Molecular Biology Simulations for Case Based Learning

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Title of Abstract: Molecular Biology Simulations for Case Based Learning

Name of Author: Karen Klyczek
Author Company or Institution: University of Wisconsin-River Falls
Author Title: Professor
PULSE Fellow: No
Applicable Courses: Agricultural Sciences, Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Cell Biology, Evolutionary Biology, General Biology, Genetics, Immunology, Integrative Biology, Microbiology, Virology
Course Levels: Introductory Course(s), Upper Division Course(s)
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: computer simulations case studies bioinformatics molecular biology

Name, Title, and Institution of Author(s): Mark Bergland, University of Wisconsin-River Falls

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Our goal is to facilitate case studies and other active learning strategies via development of computer simulations of molecular biology lab techniques. This project addresses Vision and Change recommendation to relate biology concepts to real-world examples and make biology content relevant for students. The NSF-funded Case It project has produced case studies mainly in genetic and infectious diseases, in which students use simulation software to analyze authentic DNA and proteins sequences associated with the cases. By analyzing these cases, students address several core competencies, including applying the process of science, using quantitative reasoning, using modeling and simulation, and understanding the relationship between science and society. Based in part on the recommendations in the Vision and Change report, we have developed materials designed to prepare students for research projects involving bioinformatics analysis, to extend the existing case studies and for use with student-generated experiments. The software and materials are made available free of charge on the Case It web site (www.caseitproject.org) and have been used by secondary and undergraduate schools worldwide. Case It was awarded a 2011 Science Prize for Inquiry-based Instruction (Bergland et al. 2012, Science 337, 426 (2012).

Describe the methods and strategies that you are using: Case It is an open-ended simulation that reads any nucleotide or amino acid sequence file, and includes methods for analyzing DNA and proteins. These methods include restriction digestion and mapping, polymerase chain reaction (PCR), DNA electrophoresis, Southern blotting and dot blotting, microarray analysis, protein electrophoresis, Western blotting, and ELISA. Bioinformatics capabilities (sequence alignment, tree building) have been added via integration with MEGA software. The download includes the simulation as well as all of the sequences necessary to run the cases described on the web site. The case descriptions can be viewed from the Case It home page or downloaded as a pdf file. Students read case scenarios and explore background information for the case. They then use the simulation to open sequence files associated with the case and run the appropriate procedure to analyze the sequences, generating results in the form of images that can then be incorporated into presentations or reports. At the introductory-biology level, students can assume roles of persons in the cases, such as health-care professionals, lab technicians, researchers, or hypothetical family members. They then discuss results either in person or online. The open-ended nature of the simulation encourages inquiry by enabling users to analyze any DNA sequence, including entire viral or bacterial genomes, with any probe, primer, or restriction enzyme. For example, freshmen at UWRF participating in the HHMI Science Education Alliance PHAGES project use the Case It simulation to generate virtual digests of known phage genomes for comparison with actual gels of their newly discovered phages.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Assessment of the use of the Case It materials has demonstrated that it provides an active and collaborative learning environment that engages and motivates students. Pre- and post testing as well as individual and focus group interviews were used to assess its impact on student learning and perceptions in courses at several institutions in the United States and Puerto Rico. In all courses, students demonstrated significant learning gains as a result of using the simulation to analyze case studies involving bioinformatics analysis. In addition, students reported that the activities allowed them to explore science concepts from multiple perspectives in a real world context. The instructor-independent efficacy demonstrated in these studies indicates that the use of Case It materials has the potential to be scalable in a variety of institution types.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Since 2012, the Case It software has been used by more than 10,000 students at 60 schools around the world. It was downloaded by many more faculty, from 105 different countries, so there is likely to be additional use that we have not been able to document. When we have assessed the impact on students in classes as described above, students using Case It showed improved post-test scores, and students' confidence in their knowledge also increased (Wolter et al., 2012, J Sci Educ Technol DOI 10.1007/s10956-012-9387-7). Faculty involved in software development, case writing, and assessment have been able to cite this work as scholarly activity for retention, promotion and tenure purposes.

Describe any unexpected challenges you encountered and your methods for dealing with them: Barriers to implementation of the Case It software include the need for faculty training in the use of the simulation. To address this issue, we have given many workshops at professional meetings and at the invitation of biology departments. We also have developed screencast tutorials that are posted on the web site. The web site also includes discussion forums where questions about the use of the simulation can be addressed. Finally, we are exploring the development of mobile applications of the software for use on tablets and other devices.

Describe your completed dissemination activities and your plans for continuing dissemination: We have given over 50 presentations, including workshops, oral presentations, and posters, at science education meetings in a variety of venues. In 2013 so far, we have presented at the NSF/AAAS TUES conference, American Society for Microbiology Conference for Undergraduate Educators, Science Case Network conference, and HHMI Quantitative Biology/BioQUEST workshop. We no longer have grant funding, but still plan to present at conferences as funding allows. Limited travel funds are available through the University of Wisconsin-River Falls, and from conference organizers when we are invited to present. We have published several papers describing strategies for implementing Case It and assessing its effectiveness, in Science, the Journal of Science Education Technology, American Biology Teacher, and others. In 2011 we joined the Science Case Network RCN-UBE project, and are collaborating with other case study and problem based learning projects to dissemination information and resources for faculty interesting in incorporating these active learning strategies (www.sciencecasenet.org). In 2012, the Case It web site, www.caseitproject.org, has been updated to include more interactive features and facilitate more effective dissemination of materials, and will continue to be updated.

Acknowledgements: The National Science Foundation has provided funding to support development, dissemination, and assessment of Case It materials (DUE grants 9455425, 9752268, 0229156, 0717577). Mary Lundeberg, formerly at Michigan State University and the University of Wisconsin-River Falls, has coordinated assessment of the project, with assistance from undergraduate and graduate students; in particular, Bjorn Wolter, former MSU graduate student. Chi-Cheng Lin assisted with critical aspects of the software that allowed incorporation of bioinformatics features. Rafael Tosado, Interamerican University of Puerto Rico-Metro Campus, Arlin Toro, Interamerican University of Puerto Rico-San German, and C. Dinitra White, North Carolina A & T State Unviversity, assisted in case development and assessment in their courses. Kim Mogen, Brad Mogen, University of Wisconsin-River Falls, and Eric Ribbens, Western Illinois University, have written case scenarios. Numerous faculty and student users have provided feedback on software features and ideas for new cases. The University of Wisconsin-River Falls College of Arts & Sciences and Provost’s office have provided support for faculty time and travel to conferences.

Society for Economic Botany

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Title of Abstract: Society for Economic Botany

Name of Author: Gail Wagner
Author Company or Institution: University of South Carolina
PULSE Fellow: No
Applicable Courses: All Biological Sciences Courses
Course Levels: Across the Curriculum, Faculty Development
Approaches: Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: open source, curriculum, ethnobiology, assessment, teacher development

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Goals: (1) to improve undergraduate teaching excellence; (2) model how interdisciplinarity may enhance science education; (3) provide open-source, online, peer-reviewed ethnobiological teaching and assessment materials so that even isolated faculty can join a network of other faculty. Outcomes: We produced a 2013 document called Vision & Change in Undergraduate Ethnobiology Education in the U.S.A.: Recommended Curriculum Assessment Guidelines. Since 2009, we have increased the number and variety of our modules; we are currently increasing our peer reviews of existing modules; we have increased the number and variety of instructors we have directly impacted with workshops (e.g., inclusion of community college instructors), and we have increased our advertisement to/work with other societies (e.g., ESA, SoE, ISE). Our network is becoming more international in scope.

Describe the methods and strategies that you are using: We hold hands-on teaching workshops in conjunction with professional society conferences. We provide open-source online teaching modules that range from single lesson plans to classroom tools to entire courses. We have just developed a new DRD web portal in conjunction with other societies. We invite peer and student review of modules with the aim to improve and diversify our offerings. Our 2013 document V&C in Ethnobiology, which is modeled on the AAAS V&C, proposes guidelines for developing an ethnobiology curriculum. We include an education column in our twice-yearly societal newsletter. We support student membership and attendance at our conference with reduced rates, and full members are invited to support a new online student membership for the very low rate of $10. At our societal conference we mentor students to become professionals.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: We conduct pre- and post-assessments of our teacher workshops. We conduct surveys to study our own network. We garner informal feedback from participants or people who have used our online materials.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: In late June 2013, we began distribution of our document V&C in Ethnobiology, modeled on the original V&C. Based on the reactions of conference participants, we anticipate that our document will provide the framework for the development of undergraduate ethnobiology education not just in America, but around the world. Informally, we hear from isolated instructors how much we have helped them develop curriculum and improve teaching strategies.

Describe any unexpected challenges you encountered and your methods for dealing with them: At present, only two universities offer majors in ethnobotany and none in ethnobiology. Given that SEB is a professional society with impermanent officers and committee members, and that we are very interdisciplinary rather than associated with one discipline, our impact is with individual instructors rather than departments or institutions (other than the two mentioned). And it is only through our instructors that we can assess impact to their students. However, according to OSN surveys/assessments, our impact on individual instructors (who otherwise felt isolated in their departments) is major in furthering V&C teaching recommendations. Given that the majority of our societal membership is not American and that we are an international society, it is difficult to involve and mentor undergraduate students when we meet outside of the U.S.A., as we do every several years. It will always remain difficult to involve undergraduate students in our conferences, but we do reach their instructors.

Describe your completed dissemination activities and your plans for continuing dissemination: In late June 2013 we opened a new online DRD web portal for posting open-source educational materials. The Society for Economic Botany is an organizational member of the Open Science Network and will continue to work on OSN online materials and societal teaching workshops. The V&C in Ethnobiology document is posted on the OSN web page.

Acknowledgements: Thanks to the team from the Open Science Network.

Enabling Student Success: A Learner-Centered Methodology

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Title of Abstract: Enabling Student Success: A Learner-Centered Methodology

Name of Author: Stephen Aley
Author Company or Institution: University of Texas at El Paso
Author Title: Professor
PULSE Fellow: No
Applicable Courses: and Pre-Calculus, Biochemistry and Molecular Biology, Bioinformatics, Chemistry, Ecology and Environmental Biology, Evolutionary Biology, General Biology, Genetics, Microbiology, Organismal Biology, Physics, Virology
Course Levels: Across the Curriculum
Approaches: Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: Peer-Led Team Learning (PLTL) Curricular Research Interdisciplinary Quantitative Biology Assessment

Name, Title, and Institution of Author(s): James E. Becvar, University of Texas at El Paso Ann H. Darnell, University of Texas at El Paso

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The Biology undergraduate curriculum at the University of Texas at El Paso is undergoing vast changes that address both the University Mission (a pursuit for excellence in education while providing access to the people of El Paso) and a response to the state of Texas legislature’s call for a larger percentage of students graduating. UTEP Biology undergraduate students are 85% Hispanic, mirroring the population of El Paso and reflecting national trends. The intended outcome is to graduate more students and increase participation of underrepresented students in biomedical research.

Describe the methods and strategies that you are using: The change strategy focuses on a learner-centered methodology. Beginning in 2000, the curriculum format for general chemistry changed by replacing one faculty-delivered lecture (passive learning) per week with a required weekly two-hour workshop (active learning). The workshop includes one hour of problem solving in teams guided by a Peer Leader, followed by one hour of hands-on explorations. The explorations are simple experimental activities which promote student-initiated inquiry, guided by the Peer Leaders. Many activities are based on biology, demonstrating real-world examples of the conceptual material that students encounter in lecture. Building upon this active learning approach, a 2006-awarded HHMI grant implemented undergraduate research for at least one semester, and potentially two, for all biology majors. In 2007, an NSF-funded STEP grant expanded the chemistry peer-led workshop model to mathematics and physics. In 2008, NIH provided funding for a major curricular reform where the Core Competencies (Vision & Change, 2011) of quantitative reasoning, modeling and simulation were implemented, beginning with the first introductory biology course, concluding with new course development that consolidates courses designed to prepare students for various graduate studies including Bioinformatics and Biomedical Engineering. Eleven additional undergraduate biology courses (three of which were associated laboratory courses) were either revamped or developed (NIH MARC II) with the goal of increasing the emphasis on biological modeling, computational knowledge, statistical analysis, and data analysis. This curricular reformation targeted not only the increased understanding of core concepts including the ability to make connections among interdisciplinary problems, but an increase in perception of relevance of mathematics and computer modeling in the systems approaches required today.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: 1) Successful course completion 2) Tracking students to graduation 3) Matriculation to graduate and professional school 4) Attitudinal surveys Results of these curricular modifications show that over a six year period between the fall of 2006 and the fall of 2012, the number of biological science students has nearly tripled at UTEP, with the percentage of underrepresented students, primarily Hispanic, rising 10% (to over 85%). Part of this growth is due to less attrition. Assessing degree output six years prior, the graduation rate has risen for those students who declare a major in a biology discipline (from 78% to 85%) over a six year timeframe. If we only maintain an 85% graduation rate, by 2018 we should see more than 1200 students, 85% which are Hispanic, entering the workforce or continuing at the graduate level prepared to critically address not only biology-related problems but complex interdisciplinary issues and challenges of the 21st century.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The positive outcomes of the program not only include improved student success in course, but also the enhancement of professional development gained through self-guided and team-guided inquiry, presentation, and leadership opportunities. Leaders gain significant confidence in public speaking and motivational skills. Due to our unique program implementation, undergraduates have a great opportunity to significantly enhance the program. This is because they use their own creativity and are permitted to incorporate their suggestions. The expanded knowledge and experiences gained in peer-led workshops, undergraduate research, and interdisciplinary team-based learning activities are crucial to students planning careers in the research, medical, biotechnology, or academic fields. The modified biology curriculum creates stronger thinkers and self-learners. The institutional structure was impacted with the addition of student-only research laboratories where students learn by doing. *All biology students have an undergraduate research experience built into the courses *Increased statistics knowledge *Increased graduation *Increased matriculation into graduate and professional school *Team building *Leadership skills *Communication skills

Describe any unexpected challenges you encountered and your methods for dealing with them: Maintaining curricular changes

Describe your completed dissemination activities and your plans for continuing dissemination: Presentations at multiple meetings Writing one or more journal articles

Acknowledgements: NIH, NSF, HHMI

Expanding a Research-Infused Botanical Curriculum

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Title of Abstract: Expanding a Research-Infused Botanical Curriculum

Name of Author: Jennifer Ward
Author Company or Institution: University of North Carolina at Asheville
Author Title: Assistant Professor
PULSE Fellow: No
Applicable Courses: Agricultural Sciences, Biochemistry and Molecular Biology, Ecology and Environmental Biology, General Biology, Plant Biology & Botany
Course Levels: Across the Curriculum, Introductory Course(s), Upper Division Course(s)
Approaches: Adding to the literature on how people learn, Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: assessment, consortium, inquiry, plant biology, undergraduate research,

Name, Title, and Institution of Author(s): H. David Clarke, University of North Carolina at Asheville Jonathan L. Horton, University of North Carolina at Asheville

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Our goals were to incorporate inquiry-based research experiences into undergraduate plant biology courses , including lower-division botany (required of all majors), so that all students had an authentic undergraduate research experience. We hoped to improve student learning of course content and familiarize them with the scientific process. Finally, we worked to overcome barriers of faculty time, student time/preparation, and funding.

Describe the methods and strategies that you are using: Undergraduate students developed and tested curricular modules based on their own independent research projects. These modules were tested by other research students before being used in a classroom setting. Then, undergraduate classroom students used modules in their plant biology lab courses, generating hypotheses and data related to the larger research project. In the past three years, we have involved over 300 classroom students and 12 undergraduate research mentors in this project.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: To determine if exposure to the research-infused botanical curriculum increased students' content knowledge, we administered a quiz in Moodle courseware. To assess the effects of our new curriculum on students' scientific process, we used rubric scores on two journal-style papers; the rubric was tested for intergrader reliability. All data were analyzed with SAS 9.2 with PROC GLM and PROC PAIREDT.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Student scores on journal-style papers rose after use of our curricular modules (P = 0.001), and sophomores improved their abilities to state hypotheses (P = 0.001), identify types of variables (P = 0.001), and choose appropriate statistical analyses (P = 0.017). Comparing pre- and post-test results demonstrated that students perceived significant gains in field experience, experimental design and analysis ability, writing experience, comfort with citing primary scientific literature, and recognizing the importance of plant science (P < 0.05 for all). In addition, they gained content knowledge in some botanical subdisciplines (P < 0.05). Research students also showed positive shifts in attitudes towards teaching and their own research. Our approach has now been adopted by other courses, departments, and regional universities.

Describe any unexpected challenges you encountered and your methods for dealing with them: In response to students' ongoing challenges in data interpretation, we have changed the way in which we teach these subjects.

Describe your completed dissemination activities and your plans for continuing dissemination: Results have been presented at 4 disciplinary conferences and 2 education conferences, and we are preparing them for publication. In late 2012, we created a coordinated undergraduate research network to investigate Southern Appalachian ecosystems’ resilience to environmental change. This research focus will serve as a platform for imparting botanical knowledge while advancing quantitative literacy, improving student attitudes towards STEM and NOS (Nature of Science), teaching creative STEM thinking, and encouraging higher-order cognitive processes. The place-based curricular modules that we are creating will be partially developed and administered by undergraduate and graduate research students (3 graduate T.A.s per year) and will have a direct impact on the learning of over 1000 undergraduates per year, including B.S.Ed. students.

Acknowledgements: Undergraduate research students included Scott Arico, Katherine Culatta, Jacob Francis, David Greene, Jennafer Hamlin, Ashley Hanes, Karissa Keen, Aaron Maser, Joseph McKenna, Megan Rayfield, Matt Searels, Katherine Selm, and Emmalie von Kuilenberg. This work was funded by the National Science Foundation (DUE 0942776) and the North Carolina Biotechnology Center.

Redesign of Large Enrollment Introductory Biology Laboratory

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Title of Abstract: Redesign of Large Enrollment Introductory Biology Laboratory

Name of Author: Jean Schmidt
Author Company or Institution: University of Pittsburgh
Author Title: Instructional Developer
PULSE Fellow: No
Applicable Courses: General Biology
Course Levels: Faculty Development, Introductory Course(s)
Approaches: Assessment, Changes in student laboratory approach, Material Development
Keywords: Inquiry-based labs/ Introductory biology lab/ Instructor training/ Science process skills/ CURE Survey

Name, Title, and Institution of Author(s): Elia Crisucci, University of Pittsburgh

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Large enrollment introductory biology laboratory, a mainstay of the undergraduate curriculum at research universities across the country, presents a significant and compelling challenge for implementing reform in science education. One major facet of this challenge is that models of inquiry-based lab courses designed for large enrollments are limited. Secondly, providing instruction that supports student inquiry is essential, yet this approach to teaching is unfamiliar and often uncomfortable for instructors, the vast majority of whom did not experience this type of instruction when they were students themselves. Here we discuss the very large-enrollment, introductory biology lab course sequence at the University of Pittsburgh, our ongoing redesign of the course curriculum begun in fall of 2011, and the revamping of the instructional approach by which the curriculum is delivered. Ours is a two-semester course sequence serving a diverse undergraduate population and enrolling over 1000 students in approximately 65 lab sections per semester. The primary goal of our curriculum redesign has been to shift from scripted, single-session lab exercises to inquiry-based projects that run over multiple lab sessions. Our initial efforts have been directed at the first course of the sequence, now consisting of four multi-week units over a 15-week span. Within this framework, our objective has been to develop science process skills, such as experimental design, data analysis and communication of results. Objectives also include providing greater opportunity for students to engage in quantitative reasoning, critical thinking through hypothesis-driven problem solving, and collaboration with peers. In addition to curriculum changes, our second major impetus has been on instructor training and development to support effective delivery of the curriculum. We have a relatively large team of approximately 24 part-time instructors, and we face regular turnover in staff.

Describe the methods and strategies that you are using: Curricular Change: Students spend the first week or more of each lab unit learning the tools and techniques necessary for an area of investigation. Subsequent weeks are devoted to application of these techniques in experiments designed in whole or in part by the students themselves. An example lab unit from the inquiry core of the course is entitled Dead or Alive*. This three-week investigation is presented in the context of current research into regions of the deep ocean floor, previously thought to be inhospitable to life. Student teams analyze unknown samples for evidence of life. The samples contain various mixtures of organic and inorganic substances, and are presented as coming from a deep-sea trench. The final project is a team-written grant proposal based on their analyses. Instructor Training: Weekly training sessions enable our instructors’ success as course facilitators. Session activities immerse instructors in the experience of scientific inquiry from the student perspective. We include the use of a POGIL (Process Oriented Guided Inquiry Learning)** type structure, with instructors working in teams to build answer keys for problem sets and write exam questions.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: We are using a variety of methods to assess the changes we are making to our curriculum. These methods include open-ended evaluations completed by students mid-semester and the Classroom Undergraduate Research Experience (CURE) survey*** administered near the end of each semester. The CURE survey was developed to assess research-like courses.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Since the curriculum change, our students report greater learning benefits from key course elements, including research proposals, data collection/analysis, and student-driven, open-ended projects. Students who have experienced the redesigned curriculum also report improved science writing skills, greater understanding of the evidence-based nature of science, and increased readiness for more challenging research. These course benefits are appropriate for our diverse student population since problem solving skills and scientific literacy are advantageous in any career path. Our strong instructional training program has attracted motivated candidates. A number of instructors trained in our program have advanced to academic positions in other institutions, taking some of our materials as well as our approach to inquiry-based laboratory teaching to their new posts. The institutions range from a nearby liberal arts college to the University of Kazakhstan. We expect our future impact will extend into secondary education as some instructors take positions in area high schools.

Describe any unexpected challenges you encountered and your methods for dealing with them: One major challenge we encountered when starting to redesign our introductory biology lab curriculum is that models of inquiry-based lab courses designed for large enrollments are limited. Our approach has been to review the work of colleagues and to adapt lab projects that have been successful at other institutions. In doing so, we have built on the work of many colleagues, including Jean Heitz at the University of Wisconsin in Madison, Mary Tyler at the University of Maine and Marvin O’Neal at Stonybrook University. We have also recently been accepted into formal pilot partnership with the Small World Initiative**** developed by Jo Handelsman and others at Yale University. We look forward to introducing this authentic research project, focusing on antibiotic discovery, into our introductory lab course beginning in spring of 2014. Another challenge has been developing an effective training program for our part-time instructors that will enable their success as course facilitators. Our approach has been to design weekly training sessions that reflect the student-centered and inquiry-based atmosphere that we want to have as a hallmark of our teaching labs. The training sessions include the use of a POGIL (Process Oriented Guided Inquiry Learning)** type structure, with instructors working in teams to build answer keys for problem sets and write exam questions. We have partnered with colleagues from our University Center for Instructional Design to build instructor skill in supporting student inquiry.

Describe your completed dissemination activities and your plans for continuing dissemination: While still in the early stages, our dissemination activities have included maintaining open communication and collaboration with other members of our department. Our instructor-training program also facilitates dissemination as our instructors advance to academic positions at other institutions. In the future, we hope to discuss our work at science education conferences and share key findings in publications.

Acknowledgements: * Adapted from the work of Jean Heitz, University of Wisconsin ** https://www.pogil.org/about *** CURE Survey was developed by David Lopatto, Grinnell College **** https://cst.yale.edu/swi

Problem Spaces: Supporting Student Inquiry Using Online Data

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Title of Abstract: Problem Spaces: Supporting Student Inquiry Using Online Data

Name of Author: Sam Donovan
Author Company or Institution: University of Pittsburgh
Author Title: Research Associate Professor
PULSE Fellow: No
Applicable Courses: Bioinformatics, Ecology and Environmental Biology, Evolutionary Biology, General Biology
Course Levels: Faculty Development, Introductory Course(s)
Approaches: Material Development
Keywords: data, research, bioinformatics, inquiry, analysis

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Problem Spaces were developed as an alternative to concept-centric instruction. They are designed to provide access to engaging and relevant biological phenomena that can be collaboratively investigated using publicly available research data and analysis tools. Problem Spaces are community driven curricula, that is, faculty can extend and modify the material for use in a wide range of teaching contexts and with diverse audiences. Problem Spaces are also open curricula that change with the science. The use of online links automatically incorporates new data, theory, tool modifications, and techniques. The Problem Space was developed as a model that supports learning science by doing science. In this context, the questions and investigations developed through the exploration of biological phenomena drive the problem solver to learn biological principles and its practice in the context of authentic learning.

Describe the methods and strategies that you are using: In addition to extensive use in classrooms, Problem Spaces have been used effectively in faculty development workshops to engage faculty participants in reconsidering their assumptions about teaching and learning biology. We have found that activities that engage faculty as problem solvers and scientists remind them why they initially got excited about science. We use Problem Spaces to capture faculty attention and model the type of learning environment that could transform their classrooms.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: We gauge our success based on faculty feedback from workshops and reports of how they have used Problem Space materials and strategies with students.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: There are over a dozen Problem Spaces available and they have been used by thousands of students and faculty in classroom and professional development settings (https://bioquest.org/bedrock/problem_spaces/). Several papers have been published including one research science project started in a Problem Space and a handful that address educational audiences. One notable impact of the Problem Space model on the undergraduate biology education community lies in promoting the use of data in classrooms. Several recent NSF funded projects (TUES, NSDL & RCN) have built on the Problem Space model when designing their curriculum. The TUES grant to the Rocky Mountain Biological Lab, Bringing a Field Station in the classroom, the Science Collaboratory Project, Cyberleanring at Community Colleges (C3), and the recently funded Data Discovery RCN out of Michigan State University. The Problem Space model has also influenced efforts by scientists, data providers, and professional societies to promote the use of research data in undergraduate biology education. The DryadLab project brought together scientists, science educators, and informatics specialists to create open curriculum models using research data stored in the Dryad data repository. The Ecological Society of American in conjunction with the Cornell Laboratory of Ornithology adapted features of Problem Spaces in their Data in the Classrooms project. Finally, Kristin Jenkins and I presented a half-day symposium on the use of large datasets in classrooms at the 2012 Society for the Study of Evolution meeting (https://bit.ly/SSE_EdSymposium2012).

Describe any unexpected challenges you encountered and your methods for dealing with them: The recent attention to engaging students with research data is providing Problem Spaces with a new focus. The emergence of scientific data literacy as a means for developing a technically sophisticated workforce and the ongoing attention for the development of quantitative and computational biology skills provide new opportunities for the application of the Problem Space model. The BioQUEST Curriculum Consortium (the organizational home for Problem Spaces) has long encouraged faculty to bridge science and education by engaging students in scientific problem solving. However, sustaining communities of faculty scholarship is especially challenging when the faculty members returns to their institution and is often isolated. We see potential in Vision and Change outreach as a networking mechanism to support these communities

Describe your completed dissemination activities and your plans for continuing dissemination: Some of the more mature Problem Spaces have been collected and disseminated through https://bioquest.org/bedrock/problem_spaces/ . Other projects, including a large number of workshop participant generated materials are available at https://bioquest.org/bedrock/participant_projects.php . We plan to prepare a more synthetic description of the instructional philosophy that guides Problem Spaces for publication.

Acknowledgements: The Problem Space curriculum model evolved as part of a NSF funded CCLI National Dissemination project titled BEDROCK Bioinformatics Education Dissemination. John R. Jungck was the PI of that project. Over time, the model of a Problem Space has been deeply integrated into a wide range of projects associated with the BIOQUST Curriculum Consortium. Ethel Stanley, Stacey Kiser, Tony Weisstein, Kristin Jenkins and many, many others have made significant contributions to this project.

Engaging Undergraduates, Current and Future Faculty

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Title of Abstract: Engaging Undergraduates, Current and Future Faculty

Name of Author: Sue Wick
Author Company or Institution: University of Minnesota--Twin Cities
Author Title: Professor and Director of Undergraduate Studies
PULSE Fellow: No
Applicable Courses: All Biological Sciences Courses
Course Levels: Across the Curriculum, Faculty Development
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: active learning future faculty research

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The goals of the College of Biological Sciences project to promote the Vision and Change initiative at the University of Minnesota-Twin Cities have been several-pronged: to have undergraduates actively engage with biology (“do biology, not just read about it”), to encourage current faculty to experience active learning so they can begin to use these strategies in their courses, and to help train the next generation of faculty to embrace effective active learning strategies. About a dozen instructors have offered the Foundations of Biology two-semester series of active learning courses for majors in the biological sciences for about 2800 students over the past six years. More recently about six faculty, staff and postdoctoral instructors have developed modules that bring authentic biology research into non-majors biology courses for a few thousand more students. One aim of bringing authentic research into non-majors courses is to help students understand how scientific inquiry and interpretation of results is done; another aim is to increase the level of interest in science in general.

Describe the methods and strategies that you are using: The majors courses are in active learning classrooms. Teams of nine students explore introductory biology topics through daily, weekly, and term-long activities that require higher level cognitive skills of analysis, application, evaluation and synthesis. Students experience authentic research in the second semester, working on a faculty member’s research project. Strategies for bringing authentic biology research into non-majors biology courses include a microbial metagenomics lab module in general biology; activities on sexual reproduction in bean beetles in a course on the biology and evolution of sex; and student analysis of animal photos from the Serengeti, part of a study of animal associations and migration, incorporated into an evolution and ecology course. These activities replace other lab exercises and are tested first on a small scale so they can be refined before widespread incorporation. Many faculty cite lack of suitable classrooms for active learning and difficulty imagining how active learning looks and sounds in action. We address these stumbling blocks by advertising our open door policy; as a result we have welcomed hundreds of visitors to our classes, including teams of faculty, architects and administrators from institutions poised to commit to instructional changes. Faculty from elsewhere on campus have also observed and consulted with us about how to transform their science lecture courses into ones that incorporate more engaged student learning. We also organized a program in which graduate students and postdocs learn practices of evidence-informed teaching. We met one evening a month for a year, beginning with discussions of diversity, active learning and assessment. The class divided into small groups to produce short active learning modules on topics like nutrient cycles, HPV vaccination, plasmid construction and deciphering genetic pathways. Groups presented their work to the rest of the class for feedback and refinement.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: To examine the effect of our reformed majors’ sequence, we are monitoring course alumni success in upper division coursework, in research laboratories, and in national summer research programs. We also collect surveys on students’ impressions of course effectiveness in increasing their confidence and knowledge of how science works. We are still at early stages of incorporating authentic research into non-majors courses, but plan to collect data from course surveys on whether students’ enthusiasm for science and understanding of scientific process have increased. Evaluation of our effect on other faculty is more informal, but includes assessing their willingness to participate in an intensive summer institute experience to learn more about effective active learning. To evaluate the graduate student and postdoc program on scientific teaching, we focused on the products developed. One module has been tested for its effectiveness in a freshman seminar and others have been tested on groups of undergraduate volunteers.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Our preliminary assessment of the effect of reforms to majors’ coursework indicates increases in students’ problem-solving skills and in their confidence to tackle new questions. While some students continue to resist this style of instruction, surveys indicate that many realize they are learning how to learn deeply and retain both information and skills for the future. Majors who go on to summer research programs indicated that they are very well prepared relative to other applicants, even those from elite institutions. Impacts on local faculty also are somewhat promising. Additional instructors, some of whom were initially skeptical about moving away from a familiar lecture format, have joined the ranks of the initial core faculty, and some sections of upper division courses are now also taught in active learning classrooms. Participants in the scientific teaching training program for graduate students and postdocs were positive about their experience learning teaching skills that many institutions will find desirable, and we anticipate that several of them will start developing their teaching approach from a habit of active learning instead of lecturing. An added benefit of the program is that there are now more active learning materials available for insertion into various undergraduate courses for non-majors and majors.

Describe any unexpected challenges you encountered and your methods for dealing with them: We encountered no unexpected challenges.

Describe your completed dissemination activities and your plans for continuing dissemination: Members of our active learning team have made numerous poster and oral conference presentations and given seminars on our various efforts to transform undergraduate education. We have a small assortment of publications on our pedagogical work and continue to collect data about the effectiveness of our programs with the intent to produce more publications.

Acknowledgements: Faculty, teaching postdoctoral fellows and instructional staff who have contributed to our programs to reform undergraduate education include: Robin Wright, David Matthes, Mark Decker, Robert Brooker, Deena Wassenberg, Brian Gibbens, Cheryl Scott, Sehoya Cotner, Sadie Hebert, Jane Phillips, Anna Strain, Craig Packer, Annika Moe

Class Generated Community Clicker Cases

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Title of Abstract: Class Generated Community Clicker Cases

Name of Author: tamar goulet
Author Company or Institution: University of MIssissippi
Author Title: Associate Professor
PULSE Fellow: No
Applicable Courses: Ecology and Environmental Biology, Organismal Biology, Physiology & Anatomy
Course Levels: Introductory Course(s)
Approaches: Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: Case studies, Clickers, Interviews, Involvement

Name, Title, and Institution of Author(s): Lainy B. Day, University of Mississippi Kristen A. Byler, University of Mississippi Kathleen Sullivan, University of Mississippi

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The goal of the study was to empirically test the efficacy of this novel pedagogic approach as an alternative technique to lecturing in a large, non-majors introductory biology course. In addition, multiple presentations and workshops at academic institutions, from 2-year community colleges to research-one institutions, exposed multiple faculty to this educational approach, potentially transforming their teaching.

Describe the methods and strategies that you are using: Class Generated Community Clicker Cases (CGCCC) is an innovative pedagogical approach that integrates and capitalizes on the strengths of both case studies and clickers. In CGCCC, students are given questionnaires that they fill out by interviewing members of their community, thereby creating the cases. Answers are collected in class via clickers and class discussion. Students’ data gathering advances the course content coverage, turning the disadvantage of large introductory non-major classes into an educational asset, and creates personal investment in the subject matter.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: The effectiveness of CGCCC versus lecturing were assessed using four indicators, two dealing with knowledge of biology, and two dealing with students’ perceptions of the study of biology. The indicators were: 1) Extent of students’ factual knowledge; 2) Extent of students’ ability to assimilate and apply the learned information; 3) Rates of student attendance in the class; and 4) Extent of self-reported student satisfaction with the course. This study also addressed faculty members’ apprehension of non-lecture techniques by providing data on alternative methods for teaching large introductory science classrooms. Data collection thus far occurred during the Spring 2010, Fall 2010, Fall 2011 and Spring 2012 semesters. In each semester, to control for instructor bias, the same instructor taught two class sections, one in the CGCCC approach and one via lecture. In the Fall 2010 and Fall 2011 semesters, two faculty, each teaching a CGCCC and lecture class, collected data, enabling between instructor comparison. A total of 12 class sections thus far participated in the study, 6 sections taught via CGCCC (total n = 603) and 6 sections taught in a lecture format (total n = 618). To control for a potential clicker effect, both CGCCC and lecture sections used clickers to collect student responses during the class period and during exams.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Students in the CGCCC class with more positive perceptions of the interview component of the class tended to earn higher test grades than did students who reported lower levels of satisfaction with the interview component. The CGCCC approach did affect students’ attitudes. Students described a gain from the interviews, for example the interviews connected science with their lives, they thought interviewing people was interesting, and they learned to identify central issues via the interviews. These gains may affect attitudes towards, and long-term retention of, biological content. Following my colleague's involvement as a senior personnel in my grant, my colleague applied for and received her own TUES grant in which she is utilizing case studies in an upper undergraduate level neurobiology course for biology majors. The Department Chair was supportive of testing the CGCCC approach and provided the room and section time slots that enabled comparisons of the sections.

Describe any unexpected challenges you encountered and your methods for dealing with them: The teaching approach being tested relies on students conducting interviews and reading the textbook. A challenge emerged of having the students take the interviews seriously. We therefore assigned points for the interviews. To address reading the book, we created an assignment where students had to write the page numbers that pertained to the interview questions. Students received points for this assignment. Students’ prior knowledge and students’ current academic performance affect their learning success in a non-majors introductory biology course. In tandem with applying novel pedagogical approaches, students’ perception of their ability to learn and students’ commitment to learning need to be assessed and perhaps modified.

Describe your completed dissemination activities and your plans for continuing dissemination: This project will affect both students and faculty. Due to the workshops and other dissemination venues, the project’s influence will transcend the University of Mississippi.

Acknowledgements: This study was supported by The National Science Foundation (DUE-0942290)

Integrating Bioinformatics Across the Curriculum

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Title of Abstract: Integrating Bioinformatics Across the Curriculum

Name of Author: William Tapprich
Author Company or Institution: University of Nebraska at Omaha
Author Title: Professor and Chair
PULSE Fellow: No
Applicable Courses: All Biological Sciences Courses
Course Levels: Across the Curriculum
Approaches: Assessment, Material Development
Keywords: Bioinformatics Laboratory Inquiry-based Curriculum Genomics

Name, Title, and Institution of Author(s): Mark A. Pauley, University of Nebraska at Omaha

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The overall goal of our project is to integrate inquiry-based, hands-on bioinformatics-focused laboratories across the biology curriculum. This is an interdisciplinary effort involving the Department of Biology in the College of Arts and Sciences and the School of Interdisciplinary Informatics in the College of Information Science and Technology at the University of Nebraska at Omaha (UNO). This project arose from the recognition that many of the interdisciplinary fields driving biology are only gradually becoming part of the undergraduate curriculum. The interdisciplinary nature of biological science is obvious to research teams and professionals, but the integration of emerging fields across the undergraduate biology curriculum is often slow. Bioinformatics is a prime example. Few would challenge the idea that bioinformatics is an indispensable discipline for students in biology. The future will only intensify the need for experience in bioinformatics. Even so, few undergraduate biology programs have integrated bioinformatics experiences into their biology curricula. A number of the central recommendations of Vision and Change have guided our project. As a primary goal, we are integrating core concepts and competencies throughout the biology curriculum. Our laboratories have been permanently integrated into first year biology courses and we are currently implementing new laboratories at all levels of the curriculum. By developing laboratory exercises, we focus on student-centered learning. Active participation, multiple modes of instruction, inquiry-based exercises, cooperative learning and research contexts are all incorporated into the student experience. Our project also engages the biology community. Our project team involves three diverse institutions, our materials are freely available on the project website (https://ccli.ist.unomaha.edu), and we have recently organized a research coordination network with thirteen participating institutions.

Describe the methods and strategies that you are using: The project team has developed bioinformatics laboratories for each level of the biology curriculum. Laboratories have been developed based on problems important for cellular/molecular biology and also for ecological/environmental biology. To support the laboratories, we have developed curated databases and assembled bioinformatics tools, all of which are available on the project website. This allows instructors and students in introductory courses to access data and relevant bioinformatics tools in a single location. For upper-level courses, students gain experience with the additional power and occasional pitfalls of public databases and tools. A member of the project team implements the laboratory initially. This implementation is accompanied by assessments that include pre-/posttests and student focus groups. Following revisions guided by the assessments, the laboratory is ‘handed off’ to the regular faculty member teaching the course. Continued pre-/posttest assessment together with faculty feedback leads to additional revision. Two laboratories for first year biology have completed the cycles and are permanently implemented in the curriculum at all three participating institutions. Several additional laboratories designed for second-fourth year courses are in process.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Assessment of laboratories has included learning outcomes measured by pre-/posttest results, student focus groups and review by external review panels. These assessments are conducted by an evaluation team led by a faculty member in the UNO College of Education. Results show positive learning outcomes, very favorable assessment by students and positive reviews from expert reviewers. Faculty from expert review panels have committed to implementing some of the laboratories in their own courses.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: At this stage of the project, we have implemented and assessed multiple laboratories. For a few laboratories, we have accomplished our goal of permanent implementation into the curriculum and transfer of teaching from the project team to the regular professors in the course. For example, one laboratory has been published into a laboratory manual that is used every semester in a course enrolling an average of 400 students each year. Just at the participating institutions, our laboratories have impacted well over 1,500 students. Students who have completed our laboratories are already better prepared to accomplish bioinformatics projects. When fully implemented, we expect substantial improvement in students’ ability to solve bioinformatics problems. This addresses many of the core competencies identified by Vision and Change. These include the ability to apply the process of science, ability to use quantitative reasoning, ability to tap in to the multidisciplinary nature of science and the ability to communicate and collaborate with other disciplines. Our bioinformatics project has a significant faculty development component. Many biology faculty have little training in bioinformatics and are uncomfortable in the area. We find that faculty quickly come up to speed if the laboratories are taught first by an expert.

Describe any unexpected challenges you encountered and your methods for dealing with them: A major barrier to institutionalizing the bioinformatics laboratories is reluctance of faculty to learn bioinformatics concepts. Our approach to address this barrier has been to have a member of the project team lead teaching of the laboratory initially. The regular instructor observes. In our experience, the regular instructor generally engages with students during the laboratory and becomes more comfortable with the exercise. Using this approach, we have ‘handed off’ the teaching to several instructors at the three participating institutions.

Describe your completed dissemination activities and your plans for continuing dissemination: Our laboratories are available on the project website. We have also developed curated databases and assembled bioinformatics tools, all of which are available on the same website. We have hosted expert review panels composed of faculty from regional universities to evaluate our laboratories. These faculty have agreed to implement our laboratories in their own courses. Continued dissemination will include publications in biology education journals and presentations at biology education conferences. In addition, we have recently formed a research coordination network for developing and disseminating bioinformatics educational resources.

Acknowledgements: This work is supported by Award 1122971 from the National Science Foundation. We wish to thank members of the project and evaluation teams: Garry Duncan, Oliver McClung, Letitia Reichart, Dawn Simon, and Neal Grandgenett.

Infusing Quantitative Approaches into the Undergraduate Biol

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Title of Abstract: Infusing Quantitative Approaches into the Undergraduate Biol

Name of Author: Katerina Thompson
Author Company or Institution: University of Maryland
Author Title: Director, Undergraduate Research
PULSE Fellow: No
Applicable Courses: All Biological Sciences Courses
Course Levels: Introductory Course(s)
Approaches: Material Development
Keywords: quantitative skills, MathBench, introductory biology, online modules, mathematical biology

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: A major curriculum redesign effort at the University of Maryland aims to infuse all levels of our undergraduate biological sciences curriculum with increased emphasis on interdisciplinary connections and quantitative reasoning. The overarching goals of this coordinated approach are to help students appreciate the essential role of mathematics and statistics in contemporary bioscience research and allow them to become more adept at applying their quantitative reasoning skills to biological problems.

Describe the methods and strategies that you are using: Major components of this effort include (1) developing online modules to infuse more mathematical content into fundamental biology courses, (2) strengthening the interdisciplinary connections of ancillary courses in mathematics and physics to support the development of quantitative skills in biological contexts, and (3) creating more quantitatively intensive courses for the final two years of the biological sciences degree program. Our main strategy to imbed mathematical and statistical content into introductory biology courses was the creation of a series of online modules (MathBench, mathbench.umd.edu) that are woven into the curriculum of five biology courses taken by biological sciences majors during their first two years of study. MathBench modules are designed to introduce or reinforce 10 basic quantitative skills identified by our faculty as being important for competence in upper-level biology courses. The modules use an informal tone to encourage students to apply their mathematical intuition, and then gradually build in their level of mathematical sophistication. Interactive elements with contextually appropriate feedback are imbedded throughout. A freshman taking the entire required sequence of coursework would encounter about 20 of these modules over the course of their first two years.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: The impact of MathBench on student learning and attitudes has been assessed with surveys and pre- and post-tests of quantitative skill using an instrument developed and validated specifically for this initiative.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Students who have used MathBench in their coursework show increases in quantitative skill that are independent of their previous math coursework. They also show an increase in their willingness to tackle quantitative problems and a better appreciation for the importance of mathematics to modern biology.

Describe any unexpected challenges you encountered and your methods for dealing with them: The greatest challenge has been assisting faculty in finding ways to incorporate MathBench modules into their teaching. We have developed comprehensive faculty training workshops to help them create implementation plans and have established various ways of encouraging continued communications among MathBench users.

Describe your completed dissemination activities and your plans for continuing dissemination: We are currently partnering with 32 U.S. institutions of differing type, size, and demographics to gather additional data on the effectiveness of MathBench modules in diverse educational contexts. As part of this process, we have developed workshops to assist faculty with implementing the modules and have started to build a users community for peer support. More recently, we have been approached by a group of seven Australian universities to collaborate on a grant-funded project to revise MathBench modules for the Australian educational context and assess their impact.

Acknowledgements: These projects were supported in part by grants to the University of Maryland from the Howard Hughes Medical Institute and the National Science Foundation.