Education Subgroup (EDUC)

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Sub-group minisymposia

Highlights of the Special Issue of BMB on Mathematical Biology Education

Organized by: John R Jungck (University of Delaware, USA), Raina Robeva (Randolph Macon College, USA), Louis Gross (University of Tennessee, USA)
Note: this minisymposia has multiple sessions. The second session is MS02-EDUC.

  • Midge Cozzens (Rutgers University, USA)
    "Introductory College Mathematics for the Life Sciences: Has Anything Changed?"
  • Our paper focused on issues concerning the introductory college mathematics sequence with an emphasis on students interested in the life sciences, and concentration on the time after the publication of BIO2010. It also explored the potential uses of books targeted at introductory mathematics courses for life science majors today. As relevant background, we looked at the evolution of the way that calculus has been taught over the past 50 years, including at the high school level. We also explored the implications of changes in technology and course delivery, such as online education. As we discussed different books and introductory course ideas, we focused on the needs of biology students, inclusion of real-world problems and models, the role of technology, and the impact of data science. Our paper dealt with 8 issues: Section 1 provided some personal background with calculus dating back to the 70’s, and changes in calculus prior to BIO2010. Section 2 introducesd goals for an introductory mathematics sequence and evaluates the calculus sequence in light of those goals. Sections 3-7 discussed various issues that will help to understand issues and challenges for introductory mathematics for the life sciences: Calculus in high school (Section 3), equity issues relative to calculus and other math topics (Section 4), the impact of online education (Section 5), math as a stumbling block for college students (Section 6), and the increasing importance and value of teaching data science (Section 7). Section 8 reviewed the development of books in light of these issues and challenges. The last section (Section 9) summarizes conclusions.
  • Melissa Aikens (University of New Hampshire, USA)
    "Advances and Challenges in Undergraduate Biology Education"
  • Over the last 25 years, reforms in undergraduate biology education have transformed the way biology is taught at many institutions of higher education. This has been fueled in part by a burgeoning discipline-based education research community, which has advocated for evidence-based instructional practices based on findings from research. This perspective reviews some of the changes to undergraduate biology education that have gained or are currently gaining momentum, becoming increasingly common in undergraduate biology classrooms. However, there are still areas in need of improvement. Although more underrepresented minority students are enrolling in and graduating from biology programs than in the past, there is a need to understand the experiences and broaden participation of other underserved groups in biology and ensure biology classroom learning environments are inclusive. Additionally, although understanding biology relies on understanding concepts from the physical sciences and mathematics, students still rarely connect the concepts they learn from other STEM disciplines to biology. Integrating concepts and practices across the STEM disciplines will be critical for biology graduates as they tackle the biological problems of the 21st century.
  • Raina Robeva (Randolph Macon College, USA)
    "Changing the Nature of Quantitative Biology Education: Data Science as a Driver"
  • We live in a data-rich world with rapidly growing databases with zettabytes of data. Innovation, computation, and technological advances have now tremendously accelerated the pace of discovery, providing driverless cars, robotic devices, expert healthcare systems, precision medicine, and automated discovery to mention a few. Even though the definition of the term data science continues to evolve, the sweeping impact it has already produced on society is undeniable. We are at a point when new discoveries through data science have enormous potential to advance progress but also to be used maliciously, with harmful ethical and social consequences. Perhaps nowhere is this more clearly exemplified than in the biological and medical sciences. The confluence of (1) machine learning, (2) mathematical modeling, (3) computation/simulation, and (4) big data have moved us from the sequencing of genomes to gene editing and individualized medicine; yet, unsettled policies regarding data privacy and ethical norms could potentially open doors for serious negative repercussions. The data science revolution has amplified the urgent need for a paradigm shift in undergraduate biology education. It has reaffirmed that data science education interacts and enhances mathematical education in advancing quantitative conceptual and skill development for the new generation of biologists. These connections encourage us to strive to cultivate a broadly skilled workforce of technologically savvy problem-solvers, skilled at handling the unique challenges pertaining to biological data, and capable of collaborating across various disciplines in the sciences, the humanities, and the social sciences. To accomplish this, we suggest development of open curricula that extend beyond the job certification rhetoric and combine data acumen with modeling, experimental, and computational methods through engaging projects, while also providing awareness and deep exploration of their societal implications. This process would benefit from embracing the pedagogy of experiential learning and involve students in open-ended explorations derived from authentic inquiries and ongoing research. On this foundation, we encourage development of flexible data science initiatives for the education of life science undergraduates within and across existing models.
  • Padmanabhan Seshaiyer (George Mason University, USA)
    "Conneccting with teachers through Modeling Mathematical Biology"
  • We describe some effective teaching and research practices that can help to integrate mathematics and biology efficiently to enhance student learning at all levels. One of the successful approaches proposed is to employ mathematical modeling that can help transform pedagogical practices. In this regard, we introduce some modeling activities that have been shared with teachers through professional development programs and hav been incorporated in the classrooms. We also present how engaging teachers in research experiences in mathematical modeling can help to transform their pedagogical practices and provide opportunities for students to consider pursuing areas at the interface of mathematics and biology.

Highlights of the Special Issue of BMB on Mathematical Biology Education

Organized by: John R Jungck (University of Delaware, USA), Raina Robeva (Randolph Macon College, USA), Louis Gross (University of Tennessee, USA)
Note: this minisymposia has multiple sessions. The second session is MS01-EDUC.

  • Shernita Lee (Virginia Tech, USA)
    "Mathematical Biology: Expand, Expose, and Educate!"
  • Mathematical biology has made significant contributions and advancements in the biological sciences. Recruitment efforts focus on encouraging students, especially those who are underrepresented and underserved, to pursue the field of mathematical biology, regardless of their undergraduate institution type, and raise awareness about the countless professional and academic possibilities provided by this specialized training. This article examines the need to expand, expose, and educate others about mathematical biology. To support field expansion, we give several recommendations of ways to integrate mathematics applied curricula to attract broader student interest.  With this exposure-- whether it is led by an individual, a department, a university, or researchers in mathematical biology-- each can help to promote a base knowledge and appreciation of the field. In order to encourage the next generation of researchers to consider mathematical biology, we highlight current interdisciplinary programs share popular mathematical tools, and present some thoughts  on ways to support a thriving and inclusive mathematical biology community for years to come.
  • Luis A. Melara Jr. (Shippensburg University, USA)
    "The Case for Undergraduate Research Journals"
  • We address the important role of undergraduate research journals in the undergraduate research experience. Peer review by professional researchers is identified as the most essential ingredient in establishing the relevance of these journals as venues for research dissemination. We will introduce you to examples of three such journals—Spora, SIAM Undergraduate Research Online, and the American Journal of Undergraduate Research—with demonstrated success in supporting the undergraduate research experience.
  • Meredith Greer (Bates College, USA)
    "Paying Our Dues: The Role of Professional Societies in the Evolution of Mathematical Biology Education"
  • Mathematical biology education provides key foundational underpinnings for the scholarly work of mathematical biology. Professional societies support this work via funding, public speaking opportunities, web presence, publishing, workshops, prizes, opportunities to discuss curriculum design, and support of mentorship and other means of sustained communication among communities of scholars.  Such programs have been critical to the broad expansion of the range and visibility of research and educational activities in mathematical biology. We review these efforts, past and present, across multiple societies -- The Society for Mathematical Biology (SMB), the Symposium on Biomathematics and Ecology Education and Research (BEER), the Mathematical Association of America (MAA), and the Society for Industrial and Applied Mathematics (SIAM). We then proceed to suggest ways that professional societies can serve as advocates and community builders for mathematical biologists at all levels, noting that education continues throughout a career and also emphasizing the value of educating new generations of students.
  • Kristin Jenkins (University of Texas at Austin, USA)
    "Building community-based approaches to systemic reform in mathematical biology education"
  • Starting in the early 2000’s, several reports were released recognizing the convergence of mathematics, biology and computer science, and calling for a rethinking of how undergraduates are prepared for careers in research and the science and technology workforce. This call for change requires careful consideration of the mathematical biology education system to identify key components and leverage points for change. This paper demonstrates the wide range of resources and approaches available to the mathematical biology education community to create systemic change by highlighting the efforts of four community-based education reform organizations. A closer look at these organizations provides an opportunity to examine how to leverage components of the education system including faculty, academic institutions, students, access to resources, and the power of community.

Windows and Mirrors: Latinx Women in Mathematical Biology

Organized by: Vanessa Rivera Quinones (Latinxs and Hispanics in the Mathematical Sciences (LATHISMS), Puerto Rico), Alicia Prieto Langarica (Youngstown State University, United States of America)

  • Vanessa Rivera Quinones (Latinxs and Hispanics in the Mathematical Sciences (LATHISMS), Puerto Rico)
    "Life is a cooperative game: The interplay of individual behavior in group cooperation"
  • The evolution of cooperation has been a long-standing question both from a sociological and mathematical perspective. This in part, because of the common narrative that the world operates under a 'survival of the fittest' framework. However, cooperation is not only observed in many biological systems, it can also emerge in social dilemmas under certain conditions. We explore cooperative game theory as the mathematical lens to study the emergence of cooperation as an optimal strategy in social dilemmas. In particular,  we focus on predicting when coalitions will form, what are the joining actions or behaviors that groups can take, and what is the resulting pay-off. In this talk,  we provide an overview of common examples of the evolution of cooperation in social dilemmas, and interesting directions of future study.
  • Malena Espanol (School of Mathematical and Statistical Sciences, Arizona State University, United States of America)
    "An Edge-preserving Iterative Method for Electrical Impedance Tomography"
  • Electrical impedance tomography (EIT) is a low-cost, portable, and noninvasive imaging system that does not use ionizing radiation. It has many potential applications including the continuous monitoring of patients with acute respiratory distress syndrome, which in particular is affecting many patients during the current Covid-19 pandemic. In this talk, we present an efficient numerical method that improves the reconstructed image of a human torso.
  • Selenne Bañuelos (California State University Channel Islands, United States of America)
    "A Mathematical Model with Combination Phage-Antibiotic Therapy and Immune System Response"
  • Antimicrobial resistance (AMR) is a serious threat to global health today. A renewed interest in phage therapy – the use of bacteriophages to treat pathogenic bacterial infections – has emerged given the spread of AMR and lack of new drug classes in the antibiotic pipeline. There are few mathematical models that consider the effect of phage-antibiotic combination therapy. Moreover, some biological details such as the immune system response on phage have been neglected. To address these limitations, we utilized a mathematical model to examine the role of the immune response in concert with phage-antibiotic combination therapy compounded with the effects of the immune system on the phages being used for treatment. We explore the effect of phage-antibiotic combination therapy by adjusting the phage and antibiotics dose or altering the timing. The model results show that it is important to consider the host immune system in the model and that frequency and dose of treatment are important considerations for the effectiveness of treatment.
  • Alejandra Herrera Reyes (Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, United United Kingdom)
    "Identifying unique observations in super-resolution microscopy with a spatiotemporal model"
  • Fluorescence microscopy has provided cellular biologists with quantifiable data, that can be paired with mathematical models to discover the mechanics of the imaged processes. Moreover, super-resolution microscopy achieves nanometer resolution images, allowing us to visualize the organization of proteins at nano-scales. dSTORM is a super-resolution technique that relies on the use of photo-switchable fluorophores. One known problem with dSTORM is that images obtained with this technique can suffer from recording a single photo-switchable fluorophore multiple times, possibly creating artificial features. This is especially relevant in the analysis of membrane B-cell receptors clustering, where spatial clustering might relate to immune activation. We developed a protocol to estimate the number of unique fluorophores present in the experiment by coupling their temporal (with a Markov-chain model) and spatial (with a Gaussian mixture model) dynamics within a maximum likelihood framework. Previous studies have used the temporal information, but they have not coupled it with the spatial information (both localization and localization estimation error). We present the results of our estimation protocol on simulated data, well-characterized DNA origami data, and B-cell receptor data with positive results. Our model is general enough to apply to other biological systems besides B-cell data and will enhance a microscopy technique that is widely used in biological applications.

Using modelling in mathematical biology as an educational tool: from schools to higher education

Organized by: (Natasha Ellison, University of Sheffield, UK), Alexander Fletcher (University of Sheffield, UK), Nick Monk (University of Sheffield, UK)

  • Joanna Wares and Marcella Torres (Department of Mathematics and Computer Science, University of Richmond, USA)
    "Making Sense of COVID-19: Mathematics and Data Science Activities Across the Curriculum"
  • We present mathematical modeling and data science activities created around analyzing and interpreting COVID-19 data. Some of these activities and projects address complex social issues related to COVID-19 such as inequality in testing, wealth distributions, or disparity in health outcomes. Preliminary data suggest that COVID-19 disproportionately impacts minorities and low-income households. Much of the instructional guidance provided for the activities and projects is easily adaptable to a remote learning environment, and each activity includes reflection and discussion in addition to the quantitative work. Mathematical topics covered include: modeling the spread of infectious disease, hypothesis testing, simulation, and data fitting. In addition, we share some of our experiences in teaching these activities across the curriculum, from workshops for high school students, throughout the calculus sequence, to upper-level differential equations courses.
  • Padmanabhan Seshaiyer (George Mason University, Fairfax, Virginia, USA)
    "Educational frameworks for upskilling the next generation workforce in mathematical biology"
  • In this talk, we will introduce some novel educational frameworks that provide the opportunity to not only engage students in the tools to represent, understand, analyze and solve real world problems in mathematical biology but also engage them in using tools to make data-driven informed predictions. Such upskilling approaches can help students to become life-long learners going beyond a content-based education in mathematical biology to also include a competency-based training. In particular, mathematical biology must include a variety of learning approaches including experiential learning, inquiry-based learning, challenge based learning and interdisciplinary problem-based learning. In this talk, we will consider some authentic tasks that incorporate a shared collaborative experience with innovative pedagogical practices to advance teaching and learning of mathematical biology in the 21st century.
  • Perry Hartland-Asbury (Radley college, UK)
    "Modelling Mathematics in Secondary Schools"
  • A whistle-stop tour looking at how modelling of mathematical modelling (and Biology in particular) is incorporated into UK secondary school teaching, from Key Stage 3, GCSE and A-level teaching.
  • Thomas Woolley (Cardiff University, UK)
    "Interactive mathematical biology: how to create your first shiny app"
  • This will be a live coding session in which I demonstrate how to turn the discrete logistic equation into an interactive applet that students can explore. Once you generate one app you can generate many others, or even get kids learning how to write their own codes. I’ll start with the basics in a spread sheet package, so very little coding knowledge will be needed. However, it will be useful if you download R: Download R studio as a developer environment (the free one is fine) Make a shiny account. This is the service that will host the app. Finally, having a github account as somewhere to store your code and make it accessible is also useful. By providing interactive applets you allow anyone to explore the mathematics of reproduction, modelling and chaos. This experimentation can be a useful tool for clarifying ideas for secondary school students all the way to graduate students. For those who want a sneak peak, we’ll try to create something like, the code for which can be found here

Recent Perspectives on Mathematical Education

Organized by: Stacey Smith? (The University of Ottawa, Canada)
Note: this minisymposia has multiple sessions. The second session is MS14-EDUC.

  • Kara Allum (Oxford University, United Kingdom)
    "Maths is for everyone: why interdisciplinary and DEI focused approaches should be the basis of high school outreach"
  • Mathematics is one of the most abstract topics we learn at high school and whilst the joy of problem-solving appeals to some of us, questions like “why do I need to know this?” or “how is this useful?” are typically asked by everyone else. Mathematics is inherently interdisciplinary within academia, a fact that is often not communicated within high schools or outreach projects, and leads to misinformation around the idea of what a mathematician is and where their work applies. This disconnect continues when we try to ask the question of who can be a mathematician? The primary and high schools we work with and the researchers we send both have big impacts on future engagement, and, when combined with the academic stereotype (and often reality) that every mathematician is a cisgender straight white man, we can disenfranchise a lot of young people before they get to make up their own minds. In this talk, I will describe my experiences working on different types of outreach programs, mathematical or otherwise, and put forward ideas I have learned from these projects that I believe should form the basis of mathematical outreach. I will discuss the power of storytelling, the need to protect curiosity and why we must strive to be more proactive participants within our local communities. Interdisciplinary topics and DEI work are integral factors to outreach and are key to moving the current narrative away from mathematics being exclusive to one where mathematics belongs to everyone.
  • Kathleen Hoffman (University of Maryland, Baltimore County, USA)
    "Extending Quantitative Reasoning in the Biological Sciences"
  • About a decade ago, a call to transform the curriculum in the biological sciences along with the change in the MCAT focus from courses to competencies spurred a flurry of activity surrounding interdisciplinary education, particularly quantitative reasoning in the biological sciences. Funded by HHMI, UMBC, in a joint project with three other universities, set out to develop validated competency-based modules to facilitate quantitative reasoning in the first two biology courses. Results showed a modest increase in quantitative competencies, but a discrepancy in achievement gains between direct entry and transfer students. To mediate this effect, UMBC, along with four community college partners, developed a consortium of faculty and administrators to facilitate quantitative module development in four core biology courses and to facilitate large-scale implementation. Funded by an NSF IUSE grant, the consortium will track student achievement with the intention of both mitigating the achievement gap between direct entry and transfer students, as well as understanding the effect of increased exposure to quantitative modules.
  • Shelby Scott (University of Tennessee at Knoxville, USA)
    "Things I learned as an interdisciplinary graduate student"
  • Graduate school is a confusing and difficult experience for all students, but there are particular challenges that come from being an interdisciplinary early career researcher. In this talk, I will share some of my struggles faced as a biomathematician/ecologist/statistician/data scientist and give insight to some of the positive and negative feelings many of us seem to have during our time as interdisciplinary graduate students. The goal is to open up an honest conversation about the difficulties of wearing multiple hats as an academic and to de-stigmatize some of these experiences.
  • Glenn Ledder (University of Nebraska, Lincoln, USA)
    "A Teaching Module for Mathematical Epidemiology Using Matlab or R"
  • With the enormous impact COVID-19 is having on our students’ lives, there is no better subject to motivate mathematics students than mathematical epidemiology. Add to that the significant amount of misinformation promulgated on the internet and by political actors, and it is clear we have a moral duty, as well as a mathematical one, to teach this subject. The main pedagogical problem we face is that the standard teaching materials on mathematical epidemiology focus on the theory of simple endemic disease models. This is fine as far as it goes, but the crisis we face concerns a complicated disease on an epidemic time scale. Instead of equilibrium analysis of the simplest models, we need a focus on modeling, simulation, and experiment on more realistic models as well as the simplest ones. In particular, we need to address questions about how public health measures impact the progress of an epidemic and “call bullshit” on false or misleading public statements. Our pedagogical challenges are to create materials that allow a student with minimal programming experience to set up virtual experiments in a program-based model implementation and to create meaningful modeling questions that use those experiments. To that end, I have created educational modules for the SIR, SEIR, and SEAIHRD (COVID-19) models, each of which is centered on a suite of programs that encode the model and are carefully designed to have a minimal “model-user interface”, so that students with the barest minimum of programming experience can modify the programs to address specific questions. This presentation will focus on the Matlab version of the SEIR and COVID-19 modules. I will show the programs and how easy they are for novices to use, and I will highlight a few of the experiments and accompanying questions.

Recent Perspectives on Mathematical Education

Organized by: Stacey Smith? (The University of Ottawa, Canada)
Note: this minisymposia has multiple sessions. The second session is MS13-EDUC.

  • Elissa Schwartz (Washington State University, USA)
    "Remedying the Leaky Pipeline"
  • Diversity is crucial for the success of mathematical biology education initiatives. Cultural and gender diversity among educators and researchers allows for the contribution of a wider range of ideas in mathematical biology education and research. Many trainees from historically underrepresented or disadvantaged backgrounds, however, disappear along their educational path. The loss of women scientists along the career path is common in academic systems around the world; this phenomenon has been described as the ‘Leaky Pipeline.’ It begins at early stages and continues throughout the career trajectory, gradually resulting in a small proportion of women researchers in STEM fields. To begin to remedy this issue, we conducted a virtual international workshop to connect women from underrepresented backgrounds to career advancement opportunities in STEM. In this project, we created a forum to uncover and break down barriers to progress along STEM careers experienced by women from underrepresented backgrounds. This professional development workshop contained 3 parts: a plenary talk and discussion, in which a guest speaker presented her inspirational story of her career journey; a discussion of challenges faced by participants that need to be overcome to take the next step in their STEM career development; and ‘mentoring pod’ small groups discussions (matching participant trainees with mentors in groups of 4-5 in breakout rooms) to target specific issues and facilitate development of participants’ mentoring networks. The event was attended by individuals from eleven countries: Afghanistan, Argentina, Australia, Canada, India, Nepal, Nigeria, Poland, Russia, Trinidad & Tobago, and the US. Data collected from this event (on challenges identified, solutions suggested, networks formed, and scholarship opportunities) will be used to identify which interventions actually work to mend the Leaky Pipeline, and to design similar programs in the future. Such efforts will be needed to improve retention rates in STEM, particularly among historically underrepresented groups.
  • Suzanne Lenhart (University of Tennessee at Knoxville, USA)
    "BioCalculus Assessment Tool"
  • The development and initial validity assessment of the BioCalculus Assessment (BCA) will be presented. This 20-question test was designed with the goal of comparing undergraduate life science students’ understanding of calculus concepts in different courses with alternative application emphases. The analysis of scores involved three populations (Calculus 1, Calculus 2 and Biocalculus) for which the Calculus 1 and 2 students were not exposed to applications in a life science setting while the Biocalculus students were presented concepts with a life science emphasis. Our findings show that the BCA provides a tool to assess the relative learning success and calculus comprehension of undergraduate biology majors from alternative methods of instruction.
  • Amanda Laubmeier ( Texas Tech University, USA)
    "Application-driven projects in differential equation and modelling courses"
  • Projects offer the flexibility for students to explore course material and their own understanding. Application-based projects can also reinforce connections between course material and students' interests. In this presentation, we discuss some attempts at short- and long-term projects for undergraduates. The projects are drawn from differential equations and modelling courses, and emphasis is placed on project design to encourage student creativity and exploration.
  • Stacey Smith? (The University of Ottawa, Canada)
    "Teaching While Trans"
  • Gender transitioning is on the rise among students, but it’s also happening among faculty too. This talk defines some transgender basics and highlights some of the challenges faced in mid-career academia as a result of transitioning from male to female. These include name changes and publications, university and online journal bureaucracies and interactions with students and colleagues. Finally, tips will be provided on how to be a good trans ally and small but helpful changes that can be made in the classroom to make the environment more inclusive.

Sub-group contributed talks

EDUC Subgroup Contributed Talks

  • Aneequa Sundus Indiana University, Bloomington
    "PhysiCell Training Apps: Cloud hosted open-source apps to explore different modules of agent-based multicellular simulations"
  • Multicellular systems biology is an interdisciplinary field that attracts researchers with diverse technical expertise. Simulation software are basic tools to work in multicellular systems biology. Understanding these simulation software entails a steep learning curve for interdisciplinary researchers joining multicellular systems biology research. Thus, there is a need for interactive training materials for those researchers. We have created eight cloud- hosted, interactive apps to train new users on using PhysiCell, a physics-based multicellular simulation software. These applications are open source and hosted on nanoHUB, an open and free platform to host computational simulations. We have created apps for exploring different modules in PhysiCell such as chemical diffusion, cell motility etc. In each app we fixed all parameters except those regulating one module This divide and conquer approach helps users to focus on the function of one module only. For each module user can change the parameters controlling that one aspect of simulation and run it in their browser to observe its effect. These apps can be used for training for new users as well as parameter tuning for more intermediate level users. We also added a detailed simulation where users can change all modules together to study interaction between them.
  • Chonilo S. Saldon Zamboanga del Norte National High School, Philippines
    "Remodeling students' attitudes and performance in Calculus through the use of Biomathematics modules"
  • Students often question the relevance and inclusion of Calculus subject in senior high school even if their career paths lead to Biology, medicine and allied health sciences. This query stems from the engineering-directed learning materials and the non-inclusive treatment of Calculus in the classroom. To address this polarity, biology-concept embedded learning modules and lesson exemplars were developed. Using quasi-experimental design, students' attitude towards Applied Mathematics and Calculus and performance were appraised. Results indicated that integrating biology concepts and problems in calculus classes improved both students' attitudes and performance in Calculus. Implication of the study shall be discussed in terms of students' acquisition on the interface between mathematical and biological sciences.

Sub-group poster presentations

EDUC Posters

EDUC-1 (Session: PS01)
Keith Harris Hebrew University of Jerusalem
"Biomaton: a platform for the visualisation, analysis and computation of biological models"

Biological simulations with large parametric spaces can require immense computational power and complex visualizations to provide comprehensive model analyses. As a result, published simulation results often cover only a small subset of model parameters. While the release of the simulation code is becoming a publication requirement, there are no coding standards for simulations (in terms of programming language or framework). This can represent a significant hurdle to validating model results and further exploration of the parametric space of the model by other researchers, or the wider public. We developed a platform, called ‘biomaton’, for the distribution, computation and visualization of a wide range of biological models. Biomaton is cloud-based and allows users to explore and analyze, through a simple user interface, the parametric spaces of published models uploaded to the platform. Biomaton supports multiple programming languages, and can be extended to support virtually any visualization type. We foresee the platform as a means to make mathematical and computational biological models more accessible to researchers, as well as to be used as an educational tool providing accessible visualizations of models dynamics and results.

EDUC-2 (Session: PS02)
Randy Heiland Indiana University
"Creating a graphical user interface to define model parameters for PhysiCell"

Randy Heiland, Adam Morrow, Grant Waldrow, Drew Willis, Kim Crevecoeur, Paul MacklinPhysiCell is an open source, hybrid continuum-discrete mathematical modeling system that combines off-lattice discrete agents with a reaction-diffusion framework and has been applied to a broad variety of problems in mathematical biology. Early versions of PhysiCell generally required both writing C++ code and hand-editing XML configuration files to define a model. As the framework has evolved, most of the C++ model definition code has moved into the XML, making it easier to create, run, and share models. Our poster describes the design and development of a graphical user interface to generate the entire XML model. Our goal is to help create a future where powerful agent based models can be defined and simulated with relative ease. This project, which involves several undergraduate (REU) students, provides a nice complement to a previously published undergraduate-related project: xml2jupyter.