BIOQUEST
BioQUEST arose from a meeting of the minds between John Jungck and Nils Peterson on a walk through Torrey Pines, California, in 1986. Their idea that students should practice and experience science as scientists do was crystalized in the 3P’s Philosophy of “Problem Posing, Problem Solving, and Peer Persuasion” (Peterson and Jungck 1988). This philosophy is deeply rooted in a recognition of the holistic experience of learning, addressing the interdisciplinary nature of biology, and the critical role of inclusion and social relevance in student success. Funding from the Annenberg/CPB Project, Apple Computers, Inc., the Foundation for Microbiology, and the Center for Biology Education at the University of Wisconsin-Madison supported the initial exploration of this educational approach. That educational experiment has lasted over thirty years and is still going strong.
The BioQUEST Curriculum Consortium brought together an interdisciplinary community of educators who developed software simulations to engage students in actively exploring biological phenomena through the new technology of personal computers. These initial educational modules included the Genetics Construction Kit, which despite its age is considered by many to be among the best simulations for teaching genetic concepts. The modules were made available on CDs, another cutting edge technology, in the BioQUEST Library. In 1996, BioQUEST materials moved to a new platform—the world wide web. Development of new educational materials was supported by the BioQUEST Summer Workshops, which at the time were nine very long days of intense, collaborative work. Participants often referred to the experience as “biology boot camp,” but they kept coming back. Participants continued to develop new educational materials, leveraging the use of easily accessible tools such as Excel to engage students in quantitative biology, especially in bioinformatics and evolutionary biology. In the late 1990s, BioQUEST expanded beyond simulations to include professional development around pedagogies that supported the 3P’s Philosophy such as the Investigative Case-Based Learning project, a variation of Problem-Based Learning. Recent research in effective educational pedagogies has demonstrated the efficacy of many educational practices BioQUEST has promoted over the years (National Research Council 2015), and BioQUEST continues to serve a translational role for the community of practitioners, by demonstrating how to bring research-based practices into the classroom. Another way that BioQUEST has led the way in educational reform is the commitment to generating open education resources. Most of the materials generated by the BioQUEST community were made available as open education resources, which led to broad use and adaptations that have kept the materials relevant.
The impact of BioQUEST on biology education has been recognized in various ways. In 2010, BioQUEST received the American Society for Cell Biology (ASCB) Bruce Alberts award for Excellence in Science Education. In 2014, NSF funded a study of persistent, impactful professional development organizations in STEM education reform (Kezar and Gerhke 2015). This research study identified BioQUEST (as well as SENCER, POGIL and Project Kaleidoscope) as “communities of transformation,” in that they encouraged community members not only to improve their practice but to challenge the accepted norms in a search for better solutions. The transformative impact of BioQUEST is evident in the enthusiastic community members who collaborate on papers, grants, and projects and support one another in developing educational materials and practices that challenge both faculty and students to go beyond traditional approaches. BioQUEST is a highly collaborative organization in which multiple funders, professional societies, and creative individuals have come together to address educational challenges. Funders over the years have included NSF, NIH, HHMI, and Annenberg. BioQUEST has collaborated with the National Evolutionary Synthesis Center (NESCent), the National Institute for Mathematical and BIological Sciences (NIMBioS), mathematics and biology professional societies, projects such as Shodor, and offered workshops at dozens of universities and colleges around the world.
A typical BioQUEST project is ESTEEM, which leveraged Excel spreadsheets to introduce students to quantitative models of biological phenomena. ESTEEM was a collaborative, interdisciplinary project that emerged from prior work in bioinformatics (BEDROCK) and partnerships with Shodor, MAA, and HHMI. Participants in BioQUEST workshops were introduced to ESTEEM modules, and invited to generate their own. All ESTEEM modules are publicly available, and many are still used in the classroom. This commitment to open access and engagement of community members to both develop, adapt, and use materials is a hallmark of BioQUEST’s approach. Another example is BioQUEST’s Investigative Case-Based Learning which focused on the pedagogical approach faculty use to engage students in thoughtful analysis of biological problems. This project led to a series of workshops that reached faculty across the US and around the world. The Science Cast Net, an NSF funded RCN UBE, is the current iteration of this project. Science Case Net brought together several organizations promoting case based pedagogies and supports several focused case development groups including the High-throughput Discovery Science& Inquiry-based Case Studies for Today’s Students (HITS), and the Molecular Case Net.
Today, BioQUEST continues to explore frontiers in science education and promote practices that engage all students in a relevant and meaningful learning experience. BioQUEST has become a 501(c)3 non-profit organization to continue productive collaborations addressing both emerging and persistent educational challenges, through professional development, new educational materials, pedagogical approaches, and policy leadership. Faculty may join the BioQUEST community at the annual Summer Workshop, and through collaborative projects such as QUBES and the Science Case Network. Together, this community continues to delve into emerging influential disciplines such as data science and tackle enduring challenges in providing all students with equitable, inclusive learning opportunities.
MathBench Biology Modules
MathBench Biology Modules (mathbench.umd.edu) were created at the University of Maryland (UMD) in 2004, against a backdrop of increasing emphasis on quantitative and interdisciplinary approaches to biology. The National Research Council’s (2003) Bio2010 report National Research Council (2003) had just been published, and it resonated with the growing desire of UMD biological sciences faculty members to introduce more quantitation in upper level courses to prepare students to contribute to the biological sciences research enterprise. These faculty members, led by Bill Fagan and Avis Cohen, had built their research programs at the interface of biology and mathematics, and they recognized that undergraduate students in the biological sciences needed greater exposure to the use of math in biology at every level of the curriculum. This view was reinforced by institutional data showing that success in introductory biology courses was closely linked to proficiency in mathematics.
MathBench was conceived as a series of self-contained, online modules that complemented traditional lecture- and laboratory-based introductory biology courses. From its inception, MathBench incorporated three strategies rooted in the science education literature (Nelson et al. 2009):
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Use of an informal tone, humor, story lines, and connections to real life to dispel math anxiety
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Use of interactive elements to promote student engagement and active learning
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Incorporation of individualized feedback to students to provide them with some control over the amount of instruction and practice they receive while completing the modules
Module topics (e.g., logarithms, basic statistics, and graphing) were identified via meetings between the project team (primarily lead developer Kären Nelson) and faculty members who taught the first four courses required for the biological sciences major. All faculty recognized the need for students to appreciate the relationship between mathematics and biology and develop basic proficiency in applying mathematics to solve biological problems, but not all of them were comfortable teaching quantitative concepts. Therefore, the modules were designed to be done as homework, outside of class time. In some cases, the content of the modules was revisited by the course instructor during lecture or laboratory meetings, but in other cases, it was purely supplementary material.
Initial financial support for the creation of MathBench modules came from a Howard Hughes Medical Institute Undergraduate Science Education Program grant to the University of Maryland, and the project received support for subsequent expansion and dissemination from two National Science Foundation Course, Curriculum, and Laboratory Improvement grants. This additional funding allowed MathBench to launch a collaboration with James Sniezek, then a biology faculty member at Montgomery College, a nearby 2-year institution, which in turn sparked the development of several new modules geared to the community college audience.
While MathBench was first developed specifically for UMD (and later Montgomery College) students, because the modules were freely available on the web, they quickly gained an international audience. Recently, the project has partnered with a consortium of seven Australian universities, which received funding from the Australian Government’s Office for Learning and Teaching to adapt 27 of the modules for use in Australian universities www.mathbench.org.au. This project also brought an infusion of mathematical expertise through the participation of mathematics faculty members from the Australian partner institutions.
In the early years of the project, there was little effort to establish a community of MathBench users. Each module had been created for a particular course based on the recommendations of the instructor, and each instructor had a particular vision for how the module would be integrated into their course. A social networks analysis of several UMD curriculum projects that aimed to strengthen the quantitative skills of biological sciences students showed that, rather than being a tightly interconnected network, the MathBench project resembled spokes of a wheel, with each participating faculty member connected only to the module developer (Thompson et al. 2013).
That isolation has diminished with the increasing prominence of other organizations that share a commitment to quantitative biology education. Collaboration with these organizations, particularly the BioQUEST Consortium and QUBES, has been key to the wider dissemination of MathBench and our recent efforts to establish a community of MathBench users. The BioQUEST Consortium, through its annual summer workshops, has provided a venue for recruiting and training new MathBench users. QUBES has been instrumental in providing the necessary networking infrastructure to facilitate long-term interactions among MathBench users. In Fall 2018, MathBench sponsored a QUBES Faculty Mentoring Network to provide professional development for faculty members seeking to implement the modules in their courses. This resulted in the creation of instructional materials that are being shared with the MathBench user community through the QUBESHub cyberinfrastructure. In future years, we hope to preserve the existing modules for continued use, as well as develop new modules that target additional concepts and skills identified by our community of users.
The evolution of MathBench over the years is very much reflective of changes in the national landscape of STEM education. In its early years, the project was somewhat siloed, both with respect to individual courses and campuses. As the community of adopters has broadened, we have gained greater insight into how best to implement the modules and promote a deeper understanding of quantitative biology. It is now clear, for example, that students gain little from the modules if they are perceived as an add-on rather than an integral component of the course. The highest learning gains are seen when the modules are tightly woven into the fabric of the course and the skills reinforced by the modules are required for success in the course (Karsai et al. 2015). It is also clear that student attitudes towards the utility of mathematical approaches to biology are slow to change, and therefore need to be reinforced at multiple points in the curriculum (Thompson et al. 2010).
QUBES: Quantitative Undergraduate Biology Education and Synthesis
Spurred by the interest in mathematical biology research and subsequent national STEM Education reports and National Science Foundation investment in mathematical biology education program building, many educational institutions simultaneously began to innovate in the education interface between mathematics and biology. While the flurry of attention to mathematical biology was welcome, there were re-occurring coordination issues between these siloed groups and individuals. Information about curricula was shared primarily at select sessions across multiple subdisciplinary professional societies. Faculty created materials and posted to their own websites, where it might never be used or known by faculty at other institutions. Active, but underfunded, groups of professional societies devoted to mathematical and quantitative biology education were not equipped to coordinate national scale projects to coordinate and disseminate curricula. QUBES (Quantitative Undergraduate Biology Education and Synthesis) was founded in 2013 in response to the recognition that many of these individuals and groups were establishing an emerging field of quantitative biology education, but separately and without overall coordination or guidance on best practices.
The grand idea behind QUBES was to develop a cyberinfrastructure (Hub) to provide coordination for these multiple education initiatives, but with the key feature that we recognized all professional societies and individuals had to work together to achieve this common goal (Consortium). QUBES as an idea was initially funded as an exploratory NSF Research Coordination Network for Undergraduate Biology Education. The vision of the leadership was that
“The QUBES hub will bring together a community of quantitative biology educators that can create, share, and assess curricular resources using a dynamic online network that reaches across departments, colleges, institutions, and countries.”
The proposal laid the framework for a social-cyberinfrastructure to move forward collective action on undergraduate biology education.
QUBES invited several stakeholders and potential collaborators representing biostatistics education, mathematical biology education, quantitative biology education, professional societies (such as Ecological Society of America, BioSIGMAA, Society for Mathematical Biology, the American Association for the Advancement of Science, and Association of Biological Laboratory Educators), and professional development (such as BioQUEST) to a meeting at NIMBioS. At this meeting, the network carved out a central and shared goal around quantitative biology education and agreed upon priority activities. Shortly after, QUBES was invited to participate in a collaborative effort by a team out of Radford, Pittsburgh, and BioQUEST to write an Ideas Lab proposal, which ultimately funded the current QUBES project This evolution of QUBES added a strong component of professional development and also solidified a firmer connection to a diversity of biology professional development societies [for more details see QUBESHub.org (2020)].
QUBES consists of overlapping, but complementary, activity areas:
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Consortium—facilitates collaboration and communication between a broad array of partner projects, institutions, professional societies, and the quantitative biology education community;
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Hub—the cyberinfrastructure needed to support QUBES activities from collaboration spaces and websites to cloud-run computing and modeling tools;
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Open Educational Resources—the Hub hosts and links to curriculum and software from both partner projects and the community sourced that can be freely used, modified, and shared;
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Professional Development—Faculty Mentoring Networks provide faculty support from peers and experts throughout the semester while they implement new educational resources and practices; and
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BioQUEST—grounds our virtual community with a jointly hosted QUBES-BioQUEST summer quantitative biology education workshop each year in addition to other support activities across the areas.
In addition to the five directors of these activity areas, QUBES grant funds support a web developer, a web designer, a postdoctoral research student, as well as project managers and contractors (See “About us” at QUBESHub.org). Together, we have a shared vision to support educators and advance an inclusive quantitative biology through the power of collective impact.
As of June 1, 2020, the QUBES Consortium has worked with over 100 partners and collaborators over the six years the RCN and Ideas Lab projects have been funded. QUBESHub now hosts or connects to 1134 resources (See Fig. 2), 46 open-source cloud-run tools, hosts 436 partner websites and educational project management pages, and has welcomed 11,928 registered users. Since the website launch, QUBES has partnered to help deliver semester-long virtual professional development to over 700 Faculty Mentoring Networks participants who are adopting quantitative resources, tools, and Open Educational Resources (OERs) for their classrooms—nearly half of those in the last two years. QUBES also serves approximately 80–100 people each year through our summer workshop collaboration with BioQUEST and collaborates on a number of conferences, including an NSF INCLUDES funded conference on environmental data science with NEON which reached nearly 200 on-site and virtual participants (Lauer et al. 2020). QUBES leadership and QUBES Ambassadors also routinely give talks and workshops at various professional meetings, reaching an even broader audience.
The community QUBES serves is diverse, representing a variety of institution types and around the world (though, primarily from the United States) and a variety of disciplines which act at the interface of biology and the mathematical and computational sciences. In terms of impact on individuals, we are now also beginning to see cumulative effects, for example, Faculty Mentoring Network participants report this professional development activity in their tenure and promotion portfolios, and colleges’ public relations departments highlight mentors who have led Faculty Mentoring Networks. In terms of project impacts, stories like MathBench above are one of many use cases in which projects have been able to expand their outreach into new communities and facilitate new adaptations of their resources to meet emerging or institutional needs. QUBES now routinely contracts its services, such as conference support, web design, publication systems, and Faculty Mentoring Networks to professional societies and projects looking for similar success stories.
QUBES has also invested in research and evaluation of services and products, in order to optimize practices for the shifting technological, and educational and future workforce landscapes. As a result, QUBES has been on the leading edge of providing professional development in data science education for biology. QUBES is also a leader in social-cyberinfrastructure innovation, with an open educational resource system that harnesses the power of virtual communities. Community building and Consortium efforts lead in part by QUBES, such as EDSIN and SCORE, encourage discussion specifically about supporting historically underserved communities. We have also been working with colleges and universities with Howard Hughes Medical Institute Inclusive Excellence grants. While these efforts smartly tap into a growing “new majority,” it is also crucial for our QUBES community to embrace a broader community in order to do our best work and to amplify the incredible work done within and by these communities. As a leader in education on an emerging front, QUBES takes seriously the responsibility to engage with and not just for underserved colleagues and to do our part to help close disparity gaps in STEM education. These actions are aligned with a commitment to shape a quantitative biology education that is open, ethical, inclusive, and universal.
QUBES endeavors to provide a place for all educators to find both resources and community. It is meant to be community driven, and to support this community to do its best work. While initially NSF funded, QUBES requires the continued support of community members like our readers to keep QUBES free and up to date with emerging community needs and web technologies. Being part of the QUBES community functionally means creating an account, downloading a resource, joining a group or Faculty Mentoring Network, contributing resources, and/or simply signing-up for the newsletter. For organizations, partnering with QUBES can mean sharing information across networks, partnering to offer a Faculty Mentoring Network, and/or contracting services.
The offering of contract services hints to issues on sustainability as QUBES grapples with its commitment to offer professional development and resources for free to the instructional community as our NSF funding ends. QUBES contracts go in part to support web hosting services, but also to support the human infrastructure often invisible behind online community platforms. These virtual services have become even more important in light of online shifts due to COVID-19. We are fortunate to also have attracted supplemental funding from the Hewlett Foundation for the upcoming year. In five years, we hope that QUBES is still providing an open, accessible, active, online community platform that reaches all people with tools, resources, and support relevant to the new challenges in the biomathematics education and research community.
Intercollegiate Biomathematics Alliance (IBA)
For many years, higher education has been suffering under the adverse effects of diminishing fiscal resources due to the changing political and social attitudes towards education. Overall, states have been consistently decreasing the funding for public state higher education institutions (Mitchell et al. 2018). As a result, higher education institutions have had to balance budgets by reducing faculty, limiting course offerings, and in some cases, by closing campuses. Furthermore, surviving academic programs have found themselves operating under limited resources, which made access for researchers and educators increasingly difficult. Mathematical biology is not an exception to these trends. Especially, since this is an emerging interdisciplinary field, practitioners are more vulnerable to intellectual isolation than other fields in mathematics. Naturally, lack of an already-established advanced student intellectual workforce makes scientific progress in the field even harder. Hence, lack of academic resources, lack of faculty expertise, and lack of students, advanced or otherwise, lead us to the consequence of limited curricular innovation in mathematical biology. As expected, the creation of an organization to address these issues is what motivated the formation of the Intercollegiate Biomathematics Alliance (IBA).
The initiation of IBA, a comprehensive academic collaborative entity addressing the discipline-specific needs of mathematical biology programs, was founded in early 2014 at Illinois State University (ISU). Originally conceived as a way to facilitate inter-institutional research among the three founding members, the goal of the IBA became to create a small network of universities, all contributing limited funds to a pool from which the research activities of similar collaborating groups may be supported. The early success of this initiative then led the founding members to expand this collaborative structure to other institutions with faculty of similar research interests and needs. As a result, a consortium of dues paying member institutions was formed. In this consortium, each member institution is a stakeholder where their students and faculty have unique access to a wide range of community-based support, as outlined below. In three short years, the IBA has grown from a small network of three universities to a consortium of twelve institutions with diverse size, mission, and demographic make up. As the network grew, the mission and the interests of the members naturally expanded to other scholarly activities such as but not limited to supporting undergraduate research, community curriculum, and an enhanced academic infrastructure. Based on the current goals of the consortium, the IBA states its mission as follows:
[IBA’s] mission is to provide a platform for expanding access to a diverse network of scholars and resources at the interface of biology, mathematics, and computational science to enhance research and education opportunities for researchers, educators and students. (IBA 2019)
The following highlight some of the main components of IBA’s mission.
Cross-Institutional Undergraduate Research Experience (CURE) Cross-Institutional Undergraduate Research Experience (CURE) is a workshop where IBA member students and faculty research mentors gather during an all-expenses-paid extended weekend to experience the entire process of conducting research in mathematical biology. Faculty Mentors present cutting-edge research projects that they are interested in directing and collaborating on with another faculty. Then, students visit with each Faculty Mentor to decide which project they want to work on throughout the year. The workshop continues with programming and scientific/technical writing boot camps. The workshop also includes presentations on various career directions. Current and former graduate students give presentations on graduate school experience and life as a professional working in a data-analysis related industry. Each day ends with a fun activity; a student versus faculty soccer match and a student versus faculty bowling competition. The CURE workshop without a doubt has proven to be one of the most successful initiatives of IBA. Student and Faculty Mentor involvement and the undergraduate research output, in various formats, have been increasing steadily and substantially in both quality and quantity.
Biomathematics Education with Applications and Methods (BEAM) Project BEAM will make funding available to cultivate undergraduate research at member institutions. There are two funding tracks: one that requires institutional matching and one that supports faculty with no access to institutional research funding.
Partners in Extending Education and Research (PEER) PEER is an interdisciplinary scholarly support service program that the IBA offers to educators, researchers, and scholars of cross-disciplinary fields. The PEER Program matches a cross-disciplinary researcher with a data scientist, statistician, applied mathematician, or computer scientist with a higher-level data-science expertise than what may be common in other fields. The PEER program has been so successful that the IBA’s host institution now funds a research graduate assistant position exclusively for PEER.
CLOUD for Layering, Organizing, and Utilizing DATA (IBA-CLOUD) The IBA houses a high-performance computer. Each node sports a 32 core/64 thread AMD \(\hbox {EPYC}^{\mathrm{TM}}\) 7551P processor and RAID array with full-disk encryption for maximum performance and reliability. IBA offers access to members for their research-level computing needs. IBA-CLOUD is already in use at full capacity facilitating cutting-edge research computing for members.
Graduate Certificate Program The IBA offers a flexible graduate curriculum in mathematical biology, with offerings through different options, both online and traditional coursework, students have a variety of options for obtaining a certificate in this program. This program’s innovative approach is highly praised by stakeholders.
Sponsored Journals The IBA sponsors two high quality open access refereed research journals as a part of its mission of providing avenues to the biomathematics community at large to disseminate their work. The first journal, Letters in Biomathematics, publishes peer-reviewed research articles in mathematical biology and its education as well as review articles in the field. The second journal, Spora, is the only student research oriented journal in the world dedicated to biomathematics. These two journals have filled a niche in the field each in its own unique way. The Letters in Biomathematics was the first biomathematics journal that published biomathematics education research side by side with review and research articles. Spora’s success as a platform for hosting undergraduate research has led to expanding its mission by publishing research conducted by graduate students.
Other Resources In addition to the above resources, IBA also offers unique resources to member institutions, such as (1) community curriculum, where students from member institutions may take pre-screened and approved courses offered by other member institutions, (2) faculty research retreats, where faculty members work on collaborative projects, (3) research dissemination support, where members receive financial support for open access, among others. The IBA is a unique concept which is widely regarded as an efficient and productive avenue to foster research and education in mathematical biology. What makes IBA highly efficient and productive is its approach of targeting stakeholders via the institutions in which they belong. Although other initiatives of similar kind with varying missions depend on a volunteer academic workforce, an important building block of IBA without a doubt is its dedicated staff. IBA’s leadership team consists of paid staff members who perform activities covering different parts of its functionality. In addition, IBA’s mission of supporting research and education extends to individual faculty members from non-member institutions. This way, interested and eager researchers and educators also enjoy most of the resources that are afforded to IBA’s institutional members. In fact, this model has proved to be so productive that not only other fields of mathematics but also other disciplines may benefit from a similar approach to research and education. Advancing biomathematics as well as any other scientific field is a multifaceted endeavor whose components are conducting cutting-edge research, educating future scientists, providing platforms to advance the field, providing avenues to disseminate knowledge, and sharing contemporary research tools and expertise. In this context, IBA’s very mission aspires to unify all these components resulting in the highly productive and successful enterprise serving the biomathematical community. Without the IBA’s community-based education and collaborative research philosophy, current member institutions would not have access to the resources that allow them to engage in an active research and education agenda for a rapidly emerging and changing field. Although this community-based education delivery model has started impacting a larger number of programs thanks to the increasing number of institutions joining the consortium, its impact is not yet broad enough to be considered mainstream. The mathematical biology community has an important role in embracing this novel approach in replacing the traditional thinking of “in order to offer a new program, an institution needs to have all the necessary components of this program in place before it can be offered.” Federal or state funding agencies have an important role in supporting this new research and education model as well. Seed funding will allow new institutions to experience the benefits of being a part of this community before committing institutional financial and academic resources.
An important change to the current IBA model which will increase its national profile is the addition of a scientific publishing initiative, called IBA Press. Starting in 2020, the IBA Press will serve the mathematical biology community by publishing and marketing educational and classroom materials created by its stakeholders that are proven to be successful in a single institution but not known in others. Moreover, IBA will acquire and sponsor the international research journal Letters in Biomathematics in an effort to make this well-respected and highly reputable research and education dissemination platform readily accessible to the mathematical biology community.