resources are, by their nature, at the forefront of technology and expertise, foster collaborative research environments essential for interdisciplinary science, and represent experiential learning opportunities for graduate programs. Core scientists are recognized leaders in various technologies and fields, and can be technological mentors for the next generation of scientists. As such, they are well-positioned to organize and produce educational resources such as online courses or modules that students and faculty could access in order to learn the basic principles of these new fundamentals of biomedical research. The development of educational resources that can be accessed through established repositories will greatly increase the speed with which new information can be disseminated as technologies evolve, and will facilitate the ability to ensure more uniform quality and consistency of education across institutions.

Such resources could be commissioned by a funding agency, either public (e.g., NIH or National Science Foundation) or private (e.g., Howard Hughes Medical Institute or Burroughs Wellcome Fund), and curated with assistance from an established online course purveyor, like Coursera. Additionally, students should be given protected time—class time, essentially, and ideally in a group setting—to take these courses, so that both students and advisors recognize their legitimacy and importance.

Changing from passive to active teaching methods presents a unique set of barriers. First and foremost: overcoming inertia. Although individual investigators may decide on their own to modify their teaching methods, effecting programmatic change requires time and forethought on a much larger scale, including, perhaps, bringing in outside consultants and even applying for grants to support the preparation of new teaching modalities. Another barrier is the seeming lack of importance some institutions place on teaching. Teaching is often considered a low priority for both new and established faculty, something that takes away from their time in the lab and/or writing grants, and gaining teaching experience is not a requirement for students in many biomedical graduate programs. This underscores the importance of recognizing and rewarding the efforts of educators who develop novel approaches and resources to enhance the transfer of skills and knowledge to trainees. Appropriate resources should be developed to support those individuals and their work. Failing to do so will jeopardize any and all expectations for change and enhancement of biomedical graduate education.

Topic 4: The key skills that graduate students should develop in order to become outstanding biomedical scientists, and the best approaches for developing those skills. These could include but not be limited to: a) essential skills applicable to all fields that ensure ability to design meaningful experiments and critically analyze data, b) ability to adapt new and emerging technologies or approaches and c) other skills such as team science.

Like many other professional societies, FASEB has worked to identify core competencies reflecting the skills and knowledge students should develop throughout their training. We believe that it is important not to limit career outcomes to “biomedical scientist,” because the reality today is that in the biomedical sciences, trainees will end up in a wide variety of professions. Thus, we have chosen to focus on what we believe to be the competencies necessary for success in any science-related career:

  • Discipline-specific knowledge—having detailed knowledge in a specific research area above and beyond a requisite broad knowledge of biological principles and processes
  • Professionalism—developing professional attitudes and behaviors related to the conduct of science
  • Communication skills—being able to communicate via written, oral, and visual media to audiences at all levels of scientific comprehension
  • Research and analytical skills—acquiring the wide variety of skills needed to analyze issues and situations, and propose and test rational solutions
  • Management and collaborative skills—developing the abilities to manage personnel, projects, and grants, to network successfully to achieve optimal collaborations, and to work in teams and assume leadership position
  • Lifelong learning and career development skills—understanding the importance of staying current in one’s field of research as well as knowing steps needed in order to advance and/or change one’s career.

Because the competencies described above follow closely with those identified by other groups, they could be used to establish evaluation criteria to set standards for program requirements and track trainee progress. This is an area FASEB will be exploring in the coming months.

It should be noted that “outstanding biomedical scientists” are, by definition, rigorous and responsible in their work. As instances of non-rigorous, irreproducible research have come under increasing scrutiny lately, it bears mentioning that training should lay the foundation for the conduct of high quality, reproducible research by tomorrow’s leaders. In its report Enhancing Research Reproducibility, published earlier this year, FASEB outlined the need for training to include instruction on and reinforce good practice of the following—all of which fall under the umbrella of at least one of the identified competencies—in order to optimize rigor and reproducibility in science:

  • Maintaining clear, detailed experimental records and laboratory notebooks
  • Using precise definitions and standard nomenclature for the field or experimental model
  • Critically reviewing experimental design, including variables, metrics, and data analysis methods
  • Applying appropriate statistical methods
  • Reporting findings completely and transparently.

Certainly these practices could be communicated through courses and coursework, but we feel that advisors and dissertation committees should play the biggest role in imparting them and ensuring their integration into students’ habits. For example, advisors should take note—through observation, in one- on-one meetings, and in lab meetings—of whether students demonstrate good experimental design, record keeping, and data analysis in their day-to-day work. Dissertation committees, meanwhile, need to pay closer attention to whether students show comprehension and inclusion of sound principles in their research proposals and in presentations at committee meetings.

Topic 5: Potential approaches to modernizing graduate education through the existing NIGMS institutional predoctoral training grants program to ensure that trainees have the skills and knowledge they need to be prepared to enter the workforce.

FASEB recommends that NIGMS continue to evaluate new opportunities to support the development of shared courses and other educational resources that address emerging areas of scientific knowledge, emerging technologies, and critical core competencies in the biomedical sciences, and ensure that trainees have open, efficient access to those courses/resources. Such resources could be accessed through various online repositories or course websites. Alternatively, NIGMS could provide opportunities for trainees and/or their mentors to travel to workshops and meetings that are focused on the dissemination of information pertaining to evolving areas of science, emerging technologies or the acquisition of transferable core competencies, such as communication, team-based science, leadership/management. We further recommend that NIGMS continue to support and promote the open exchange of best practices and resources across institutions, and provide opportunities to bring faculty together so that they can share those ideas and practices. Finally, FASEB cautions against being overly prescriptive in the implementation and application of these practices, keeping in mind the differences in expertise and resources at any given institution.

Topic 6: Anything else you feel is important for us to consider.

FASEB appreciates the opportunity to respond to the NIGMS Request for Information: Strategies for Modernizing Biomedical Graduate Education. The issues presented for discussion are of significant interest to FASEB and its member societies, and will have significant impacts on the success of the biomedical research enterprise going forward. In this regard, FASEB would like to continue to work with NIGMS through a bi-directional partnership to foster the continued exchange of ideas and information.

ABRF Announces September 13 Webinar: Advancing Clinical Metagenomics Via CLIA/CAP Accreditation



Clinical metagenomics is still in its infancy, and maturation of the field requires an appropriate accreditation program to ensure quality testing and patient safety. Please join J. Russ Carmical, PhD, Assistant Professor, Baylor College of Medicine & Sequencing Director, Alkek Center for Metagenomics & Microbiome Research and Nadim J. Ajami, PhD, Assistant Professor, Alkek Center for Metagenomics & Microbiome Research on September 13 at 1:00 pm ET for an overview of how one metagenomics lab — the Alkek Center for Metagenomics & Microbiome Research (CMMR) at Baylor College of Medicine — is pursuing CLIA/CAP accreditation.


J. Russ Carmical PhD


Nadim J. Ajami PhD

An integral component of the accreditation process is proficiency testing (PT), which utilizes pre-established criteria, or measurement standards, for inter-laboratory comparisons. To date, commercially available metagenomic PT offerings are not available, which puts the burden on individual laboratories to develop an alternative assessment. In order to address the need for PT in metagenomics, the CMMR utilized a combination of previously sequenced samples (e.g. “blinded generous donor samples”), synthetic DNA standards, and mock communities to evaluate microbial DNA extraction, library preparation, and sequencing. In addition to developing PT specific to metagenomic analyses, the CMMR developed a quality system with standard operation procedures (SOPs), competency testing, a laboratory information management system (LIMS), and asset management software in compliance with CLIA/CAP standards. This webinar is the second on metagenomics under the GenomeWeb/ABRF 2016 Webinar Series. The first webinar in the series is available on demand here.