BioQUEST / HHMI / CaseNet Summer Workshop 2015
Presentation descriptions
This page contains descriptions of the workshop sessions and presentations. The sessions and presentations are listed in the schedule. Inside the schedule, you can click "more info" next to a session/presentation to be directed to the descriptions posted below.
Quantitative reasoning: Interdisciplinary STEM 21st century reasoning modality
Robert Mayes
Georgia Southern University
Date & Time:
Wednesday, June 17 @ 9AM
Description:
The Next Generation Science Standards (NGSS 2013) and the Common Core State Standards for Mathematics (NGA 2010) call for improving scientific, engineering, and mathematical practices. Among the practices called for are model-based reasoning which engages students in developing and using models, analyzing and interpreting data, and using mathematics and computational thinking. Fundamental to these processes is quantitative reasoning (QR), which for this project is defined as:
Quantitative reasoning is mathematics and statistics applied in real-life, authentic situations that impact an individual’s life as a constructive, concerned, and reflective citizen (Mayes et al. 2014b).
In the NSF project, Culturally Relevant Ecology, Learning Progressions, and Environmental Literacy (or simply the Pathways project) a QR learning progression was developed to explore the trajectory of QR development across 6th to 12th grades. The QR progress variables for the QR learning progression include the Quantification Act (QA) - mathematical process of conceptualizing an object and an attribute of it so that the attribute has a unit measure; Quantitative Interpretation (QI) - ability to use models to discover trends and make predictions; and Quantitative Modeling (QM) - ability to create representations to explain phenomenon and to revise them based on fit to reality. Three parallel diagonistic assessments for QI were developed to inform the learning progression and provide an instrument to assess students QI ability. An overview of 21st century STEM reasoning modalities will be provided, including complex systems reasoning, scientific model-based reasoning, computational reasoning, engineering design, and quantitative reasoning. The QR learning progression will be presented, leading to a discussion of the three QI assessments and efforts to research their validity and enhance future versions. Outcomes of Rasch analysis of data gathered from administration of the assessments to a large sample of students from 6th to 12th grades will be discussed.
Additional resources:
Robot vs. Disease: Using CellProfiler to model biomedical research in your classroom
Mark Bray
Broad Institute of Harvard and MIT
Date & Time:
Saturday, June 13 @ 2PM & Sunday June 14, @2PM
Description:
In this session, I will introduce the open-source and freely-available software package CellProfiler, designed to quantify cellular images obtained by fluorescence microscopy. There is strong and growing demand for software to analyze such images, as automated microscopes collect images faster than can be examined by eye and the information sought from images is increasingly quantitative and complex. CellProfiler provides powerful image analysis algorithms in a user-friendly interface, making it a useful introductory tool for students new to quantitative cellular analysis. During this session, I will demonstrate the software, provide vignettes of interesting research enabled by the software and give examples of prior educational applications.
John Jungck
University of Delaware
Date & Time:
Sunday, June 14 @ 10:30AM
Description:
In this workshop, I will focus on ten different kinds of hypothesis testing via mathematical analysis of visuals in biology: (1) Phenomenological; (2)
Topological; (3)
Geometric; (4) Spatial Statistics; (5) Networks; (6)
Iterative Fractal Generation; (7) Fractal Measurement; (7) Bioorthogonal Transformations: Warping, Morphing, Morphometrics, Landmarks; (8) Cellular Automata; (9) 3D rendering; and (10) Hyperbolic space. In each case, I argue that visual representations are testable hypotheses, help us reason about biological causation, and help us communicate our inferences. For students to be empowered as scientific investigators, I argue that they need more visual tools than linear regression of an X-Y scatterplot of points or a histographic display of frequencies or compositions.
Open science, open data, open source projects for undergraduate research experiences
Kam Dahlquist
Loyola Marymount University
Date & Time:
Saturday, June 13 @ 2PM
Description:
In this workshop, I will demonstrate a suite of open source tools that students use in my courses to conduct original research in my courses. In a team-taught, cross-listed Biological Databases course, students use the XMLPipeDB suite to create a gene database for a microorganism and use it to analyze published DNA microarray data. In a team-taught, cross-listed Biomathematical Modeling course, students use the GRNmap software to perform differential equations modeling of a medium-scale gene regulatory network and the GRNsight software to visualize the results. Each of these courses is taught "in the open" on a publicly-accessible course wiki. The results of student research are published on the web for the scientific community. There is a special emphasis in the courses on interdisciplinary teamwork, computer literacy, data literacy, and information literacy.
I will discuss how you can adopt and adapt these exercises and/or framework in your courses.
Additional resources:
Mathematical modelling open source software
Visualization open source software
Biological Databases course website
Biomathematical Modeling course website
Bioinformatics Laboratory course website
A biologically themed introduction to computing
Eliot Bush
Harvey Mudd College
Date & Time:
Saturday, June 13 @ 2PM
Description:
As biology becomes more quantitative, there is an increasing need to train biologists who will be sophisticated users of computers. We have developed a first-year undergraduate course that teaches the foundations of computational thinking and programming in the context of biological problems. This is more than just an introductory computer science course: every assignment has a strong biological theme. In this session we’ll give an overview of the course, and then provide attendees an opportunity to work on one or more Python programming assignments. These include developing a simple gene finder, and implementing an RNA folding algorithm.
A variety of materials from the course are available:
Collection of homework problems
Avida ED: An artificial life platform for teaching evolutionary principles and the nature of science
Jim Smith1, Wendy Johnson1, Amy Larke2, Louise Meade1, & Robert T. Pennock1
1Michigan State University
2Michigan Technological University
Date & Time:
Saturday, June 13 @ 2PM
Description:
Participants in this session will learn how to implement the artificial life platform, Avida-ED (avida-ed.msu.edu), in their classrooms. We’ll begin by describing the Avida-ED instructional sequence and lab manual that we implemented in an Introductory Cell and Molecular Biology course at Michigan State in 2014. Avida-ED was used in the teaching lab, in parallel with a bacterial antibiotic resistance experimental research stream, allowing students to draw connections between Avidian evolution and the evolution of antibiotic resistance in microbial populations. After downloading the Avida-ED program and Lab Manual, participants will participate in a short set of exercises, each focused on teaching particular evolutionary concepts, that we used to familiarize students with Avida-ED. We’ll then describe independent Avida-ED research projects carried out by our students, the results of which were presented as posters to scientists in MSU’s BEACON Center in fall 2014. These will provide the basis of a discussion about how workshop participants might implement Avida-ED research projects into their own courses. We’ll also present some of the results of our DBER work showing that Avida-ED appears to have a significant positive effect on student learning of evolutionary concepts, in particular the random nature of mutation, which is considered by some to be a threshold concept in evolution education.
Additional resources:
Sarah Orlofske
Northeastern Illinois University
Date & Time:
Saturday, June 13 @ 2PM
Description:
This workshop will investigate two biological examples for how to integrate mathematical concepts into both introductory and upper level undergraduate biology classrooms. Using two different case studies involving food webs, directed at beginning and then more advanced students, we will explore how students can learn through building conceptual models and then add in components of network modeling and analysis. Similarly, we will explore how building evolutionary trees (phylogenies) can move through the process of conceptual modeling through simulation, and again to computer based phylogenetic analysis. Throughout the workshop participants will have the opportunity to work through different aspects of the inquiry-based lessons and gain hands on experience as well as discuss implementation and assessment.
Additional Resources:
Mesquite - a phylogenetic analysis software, click here to run on QUBES Hub
R Studio - statistical software, click here to run on QUBES Hub
Colleen Jonsson
NIMBioS
Date & Time:
Saturday, June 13 @ 6:30PM
Description:
TBA
Julie Morris
University of Denver
Date & Time:
Sunday, June 14 @ 10:30AM
Description:
In this session, we will introduce Data Nuggets (http://datanuggets.org/). Data Nuggets are classroom activities, co-designed by practicing scientists and teachers, which give students experience interpreting quantitative information and making claims based on evidence. They are created from ongoing scientific research and provide a brief background about scientists and their study systems, as well as real datasets from their research. Students are challenged to answer a scientific question using the dataset to support their claim. The goal of Data Nuggets is to engage students in the practices of science through an innovative approach that combines scientific content from authentic research with key concepts in quantitative reasoning. The workshop will include an introduction to Data Nuggets from the student perspective, and will present strategies for modifying existing Data Nuggets to teach a range of quantitative skills and levels (from simple graphing skills to calculating basic statistics). Participants will gain hands-on experience allowing them to adapt Data Nuggets to their own course needs and specific student learning goals, and will also be introduced to a template that can be used to create new Data Nuggets from any original data.
Sam Donovan & Lou Gross & Arietta Fleming-Davies
University of Pittsburgh; University of Tennessee
Date & Time:
Sunday, June 14 @ 10:30AM
Description:
Join us for an education workshop where you will get hands on experience using a variety of freely available scientific tools (particularly R and Netlogo) to explore biological problems. Our primary goal is to help participants adopt and adapt existing curriculum modules that address two of the core competencies outlined in the Vision and Change report (“Ability to use quantitative reasoning” and “Ability to use modeling and simulation”). The tools and modules we will present are appropriate for use in introductory biology and upper-division course and laboratory settings. One tool introduced will be the R package, a freely available statistics and modeling package available on multiple platforms that has become prevalent in many areas of biology. Attendees will work with examples of its use with naive students to enhance quantitative analysis of data. Topics will include data analysis / visualization, agent based modeling, and general strategies for engaging students quantitative reasoning.
To run R on the Hub website, click here
Evo-ED: Integrative cases for teaching evolution across the biology curriculum
Jim Smith, Merle K. Heidenmann, & Peter J.T. White
Michigan State University
Date & Time:
Sunday, June 14 @ 10:30AM
Description:
Participants in this session will be introduced to and gain experience working with a set of online cases that we developed to help students learn evolutionary concepts (www.evo-ed.org). Our underlying assumption in developing these cases was that a complete understanding of evolution requires knowledge that spans many biological sub-disciplines. However, students are often taught evolution in the context of ecological systems, isolated from molecular, genetic and cellular concepts. To address this, each of our six online cases tracks the evolution of traits from their origination in DNA mutation, to the production of different proteins, to the fixation of alternate macroscopic phenotypes in reproductively isolated populations. Each case consists of a set of web pages, a PowerPoint slide set, and in some cases games and simulations. Two of the cases have been developed for inclusion in the National Center for Case Study Teaching in Science and thus have an expanded set of teacher resources. In the HHMI/BioQUEST/SCN session, we’ll illustrate how we’ve used the cases in our own teaching in both the introductory and advanced biology courses, share some additional teaching resources we’ve used to accompany these class sessions, and work with participants to think about ways they might use the cases. We’ll also share some of the results of our published DBER work in which we described implementation and assessing the effectiveness of the Evo-ED cases.
Additional resources:
Buffalo cases:
- Joel E. Greengiant Learns About Peas: From Nucleotides to Selection
- The Evolution of Color Vision in Monkeys: From Nucleotides to Ecology
Tony Weisstein
Truman State University
Date & Time:
Sunday, June 14 @ 10:30AM
Description:
In this session, I will introduce the Biological ESTEEM Collection, an online suite of Excel-based modules that facilitate mathematical exploration of a wide range of biological concepts. These modules are designed to guide early learners step-by-step through the reasoning that underlies a particular model or analysis, while advanced users can modify the default calculations to better reflect the actual features of a given biological system. Today, we will focus on two modules: (1) Island Biogeography, in which students determine which biotic and/or abiotic factors best predict species diversity in discrete habitat patches; and (2) SIR BuildIt, in which students first model the spread of a generic infectious disease, then refine the model to reflect more precisely the properties of a specific disease of their choice.
Additional Resources:
Data-based inquiry in the classroom using authentic research data from the Dryad Digital Repository
Samantha Swauger
DryadLab
Date & Time:
Sunday, June 14 @ 2PM
Description:
Looking for real datasets to use in the classroom? DryadLab modules encourage students to focus on core competencies such as critical thinking and data analysis by promoting an active learning environment for all students. Through the use of authentic data sets, students develop an ability to analyze and represent data to solve a problem, understand the relationship between the data and the hypothesis, cope with missing data, recognize confounding factors, interpret ambiguous results, and come to better understand how scientific knowledge is constructed – come learn how to use these materials in your classroom!
Studying DNA structure with mathematical and computational methods
Mariel Vazquez
University of California, Davis
Date & Time:
Monday, June 15 @ 9AM
Description:
I will discuss a course where we introduce students from mathematics, biology, computer science, statistics, and related disciplines to common mathematical and computational techniques used in the analysis of the three-dimensional structure of DNA. The structure of DNA is used as a guiding thread for the presentation of the quantitative methods. Students learn different ways to model DNA that will depend on the biological question to be answered, and they devote 6-8 weeks to a research project. This can be used as a template for courses aimed at a highly interdisciplinary audience where a strong interaction between mathematics and biology is emphasized.
Joining a movement? Consideration of the national landscape of STEM reform
Adrianna Kezar
University of Southern California
Date & Time:
Monday, June 15 @ 1PM
Description:
Dr. Adrianna Kezar will describe various national efforts aimed at STEM reform as well as emerging research about the viability and trends in such efforts. She will explore how communities of practice – like BioQUEST fit into this larger landscape as well as the research on benefits of participation in these groups for both faculty as well as the institutions they are a part of. She will also explore avenues for creating more local change efforts such as learning communities on your own campus that bridge math and biology faculty.
Open Education Resources (OER) for science teaching - an evolving landscape
Ahrash Bissell
Monterey Institute for Technology and Education
Date & Time:
Tuesday, June 16 @5PM
Description:
OER are teaching, learning, and research resources that reside in the public domain or have been released under an intellectual property license that permits their free use and re-purposing by others. While debates continue regarding best practices in licensing choices, publishing models, and appropriate technical formats, we can safely leave such esoteric topics aside and instead examine the real and potential impacts of OER on teaching and learning, especially in science. We’ll look at some key issues and trends in open science education, including flagship OER repositories, production and adaptation practices, open-centric pedagogical models, and persistent or emerging challenges and opportunities.
Additional Resources:
List of links to Open Education Resources
Designing active learning exercises for ecology, evolution, and mathematical biology classes
Stephen Adolph
Harvey Mudd College
Date & Time:
Sunday, June 14 @ 2PM
Description:
In this workshop I will share a few of the in-class active learning exercises that I have been using in my undergraduate courses. These exercises guide students through quantitative topics in ecology, evolution and some other fields. We will then work on developing in-class activities that are tailored to your own courses and students.
Kristin Jenkins and Stacey Kiser
BioQUEST and Lane Community College
Date & Time:
Sunday, June 14 @ 2PM
Description:
These modules introduce students (and anyone else who's interested) to the mathematical underpinnings of what they learn in introductory biology courses. But unlike a textbook, the modules are not full of equations and proofs. Instead, we try to bring math to life using intuitive approaches, everyday situations, and even humor. The modules contain hundreds of interactive activities, games, and questions. They range from the relatively simple (what to do with division) to the relatively abstruse (discrete diffusion models).
Additional Resources:
A hitchhiker’s guide to the case study
Annie Prud'homme-Genereux
Quest University Canada
Date & Time:
Saturday, June 13 @ 2PM
Description:
This session is for instructors who are curious about case studies. Case studies are narratives that scaffold the learning experience. They allow students to “think-like-a-scientist,” collaborate with peers, understand how knowledge is applied in the real world (which is often more messy than it is presented in a textbook), and the stories help students remember information by placing it in its larger context and linking it to other knowledge. In the first half of the workshop, we will simulate a case study class; you will put on your student hats and experience the case discussion method from the point of view of the learner (I promise: the case study used for this purpose will puzzle and fill you with wonder!). You will then reflect on your experience and engage in a discussion about the strengths and pitfalls of this method (and we will come up with solutions for remedying the potential pitfalls). In the second half of the session, you will be introduced to variations in using cases in the classroom (that might be more suitable to your particular context), resources, and we will discuss how to integrate quantitative reasoning into the case method. In preparation for the session, you might wish to brush up on your basic high school Punnett Square knowledge, but no background is required. Just put up your thumb; this school bus picks up hitchhikers on the way to case study nirvana!
Additional resources:
Annie Prud'homme-Genereux
Quest University Canada
Date & Time:
Tuesday, June 16 @ 1:30PM
Description:
Research papers are stories. They recount the heroic journey taken by scientists in their quest for hidden treasures. We often use these tales to transmit our scientific culture and to inspire our apprentices. Using these stories is a good idea, but the articles themselves may not be the best way to encourage students to become heroes of tomorrow’s stories. For one thing, research papers are infused with secretive language and refer to the use of magical tools that are unfamiliar to a trainee. The heroes of the stories are presented as successful, wise, and all-knowing and leave apprentices with little confidence that they could have done better. Perhaps most importantly, a journal article is presented in a continuous narrative and it doesn’t give students the opportunity to consider the paths they would have taken when faced with a similar quest; it doesn’t give them a chance to make hypotheses, to design experiments, to predict results, and to critique them. In short, a journal article does not give students the opportunity to practice the skills of thinking like a scientist. A case study based on a journal article side-steps these shortcomings. It gives students a chance to be the hero in a story. It is easy to transform a research paper into a case and is a good place for first-time case writers to get their feet wet. In this workshop, you will be introduced to a “formula” for transforming your favourite research article into a case study that develops your students’ ability to think like a scientist. You will have the opportunity to practice converting a journal article into a case and will receive feedback from peers and from the facilitator. The goal is for you to feel comfortable writing a journal case study on your favourite experiment by the end of this session.
Additional resources:
Development of BioSQuARE, an instrument to assess undergraduate biological quantitative skills
Jason Belitsky
Oberlin College and Q6 Project
Date & Time:
Thursday, June 18 @ 1:30PM
Description:
This session will feature the Biological Science Quantitative Reasoning Exam (BioSQuaRE), an instrument designed collaboratively by members of seven institutions interested in innovative approaches to strengthening quantitative reasoning among our students. BioSQuaRE is aimed to assess the performance of introductory biology students in the quantitative areas that are becoming essential for success in modern college biology. We will present the motivation for the project, the iterative development of the instrument, and examples of items and the responses from initial trials. We will describe the process for collaborative development and implementation of this new assessment tool. Participants will be invited to discuss how BioSQuaRE and other assessment initiatives can be used productively to advance student learning.
InterLACE: Interactive Learning and Collaboration Environment
Leslie Schneider
Date & Time:
Wednesday, June 17 @ 9:00AM
Description:
Initially funded by an NSF Grant to Tufts University, InterLACE (Interactive Learning and Collaboration Environment) is a web-based Computer Supported Collaborative Learning (CSCL) environment that supports scientifically meaningful collaborative activities and promotes a broad range of knowledge building and science process skills (Hynes, et al 2012). The platform was explicitly designed to support interactive learning and adaptive instruction in both face-to-face and online environments. Accessible from any web-enabled device, InterLACE’s interactive digital whiteboard delivers content in way that encourages students to quickly capture, share, analyze, and improve their ideas. It provides both students and instructors with continuous feedback about the learning process, enabling active learning in ways that were previously unimaginable. Online collaboration and discussion of concepts identify the key questions and issues for face-to-face classroom discussion. Embedded learning analytics help educators identify in real-time those students who understand key concepts and those who do not, making sure that no student falls through the cracks. The platform’s highly visual presentation allows both teachers and individual students to embed videos, graphics, and interactive media.
InterLACE is used by thousands of educators and students at both universities and high schools worldwide. Research has confirmed that high school physics students in InterLACE classrooms are highly engaged and achieve significant gains in conceptual knowledge on standardized tests vs. comparison groups. Interviews with teachers revealed that InterLACE supports active and sustained learner engagement and provides analytical tools to measure and maintain it. Teachers also observed that both student collaboration and metacognition improve with InterLACE use.
Additional Resources:
InterLACE activity (password: pass)
Date & Time:
Sunday, June 14 @ 6:30PM
Description:
We will have a traditional poster session on Sunday night. This session is an opportunity for you to share resources and programs in which other workshop participants might be interested. Please let us know if you plan to present a poster so we can prepare enough space. You do not need to create a new poster for this event if you have something appropriate from another event.
Additional resources:
How to print a poster on fabric
4H Sharing Session
Date & Time:
Wednesday, June 17 @ 7:30PM
Description:
A second event, the annual 4H Sharing Session, will be held on Wednesday night. Each person who wishes to share will have 3 minutes to describe whatever they would like to share - a resource, an activity, a website, etc. You do not need a poster for this, but prepare a couple slides and handouts if you wish. We will have a sign up sheet for this event at Registration.