Genomics Education Partnership, The University of Alabama

Laura Reed, The University of Alabama

The Genomics Education Partnership (GEP) is a consortium of faculty from more than 100 colleges and universities in 31 states, the District of Columbia, Puerto Rico, Canada, and Taiwan. The typical GEP faculty member teaches genetics at a mid-size Primarily Undergraduate Institution, but the consortium also includes faculty from community colleges and research universities. Faculty implement the GEP program in a variety of ways, ranging for short modules within a larger introductory lab course, a dedicated upper division lab course, a significant portion of a lab course, or as an independent study with one or a few students. The GEP approach is modular and extendable to fit the specific implementation conditions of the faculty.

Much of the GEP's success stems from its scientific and pedagogical strategy: to identify questions that rely on comparative genomics, then enlist students to generate annotations of the relevant genes in eukaryotic genomes. The Genome Browser, used as the organizing web-based tool for student projects, presents students with multiple (and potentially conflicting) lines of evidence for the location and structure of a gene or genomic feature. The students then evaluate these sources of information to produce an original, data-supported gene model. Pooled student results have allowed us to examine the evolution of a largely heterochromatic domain (F element) of the Drosophila (fruit fly) genome, and new current projects include analysis of venom evolution in parasitoid wasps and signaling pathway evolution in Drosophila. This strategy of producing high-quality curated gene models with the help of undergraduates can be applied to diverse biological questions. In addition to providing research experiences for more students, the GEP has played a major role in bringing bioinformatics into the curriculum at these colleges and universities, with approximately half of our members reporting that their departments had no bioinformatics courses or modules prior to their training, while almost all now do (unpublished GEP survey, 2017, 92% response rate).

CURE Development

The Genomics Education Partnership (GEP) was established by Dr. Sarah Elgin at Washington University in St. Louis in 2006. It was motivated by the need for much human cognitive effort to improve assemblies and annotate genomes in order to answer interesting questions about the role of genome structure on gene expression. Dr. Elgin recruited a handful of like-minded undergraduate educators at diverse institutions to establish the GEP CURE and they built the culture and expectations of the group that has expanded over the years since.

Different institutions have implemented GEP in different ways. Some faculty implemented short modules within introductory courses; others are semester-long, intensive research experiences as part of a required or elective upper division course. Further, some faculty use the GEP as the basis for an independent study course.

As the field of genomics has developed, so too has the GEP curriculum and projects. The GEP faculty are able to build on basic skills to adapt to new questions and scenarios with substantial support from the centralized GEP staff. The essential strategy of the GEP student projects has remained fairly constant as the unit of the student work can be integrated into different kinds of scientific questions.

The GEP has a very successful model, but it requires money to run. Funds are necessary to support in-person trainings, annual alumni meetings, and staff to help with the diverse questions and problems that GEP faculty encounter. We have been lucky in securing grant funds to continue and expand the work of the GEP. Going forward, we will be testing whether online training can be similarly effective as in-person training for on-boarding new faculty in a more cost-effective manner.

We will need to transition to a non-profit model in the near future to allow for more diverse strategies for securing funding. A significant barrier to making that transition is our collective lack of understanding and experience on the business/legal side of establishing and maintaining a non-profit. The GEP has been discussing transitioning to 501c3 status for several years. There are benefits and costs to becoming a 501c3, and one of the trade-offs is literally the cost of running a non-profit. Currently, the GEP is using the administrative infrastructure of our host institutions (e.g., University of Alabama, Washington University in St. Louis) to deal with issues like benefits and taxes for our employees. If we become an independent entity, we would have to manage those issues ourselves. The most likely strategy would be to hire an accounting firm to deal with the finances related to the non-profit and this might be cheaper than University overhead on grants. So, it would be more of a hassle perhaps but might be more cost effective in the long run. Another possibility would be to join an already established 501c3 with a related mission (e.g., Phoenix Bioinformatics,, in which we would turn over most of the administrative responsibilities to the parent organization and focus our efforts on GEP-specific activities. A potential disadvantage of this approach would be possibly losing leadership control of the GEP if the parent organization's board decided a different course of action for the GEP was preferable. Some other benefits of becoming a 501c3 would be that we could collect financial support from a variety of sources (e.g., subscriptions, donations, grants, sponsorships) without having to comply with university-specific rules or having the finances of the organization tied to a specific institution. If leadership of the GEP changed, and thus the institution of the program's PI, the GEP entity would be free of the challenges of disentangling itself from a specific academic institution. Other considerations include questions about in which state the national program should incorporate, how is the board of directors determined when the major players in the organization tend to be employees of the GEP, etc. As science academics, the GEP steering committee has quickly come to feel overwhelmed by the various legal permutations of these options and determined that we needed legal advice. We turned first to the University of Alabama's non-profit law clinic in the School of Law and then to the corresponding clinic in the Georgetown School of Law. Both clinics turned down our application because our national program was not of sufficient benefit to the immediate interests of the University (e.g., program would not have a large impact on Western Alabama specifically). In the meantime, we have received grant support which has lessened the pressure to solve our 501c3 status question since we are no longer pressed to identify strategies for fundraising. Thus, we are currently in suspension on this question. We do eventually want to properly explore a transition to 501c3 status, but since we do not presently have a legal advisor identified, we are not currently making progress on this front.

Indicators of success:

Since its beginning, GEP has collected data on whether student learning gains in the relevant genomic and students' perceptions of their ability to be scientists. On both of these fronts, GEP has had a very strong record thus far. In preparing our grant proposals to the NSF IUSE and NIH IPERT programs, we also conducted a survey of the GEP faculty in the Fall of 2017. The survey was drafted at our summer alumni workshop in the summer of 2017 and then further refined by the GEP leaders before deploying via Qualtrics. We intended to use this data only for grant writing purposes and so did not seek IRB approval of the survey protocols. In this survey, we asked questions like:

  • What was your initial motivation for joining the GEP?
  • Why have you stayed as an active member of GEP?
  • What GEP resources or activities have helped you maintain genomics research in your courses or curriculum (sustainability)?
  • (1-5 agreement scale) I believe that my participation in GEP helped increase inclusion of genomics/bioinformatics in the curriculum of my department
  • To what extent does the organization/infrastructure of the GEP promote a sense of community?
  • To what extent do you feel a sense of responsibility for the success and continued sustainability of the GEP?

Based on the answers to these and other questions, we were able to identify several important themes:

  • GEP membership provides opportunities for professional development and research publication authorship.
  • Most departments have no bioinformatics or genomics course opportunities for their students prior to GEP starting at their institution.
  • Many faculty felt their Tenure & Promotion process was strongly positively influenced by their involvement in GEP.
  • We identified specific aspects of the GEP organization that were most impactful for retention of current members.

We were then able to both use that data as evidence of our success, and to justify the need for funding to enhance the aspects of GEP that seem most effective. Also, using this data we were able to pose new research questions such as; if we use alternative strategies for training new members (e.g., on-line, through regional level events vs. the traditional method of national trainings) will there be negative/positive impact the outcomes for both our faculty and their students, and what is the cost benefit ratio of alternative methods for group induction.

Our CURE has produced scientific (and science education) products. Our scientific publications include both GEP faculty and students as co-authors. In future work, we will be producing micro-publications, in addition to our regular publications, to allow the student's work product to be made available to the scientific community more quickly.


Initially, the GEP was supported by a grant from the Howard Hughes Medical Institute obtained by Dr. Elgin. Later the program was support by federal grants with current funding from both the NSF and NIH. The GEP has been fortunate to maintain nearly continuous grant support.

The GEP's NIH grant funds a new strategy for training and engaging GEP members. From our faculty surveys, it was clear that the GEP members have a strong sense of community with and obligation to the GEP that derives from regular annual interactions among the members at the annual alumni meeting. The challenge is that the national alumni meetings do not scale well in cost or in effectiveness (e.g., if it gets too big, we lose the sense of community), so we proposed to start regional "node" events to help faculty engage in the GEP community on a more cost-effective, regional scale. Thus, by proposing a new method for training new members, we were able to obtain federal funding.

In GEP's most recent NSF grant, we proposed to study alternative methods for training new members. We have a long track record of training and retaining faculty that join the GEP through a national training event and then reunite at annual national alumni workshops. The new NSF grant funds online training methods and gives us the opportunity to research whether alternative methods of training (regional, national, online) influences the ability of the GEP to retain members and sustain our community. If we can achieve a similar level of community commitment using the more cost-effective methods of online training or regional events, then we can provide that as a model for other similar educational efforts.

The GEP conducts both educational and scientific research. As we have transitioned to a distributed leadership model, we have also broadened our scientific questions. We have determined the responsibilities of what we are calling "scientific partners" that may bring new scientific projects to the GEP. It is the responsibility of the scientific partner to provide the funding for genomic data generation, providing science-specific analyses (e.g. meta-analysis of student generated gene annotation models, and writing the scientific publications). Thus, the GEP as an entity is only financially obligated to maintain its centralized curriculum, IT infrastructure, and assessment research. The GEP and the scientific partner would collaborate to generate specialized resources needed for the students on a particular scientific project (e.g., curriculum specific to the science project).

The GEP has made good use of institutional resources of some of its members. Administrative staff at Washington University in St. Louis (WUSTL) help with administering student assessments and WUSTL also hosts the servers for the GEP websites. The University of Alabama has provided site license support for important collaboration software (e.g., Zoom and Box) and we have used student teams doing their senior projects from the Management Information Systems major to give advising on technological solutions to our communication challenges across a nation-wide organization.

We have also made some collective financial decisions to keep the costs of running the GEP low. For example, collectively, we all agreed that we were willing to use dorm housing (instead of hotels) for our summer alumni workshop at WUSTL to increase the number of people we could afford to bring to the workshop.

Stakeholder Buy-In

Students typically participate in the GEP CURE as part of their normal biology lab curriculum at various institutions. In some cases, the CURE is offered as an elective or independent study experience. The promise of contributing to real scientific research (instead of performing canned lab exercises) was a big motivator for the students to take the experience seriously and give their best effort.

Faculty are typically recruited by presentations at professional conferences and by word-of-mouth. GEP faculty are trained in the program through an in-person, 3-5 day workshop or using online faculty mentoring networks through QUBES. GEP faculty are expected to implement the curriculum in their course(s) as a condition of receiving the training and are encouraged to remain engaged in the community through annual participation in Summer Alumni Workshops. Faculty supervisors (e.g. department heads or deans) were also required to sign a letter of support stating that the faculty member would be assigned to teach classes where the GEP curriculum would be used. GEP is pitched to potential faculty as an opportunity to fundamentally enhance undergraduate education in their institutions. Faculty have reported that they are motivated to participate to improve their teaching outcomes and for their own professional development, which included training in genomics, joining a community of practice focused on science education, and co-authoring publications.

The institutional and academic context of the individual faculty member varies dramatically across the GEP membership and the degree of support needed from centralized staff varies correspondingly. We have determined that the support provided by the highly competent GEP staff has been critical to successful implementation of the GEP CURE at some institutions.

A primary barrier to doing genomics research for most biology faculty is a lack of background and training in computational methods. GEP lowers the barrier to entry by making the tools easy to use so that the faculty (and their students) can focus on the concepts instead of writing code. The availability of GEP staff to help troubleshoot with a short turn-around has also been critical to the success of GEP. Faculty aren't left stranded without direction on where to go with their class when something goes wrong.

Sustaining Change

Institutional support has been a key element in making the CURE sustainable. Also, a charismatic leader (Dr. Elgin) inspired many faculty to persevere through frustrations in their implementations.

At the planned retirement of Dr. Elgin, there was a critical point at which the GEP faculty had to decide what they wanted to have happen to the project; have it sunset or identify an alternative leadership strategy. Due to the strong sense of community among the GEP faculty, it was decided by the group to keep the GEP an active organization lead by a distributed leadership model. At the 2017 Alumni Workshop, GEP members established a GEP management structure supporting four major functions: Science & IT, Assessment, Curriculum, and Professional Development & Mentoring. We developed by-laws (regarding quorums, succession, etc.) through consensus. We plan a three-year term cycle for committee chairs where individuals start as vice chairs, move to chair, and then past-chair for most standing committees. This will help maintain continuity and mentor developing leaders. Committee leadership and membership is determined by the self-identified interests of the faculty members. For example, people especially interested in assessment and science education lead the assessment committee, while others more motivated by the scientific questions are part of the Science and IT committee. The structure of the committees has evolved from the initial conception (e.g. defining specific roles within committees like Director of New Member Training within the Professional Development Committee) as we became to better understand our collective duties as an organization. There is also a steering committee coordinating the overall activities of the GEP. We also established titles for leaders within GEP to provide leaders recognition on their CVs.

Maintaining open communication across such a diverse group of faculty is challenging. We organize all of our tasks using a collection of free software (Google Groups, Google Drive for living documents with collaborative editing, Trello for task management, Campuswire for Q&A) and tools provided by site license at a couple of our larger member institutions (Drop Box for long-term document and data storage, Zoom for teleconferences). We also have our public facing website where resources for students are posted. All of our teleconferences are recorded and the recordings, along with meeting agendas and minutes are posted in a private virtual space where any GEP faculty member can access them. We also have a monthly newsletter to all GEP members that is collectively generated and edited by the Steering Committee. Having a diverse membership means there is a broad distribution of level of comfort with electronic tools, and the proliferation of electronic tools is proving to be a barrier to engagement for some GEP members. We are actively discussing strategies to minimize the burden to engagement while simultaneously maintaining the versatility and low cost of our current model.

GEP faculty attend annual "alumni workshops" that help them to feel connected to the other members of the community while keeping their knowledge of the science and the curriculum current. There is extensive support from the centralized computational staff that provide timely answers to questions and maintain the computational infrastructure for the program.

The faculty of the GEP have had remarkable retention. This has partly resulted from creative strategies faculty have used to keep the curriculum as part of their teaching repertoire even as their specific teaching assignments have changed. The adaptable nature of the curriculum has allowed for creative implementations. Additionally, many faculty have identified help from Teaching Assistants (TA's) as a key to their continued engagement. Earlier in GEP's history, grants supported training not only the primary faculty member who would implement GEP, but also a TA or other supporting staff/faculty member who would assist in the initial implementation. Since then, many people use talented undergraduate students from prior classes to serve as TA's for their current implementation.

I (Laura) have remained involved because the underlying science and the educational philosophy of the GEP appeals to me. I have a sense of community in the GEP that I do not necessarily get in other realms of my professional life. I took over leadership of the GEP because I was one of the few members in a position to do it both professionally (post-tenure at a R1 research institution) and in terms of my scientific interests (evolutionary genetics). I was excited to both facilitate a program that had been so supportive of me pre-tenure and to expand the breadth of the scientific questions I could explore. If I left my institution, the CURE would come with me as long as I moved to another similar institution with a similar level of administrative support.

Advice for Implementation

My entry into my role (Laura Reed) leading the GEP has been a gentle one. I started as a regular new member implementing GEP curriculum in my course. By participating as a regular member over several years I was able to glean much information about STEM education from interacting with my more experienced peers. When the possibility of a transition into leadership arose, I had accumulated enough vicarious experience to think that I might be capable of assuming leadership. One critical element of that decision was knowing that I could develop and answer my own scientific questions within the GEP framework to augment my own scientific research program.

One of the things that has helped the GEP to sustain has been the varied group of faculty who are engaged. As individual career and life circumstances change, we are able to shift responsibilities among group members to compensate. So, having a team is helpful. Also, the core student project within the GEP is fairly uniform in overall structure allowing us to optimize broadly useful curriculum. While we are constantly updating we are not having to reinvent the wheel with every new round of student projects.