The Genomics Education Partnership: Shared Research

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Title of Abstract: The Genomics Education Partnership: Shared Research

Name of Author: Sarah C R Elgin
Author Company or Institution: Washington University in St Louis
Author Title: Professor
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Evolutionary Biology, Genetics
Course Levels: Independent study / research, Introductory Course(s), Upper Division Course(s)
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.)
Keywords: bioinformatics comparative genomics eukaryotic genes/genomes research lab course collaborative network

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The Genomics Education Partnership (GEP) was founded in 2006 to provide undergraduates with an opportunity to participate in a large-scale genomics research project. By incorporating genomics research into the undergraduate curriculum, the GEP faculty members can provide a research experience for a larger number of students than can generally be accommodated in a traditional summer research program. Our major research goal has been to examine the evolution of the ‘dot’ chromosome (Muller F element) of Drosophila, an unusual domain that exhibits both heterochromatic and euchromatic properties. (Our first publication is Leung, W. et al. 2010 Genetics 185: 1519-1534, Evolution of a distinct genomic domain in Drosophila: Comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. Our second publication, in preparation, will have ~500 student and ~50 faculty co-authors.) Future projects will focus on the expansion of the F element in a subgroup of species, and on the search for conserved motifs specific to this element and its genes.

Describe the methods and strategies that you are using: Bioinformatics research typically requires only access to computers and the Internet, and thus has lower costs and fewer lab safety concerns than most life science research. While GEP faculty members teach students a common set of bioinformatics protocols, each student in the class applies their knowledge to a unique region of a genome, taking responsibility for their own project. We find that students can effectively acquire many bioinformatics skills through peer instruction, allowing a team approach to the research. A genomics-based course has the advantage that a central website (maintained by W. Leung and C.D. Shaffer, Washington University in St Louis) can support the efforts of a large number of faculty and their students across the country, providing cost-effective implementation. An anonymous survey of the GEP faculty has shown that this central support is of critical importance in enabling the faculty to introduce this novel, research-centered curriculum to their campuses.

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 assess the undergraduate experience, students are asked to take a pre/post course quiz and survey. The quiz tests student knowledge of eukaryotic genes and genomes. The survey examines science-related attitudes, and includes 20 questions that are identical to the nationally utilized Survey of Undergraduate Research Experiences. All research projects (~40 kb segments of the domain of interest) are completed at least twice independently by students at different schools, and the results reconciled. Final results are submitted to GenBank and connected to FlyBase.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Student members of the GEP have improved over 7 megabases of sequence (from the F element, and a euchromatic reference region at the base of the D element) and produced more than 1,000 manually curated gene models, as well as annotating other features of these domains. Last year over 1000 students from 54 colleges and universities participated in GEP-affiliated lab courses. Student results for four Drosophila species are currently being assembled and analyzed to better understand the evolution of this domain (manuscript in preparation). Students show significant gains on the quiz, which tests their understanding of the structure and function of eukaryotic genes and genomes. Their responses on the CURE survey are generally the same or better than responses from students who have spent a summer in a mentored research experience, assessed by the parallel SURE survey (supervised by D. Lopatto, Grinnell College). The pedagogical results confirm and extend our prior findings (Lopatto et al. 2008 Science 322: 684-85, Undergraduate Research: Genomics Education Partnership; Shaffer et al. 2010 CBE-Life Sci Educ 9: 55-69, The Genomics Education Partnership: Successful integration of research into laboratory classes at a diverse group of undergraduate institutions). Positive responses on the quiz and survey show little correlation with characteristics of the home institution (e.g. private vs. public, school size, etc.), but do correlate with the amount of time that the faculty member can schedule for GEP-related work (lecture/discussion plus lab time); more time enables a more beneficial research experience. As GEP member schools are very diverse, these results are consistent with the interpretation that students from all backgrounds, working in a variety of settings, will benefit from participating in a research-based lab course.

Describe any unexpected challenges you encountered and your methods for dealing with them: While a centralized project such as that run by the GEP is an excellent way for faculty to begin teaching research-based laboratory courses, ultimately one would like that research to be directly tied to the research interests of the individual faculty member. Better bioinformatics interfaces (for example, an easy route for loading a new genome into a browser such as the UCSC Browser) are needed to reach this goal.

Describe your completed dissemination activities and your plans for continuing dissemination: Since its inception, the GEP has grown substantially, and now has over 100 partner schools (see current members at https://gep.wustl.edu). Members join by attending a 3 - 5 day workshop at Washington University. All curriculum is freely available on the GEP website under a Creative Commons license. We find that the collaborative nature of a shared research effort helps to make this an enjoyable and effective way to teach. The results suggest that such national projects are cost-effective, can have a widespread impact on life-science teaching, and should be supported in greater number.

Acknowledgements: I thank all faculty members of the GEP (see https://gep.wustl.edu/community/current_members) and their students; Jeremy Buhler, Elaine Mardis, Chris Shaffer, and Wilson Leung, all of Washington University; and David Lopatto, Grinnell College, for their participation in this project. This work has been supported by the Howard Hughes Medical Institute through grant #52007051 to SCRE and by Washington University in St Louis.

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.

PRIMER: Authentic Research on Environmental Microbiology

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Title of Abstract: PRIMER: Authentic Research on Environmental Microbiology

Name of Author: Jose Perez-Jimenez
Author Company or Institution: Universidad del Turabo
Author Title: Associate Professor/Director
PULSE Fellow: No
Applicable Courses: Agricultural Sciences, Bioinformatics, Biotechnology, Ecology and Environmental Biology, Microbiology, Research courses, Virology
Course Levels: Across the Curriculum
Approaches: Authentic Research Experience
Keywords: authentic research, microbiology, bioprospecting, biotechnology, mycology

Name, Title, and Institution of Author(s): Yomarie Bernier, Universidad del Turabo

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The overall goal has been to develop research skills and attitude among undergraduate students that energize them towards academic progress (retention) and success (graduation).

Describe the methods and strategies that you are using: Puerto Rico Institute for Microbial Ecology Research (PRIMER), as an authentic research experience model, has provide diverse levels for engagement for students. The skills development has three stages: apprentice (help others to conduct protocols and initial understanding), novice (perform protocols with minimal supervision and are capable of explaining the applied scientific method), and fellow (address new questions with the mentor and are capable of scientific writing with supporting literature). Students develop initial expertise in particular protocols that later teach to peers: a community of learning has evolved. Intellectual development is fostered throughout discussion sessions: regular laboratory meetings, oral presentations at local student forum, and poster presentation at scientific meetings (local and national). Participation at SACNAS National Conference is aimed every year.

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 have noticed increase level of personal and academic confidence along the PRIMER process of research, collaboration, and dissemination. We lack a formal evaluation methodology.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Students that took the opportunity with responsibility and dedication (~90%) has experienced academic success: retention, graduation, formal jobs, and pursue of graduate/professional education. In 1998, the undergraduate research experience motivated an interdisciplinary faculty team in biological sciences to strengthen institutional effort with formal dissemination forums and opportunities. Recently, students presentations have become part of the Researchers Forum (originally established for faculty).

Describe any unexpected challenges you encountered and your methods for dealing with them: PRIMER has operated as an extracurricular program that demands a lot of time on mentoring/training by the faculty and research/dissemination by the students. A learning community has evolved from learning protocols among more expert students, recruiting assistant mentors, and regular meeting aligned with dissemination commitments. We have formally proposed to organize research course in fixed schedule for more efficient time management and rigorous evaluations.

Describe your completed dissemination activities and your plans for continuing dissemination: Dissemination activities have been based on active participation with presentations at scientific forums (university, state, and nation). Recently, PRIMER was portrayed in the new magazine for the Chancellors office. Additionally, newsletter has been prepared and distributed on campus and NSF ATE-related events.

Acknowledgements: Research was supported in part by 'Richness and endemicity of sulfate-reducing bacteria in Neotropical environments' (NSF-RIG MCB-0615671), 'PRIMER Tropical Bioprospecting Venture at CETA' (NSF-ATE DUE-0903274), and 'PRIMER Bioprospecting for Bioenergy' (US Forest Service 11-DG-11330101-111) to Dr. Perez-Jiminez. We are thankful to Diana L. Laureano, Aracelis Molina, and Darlene Muñoz for administrative assistance. We are especially proud of the students than embraced the opportunity with responsibility and dedication to transform their lives.

Connect Classroom Learning with Real World Applications

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Title of Abstract: Connect Classroom Learning with Real World Applications

Name of Author: Xiao-Ning Zhang
Author Company or Institution: St. Bonaventure University
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Biotechnology, Plant Development and Physiology
Course Levels: Upper Division Course(s)
Approaches: Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: Research-based laboratory Design Interdisciplinary Collaboration Peer Teaching Peer Plant Development and Physiology Molecular Cell Biology

Name, Title, and Institution of Author(s): Paula Kenneson, Saint Bonaventure University

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The goals of this project are: 1) to test the feasibility of using real research projects in teaching labs; 2) to bridge the gap between knowledge lectured in the classroom and applications of the knowledge; 3) to train undergraduate students to become scientific learners and critical thinkers. 4) to train undergraduate students to speak of biology research to the general public. The intended outcomes are : 1) A set of teaching materials including detailed pedagogies, lab manuals, syllabi including learning goals and outcome assessment tools, and corresponding rubrics to support student learning; 2) A collection of quantifiable data for statistical analysis as well as qualitative measurements of student learning and the dissemination of the information in the teaching and learning community.

Describe the methods and strategies that you are using: These goals have been tested in two different courses: Bio406 Plant Development and Physiology (lecture and lab) in 2011 and 2013 and BioL466 Cell Molecular and Biology Lab in 2012. In Bio406, we used a three-prong approach: lecture, discussion and laboratory being interconnected, equally important and supportive to each other to promote active learning. The lecture content was extracted from ‘Teaching Tools’ published on The Plant Cell. Information from textbook and current literature was added when necessary. In the lab portion of this course, newly identified Arabidopsis mutants were used as the common cue throughout the semester to let students characterize mutant plants throughout the life cycle. By doing this, students applied the new knowledge from the concurrent lecture and see how different lab techniques could be put together to answer a general experimental question - how are new mutants different from the wild type? At the end, students summarized their results from different tests and came to their own conclusions. All students paired up to practice as Teaching Assistants to lead different lab sections and to generate summary figures. During the discussion, students worked in groups to solve problems that deepened their learning. These problems are focused on understanding literature, experimental design and real world applications. In BioL466, the effort was focused on how to tailor the research project to a manageable level for a weekly 3-hr meeting time. Students worked in groups to test instructor-provided hypotheses. They learned techniques required for molecular cloning, protein expression and various tests for protein-protein interactions. Based on findings, each student proposed a new hypothesis for future research. We also provided writing exercises and guidance on public speaking presentation to enable students to become proficient in presenting their research to a variety of audiences.

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 common evaluation tools for both courses were standard lab report or lab summary, poster presentation and research proposal. For Bio406, exams were used to evaluate basic knowledge from lecture and critical thinking on science questions; term papers were used to connect textbook learning with real world phenomena and to practice scientific writing; lab leader evaluation to assess the effectiveness of 'peer teaching peer'; literature presentations were used to measure the understanding of science being presented and to measure public speaking and student feedback was used to assess student interests and the feasibility of using real research project in teaching labs. Both labs suggested that although not all research experiments are practical for teaching labs, it is definitely feasible if a project can be broken down into several small tasks and each task can be accomplished in a three hours.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: There were 16 students in 2011, 11 students in 2012 and 12 students in 2013 who have enrolled in either Plant Development and Physiology or Molecular Cell Biology when this change project was delivered. Involving students in the change project stimulates their interests more effectively and builds a bridge to minimize the gap between abstract knowledge from lecture and their applications. The change project allowed students to become a part of something much bigger than what they have done. In doing so, they have applied their learning scientifically and become critical thinkers. They are also more likely to seek for research opportunities in the future. It turned out to be a better way for teaching and learning. Some of these students just entered medical schools, while others are still at SBU. Their performance will be followed up in 5 years. Through this continuing effect, the Department of Biology started to be more open to change in promoting active learning among students. The instructor for freshman biology lab has agreed to use one of my research experiments in her lab course to test mutant responses to environmental conditions. Not only did this project open the dialogue about the scholarship of teaching and learning but also implemented co-teaching and collaboration in the Biology classes between the authors and their respective schools. For the first time, a faculty member from School of Education (Dr. Kenneson) and a faculty member from Department of Biology in School of Arts and Sciences (Dr. Zhang) started a collaboration to enrich the impact of this change project. The change project and its impact on students were introduced successfully to current donors of the university in May 2013. Publicizing this change project at the university level is in the plan and will be carried out in fall 2013.

Describe any unexpected challenges you encountered and your methods for dealing with them: A major difficulty that prevents the change to continue is time. Implementing research-based teaching labs requires significantly more hours of dedication. Under the current teaching load requirement, it was very stressful. Ongoing discussions on campus are to find ways to address issues on teaching load hoping more time being allocated toward research-related activities. There have also been several university-wide conversations on scholarship in teaching and learning. I anticipate this new learning community will promote the dialog and facilitate for change in other courses on campus. Another challenge we encountered is the resistance to change from some students. Since these course designs are very different from all other biology lab courses that students have been used to for years, it is difficult for some students to embrace this new idea quickly. We had to explain repeatedly why we do this, how it is related to the big picture and what qualities are expected in order to prepare for the future. We hope that when more biology courses are on board with new designs, this climate will change.

Describe your completed dissemination activities and your plans for continuing dissemination: Preliminary lab activities of this project has been presented as a poster “Characterization of the Arabidopsis sr45-1;oif-ler mutant in BIOL406: Plant Development and Physiology Laboratory” at Plant Biology Meeting in August 2011. A more systematic design of the course has been presented as a poster “Aligning biology lab planning, instructional design and common core college and career readiness writing standards to increase student learning” at PKAL Upstate New York Regional Network Meeting in April 2013. This poster led to an open dialog with local major universities, University of Rochester and Rochester Institute of Technology, and will continue in the near future. The results from BioL466 were presented as a poster at the Gorden conference - Plant Molecular Biology in July 2012. The idea, strategies and data of this project will be presented to the university community in fall 2013. The continued collaboration between the Biology Department and the School of Education will also add to future research in the success of the Common Core College and Career Readiness Standards in preparing high school students to meet the challenges of university level study and research.

Acknowledgements: This project is supported by the National Science Foundation (0950158) and Keenan Award at St. Bonaventure University.

Multidisciplinary Effort to Address Education in New Biology

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Title of Abstract: Multidisciplinary Effort to Address Education in New Biology

Name of Author: Kari Clase
Author Company or Institution: Purdue University
Author Title: Associate Professor
PULSE Fellow: No
Applicable Courses: Biotechnology
Course Levels: Introductory Course(s)
Approaches: Mixed Approach
Keywords: undergraduate research; representations; biotechnology; technology; biological systems

Name, Title, and Institution of Author(s): Kristy Halverson, University of Southern Mississippi Robin Heyden, Heyden Ty Jenna Rickus, Bindley Bioscience Center

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Biology as a discipline is changing, integrating more quantitative tools and technologies to tackle increasingly interdisciplinary global challenges. Change provides opportunities for collaboration across disciplinary boundaries and a need to engage students in the New Biology as discussed in recent reports. Change in biology can happen successfully outside of the traditional departmental barriers and current initiatives in engineering and technology can synergize with the changes in biology, resulting in changes with greater impact. However, opportunities for multidisciplinary collaborations must be encouraged and environments that encourage creative and innovative thinking should be nurtured. Just as biology research no longer resides within a single biology department, innovative biology education can cross departments and colleges as well. Students should be provided with opportunities to learn how to tackle these problems by integrating scientific ways of thinking with thinking from other disciplines such as engineering and technology. In response to these changes, a biotechnology minor was created as a collaborative effort among the Colleges of Agriculture, Pharmacy, Science and Technology at Purdue University. Curriculum was developed to reflect the changing biology and draw students from science, technology and engineering majors across campus. The unique course content and delivery demanded new approaches to assessment and measurement of student learning outcomes that led to new collaborations beyond the university. The multidisciplinary team that facilitated implementation includes expertise in biochemistry and molecular biology, biological engineering, educational technology, and biology education research.

Describe the methods and strategies that you are using: An authentic student research experience was implemented through participation in the Howard Hughes Medical Institute’s (HHMI) Science Education Alliance. Interactive virtual world learning activities were integrated into the experience and students engaged in activities related to visualizing genomes, kept records of their experiences in an electronic lab notebook, posted about their experiences in a blog, annotated genomes in virtual research environments and presented their results in virtual world environments. Virtual learning environments had value in helping build a research community and the collaborative, social environment also contributed to student learning. The virtual learning environments offered new ways to explore questions of representation that were transparent in the types of representations students later generated. Students learned how to collaborate and share data using virtual resources in addition to practical laboratory skills. The use of technology also helped students to accurately develop a conceptual understanding of annotated genomes and they supported their genome definitions with data--this way of thinking was reflected in both their drawn representations and their verbal discussions. Engaging students in an authentic interdisciplinary research space helped them take ownership of their project and prepare for more real world scenarios because of the interactive nature and decision making required.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Qualitative data gathered from student responses, generated representations provided on questionnaires, interview transcripts, and observations during the virtual presentations were used for the data analysis. Approximately fifty students have been interviewed to examine the impact of the environment on their thinking about biological systems through genome representations and discussions. Open-ended pre-questionnaires were administered at the start of the courses that focused on student understanding of biological concepts and attitude questions. Students were also asked to draw and explain a representation for genomes as well as describe what they view as the purpose of a genome. Each student participated in multiple virtual and wet lab activities related to the research project.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Global efforts were achieved by student demand for authentic undergraduate experiences and engagement of other faculty. Efforts were made to align initiatives with the strategic direction of collaborating departments, colleges and ultimately the learning outcomes and strategic educational initiatives at the university level. The learning outcomes for the courses also align with the ABET standards for engineering resulting in their integration as science electives in engineering and technology major plans of study. Administration supported early pilot efforts with resources, including the flexibility to teach courses beyond departmental boundaries. Administrators also supported the creative use of an interdisciplinary bioengineering research space for the project, allowing students to take ownership of their research and contributing to the authentic experience.

Describe any unexpected challenges you encountered and your methods for dealing with them: Initially, it was a challenge to build fruitful collaborations and find the right fit for the needs and future direction of the project. Synergy was found by collaborating with faculty in other departments in science, engineering and technology that were also in the midst of change. Interdisciplinary conferences and seed funding opportunities have been critical for the initial success of the project and building collaborations across disciplinary and institutional boundaries.

Describe your completed dissemination activities and your plans for continuing dissemination: The project team has been working to effectively communicate the synergy between science, engineering and technology and support the value and impact of interdisciplinary collaborations through conference presentations, publications and research funding.

Acknowledgements: This research and interdisciplinary collaboration was supported by a visionary Grant from the Gordon Research Conference on Visualization in Science and Education (2009), the National Institute of General Medical Sciences (8 P20 GM103476-11) from the National Institutes of Health, and Howard Hughes Medical Institute.

Assessing a Year-Long, Research Lab in a Core Biology Course

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Title of Abstract: Assessing a Year-Long, Research Lab in a Core Biology Course

Name of Author: Marcy Kelly
Author Company or Institution: Pace University
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Cell Biology, Genetics
Course Levels: Introductory Course(s), Upper Division Course(s)
Approaches: Material Development, Research projects in the teaching laboratory
Keywords: microarray, nextgen RNA sequencing, year-long core biology course, novel research

Name, Title, and Institution of Author(s): David S. Zuzga, LaSalle University

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: It is anticipated that enrollment in this year-long laboratory program will yield the following outcomes for the students: 1. Develop a strong foundation in the following core concepts associated with biological literacy: (a) Structure and function at the cellular and molecular level; (b) Information flow, exchange and storage through genes and proteins; (c) Pathways and transformations of energy and matter involved in cellular communication and responses to the environment 2. Become proficient in the following biological core competencies and disciplinary practices: (a) Realize the steps involved in the process of science including the examination and critique of scientific literature, hypothesis generation, experimental design, data interpretation, trouble-shooting and experimental revision and, the generation of biologically relevant datasets; (b) Development of quantitative reasoning skills to interrogate large datasets; (c) Appreciate the interdisciplinary nature of science by navigating biological data repositories and Bioinformatics to obtain information pertaining to specific genes and gene families; (d) Communicate and collaborate with other scientists in graphic form, written form, and verbally.

Describe the methods and strategies that you are using: The year-long program is completed by all biology majors and is spread over two courses: Genetics (BIO231) and Introduction to Cellular and Molecular Biology (BIO335). During the first semester (BIO231), students examine global changes in gene expression in response to osmotic stress in S. cerevisiae. Students perform an osmotic stress experiment, isolate RNA and prepare samples for analysis by either microarray or nextgen RNA sequencing, apply bioinformatics to examine differential expression in a large data set, and, importantly, interrogate the dataset with Gene Ontology tools to identify candidate genes not previously described as functional regulators of the osmotic stress response. Linking the two semesters, students write proposals for conducting functional studies of candidate genes and engage in peer review sessions to rank proposals and select candidate genes for investigation in the subsequent semester. In BIO335, students develop a cloning strategy for a selected candidate gene and design experiments to characterize the function of the gene products in osmotic stress. Thus, students are provided with an authentic research experience and the opportunity to identify novel roles for genes in the stress response.

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 two outcomes for the year-long laboratory course can be simplified for the means of describing the assessment plan. The first outcome, develop a strong foundation in the core concepts associated with biological literacy, focuses on the acquisition of biological content knowledge by the students participating in the year-long laboratory program. The second outcome, become proficient in biological core competencies and disciplinary practices, focuses on the enhancement of the critical thinking skills of the students participating in the year-long laboratory program. Several quantitative and qualitative assessment tools will be utilized to assess whether or not the students participating in the year-long laboratory program made gains in biological content knowledge and critical thinking skills: (a) Writing assignments required for the BIO231 and BIO335 laboratory courses; (b) Pre- and post- program open ended questions; (c) BIO231 and BIO335 final course grades; (d) Performance on the Department of Biology and Health Sciences-NYC major assessment exam; (e) Participation in the Classroom Undergraduate Research Experience (CURE) survey.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The implementation of the laboratory program has yielded significant impacts at the student, faculty, and institutional level. Student Impact: The year-long lab course is integrated into core courses, ensuring that all biology majors will obtain authentic research experiences. At Pace, these courses have an enrollment of approximately 60-80 students per year. It is anticipated that participation in the lab program will enhance students’ potential to conduct scientific research. Projects initiated during the year-long laboratory program may be pursued in faculty mentored, independent research courses. Indeed, four students are continuing their investigations. Faculty and Institutional Impact: A Phase I TUES grant from the NSF was recently awarded to support the expansion of the program to peer institutions. Two participating faculty members (from Pace and La Salle University) recently attended an NSF and HHMI funded GCAT-SEEK workshop to develop RNA sequencing laboratory protocols to broaden the methodological framework of the program. Indeed, the laboratory program itself is modular and scalar - the framework of the program, generation and analysis of a transcriptome database, selection of candidate genes, cloning, and design of an experiment to test the functional role of the candidate gene can be readily adopted by Biology Departments at other institutions. The core courses in which the proposed laboratory program are integrated are ubiquitous offerings in the undergraduate setting, negating the need for partner institutions to develop courses de novo. Moreover, the program can also accommodate a breadth of faculty research questions, providing the opportunity for faculty to integrate their own research into the lab program, thus leveraging faculty expertise in the course. Indeed, the program will be adopted at La Salle University and further efforts will be made to recruit partner institutes in anticipation of a Phase II TUES proposal.

Describe any unexpected challenges you encountered and your methods for dealing with them: Hurricane Sandy struck the New York City metropolitan area in October 2012. The students enrolled in the BIO231 course at that time had isolated their RNA and were getting ready to send it out for analysis. Unfortunately, due to power loss from the storm, all of the student RNA samples were lost. The students were provided with the data sets obtained by the students enrolled in BIO231 the year before. This enabled us to continue with the work as planned without any interruption to our schedule. As we continue to implement this program, the datasets we employ will become increasingly robust and can be interrogated by the students in the advent of challenges - whether they are experimental or otherwise.

Describe your completed dissemination activities and your plans for continuing dissemination: To reach as broad and audience as possible, the program outline and accompanying assessment data will be presented at the major annual meetings of faculty associated with this program and reported in journals with a pedagogical foci. Furthermore, faculty involved in this program have diverse research interests which allows for the program to be introduced at major meetings for societies that include pedagogical sessions. These include the annual meetings of the, the American Society of Microbiology (ASM) and the American Association for Cancer Research. Finally, assessment data and the program structure will be disseminated among faculty with interests in novel pedagogical ideas via ASM’s Biology Scholars Program Listserv and GCAT SEEK’s Listserv. In each of these venues, emphasis will be placed upon 1) the success of the program in enhancing student learning and 2) the adaptability of this program by any institution.

Acknowledgements: We would like to thank and acknowledge GCAT-SEEK for the nextgen sequencing training and analyses and Dr. David Lopatto for allowing us to participate in the CURE survey (https://www.grinnell.edu/academic/csla/assessment/cure). MPK would like to acknowledge the American Society of Microbiology’s Biology Scholars Program (NSF Award # 0715777) for helping her develop the research ideas for this assessment study. Support for the development and assessment of this year long laboratory program is from an NSF Type 1 TUES grant to MPK (NSF Award # 1246000).

New Tools for Learning about Biological Energy Transfer

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Title of Abstract: New Tools for Learning about Biological Energy Transfer

Name of Author: Ann Batiza
Author Company or Institution: Milwaukee School of Engineering
Author Title: Director, The SUN Project
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Biotechnology, Ecology and Environmental Biology, General Biology, Plant Biology & Botany, Teacher In-service
Course Levels: Across the Curriculum, Introductory Course(s), Teacher In-service, Upper Division Course(s)
Approaches: Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development, Mixed Approach
Keywords: cellular respiration photosynthesis models analogy energy

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: All of our work is motivated by the desire to increase understanding of 'what powers life.' Our previous work, funded by the Institute of Education Sciences and called The SUN (Students Understanding eNergy) Project, was recently published in CBE-Life Sciences Education (Batiza et al., 2013). It provides causal evidence through a randomized, controlled trial of immediate and long-lasting (year later) effects of a new way to teach biological energy transfer. Large, significant effects on knowledge and self-efficacy were reported for 19 regular biology teachers (vs. 20 controls) who attended a two-week workshop about cellular respiration (CR) and photosynthesis (PS). The workshop introduced a series of physics and biology-based mental-model-building experiences to help the teachers understand both the 'why' and the 'how' of biological energy transfer. Our approach uses a hydrogen fuel cell and physical and digital manipulatives to emphasize the flow of electrons as the basis for biological energy transfer. A mechanical ATP synthase demonstrates how the concentration of protons originally stimulated by electron movement allows for the production of ATP. Now, with NSF funding we are adapting those materials for the undergraduate level and we have created additional materials including the SUN Chloroplast eBook, which can be accessed at https://www.msoe.edu/academics/research_centers/sun/about.shtml. We are currently pilot-testing adaptation in a variety of undergraduate institutional settings and in a variety of courses that range from an introductory cell biology course for ~115 honors biology students at the University of Wisconsin-Madison to a small bioengineering course at Milwaukee School of Engineering for 14 participants. This year we will follow up regarding long term effects on UW-Madison students and also test the adapted materials in an intimate Energy and the Environment Physics class for non-majors at UW-Milwaukee and in a large biochemistry class.

Describe the methods and strategies that you are using: Our original work on these materials, as stated above, used a randomized, controlled trial to study effects upon high school regular biology teachers (Batiza et al., 2013) and a cluster, randomized controlled trial for effects on their students (paper in preparation). Importantly, we found moderate to large, significant effects in both populations. Teacher-level data in terms of a drawing with written explanation, a multiple choice test, and an established survey of self-efficacy modified for biological energy transfer were gathered not only before and immediately after the workshop, but also one year later. In addition, teachers deposited implementation data online every two months. Student data in terms of a drawing with written explanation and a multiple choice test was also collected. At the undergraduate level we have continued use of the drawing with written explanation as a pre and post test and at the various institutions we have included some appropriate multiple choice and/or short answer pre/post content questions. Pre and post surveys provide for ethnographic and self-efficacy data as well as evaluation of the various instructional materials used. We are also developing a script to videotape a subset of students whom we will follow up for long term effects of these materials.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: For the original biology teacher effects, the pre/post gains of teachers who took the workshop were tested for significance using the paired-samples t-test. In addition, scores between groups were tested for significant differences using analysis of variance (ANOVA). Similarly, the multiple-choice and likert-scale survey responses of the UW-Madison Treatment and Control groups were analyzed using a paired samples t-test and ANOVA. The achievement and self-efficacy of the small bioengineering group was tested for significance using the paired samples t-test. Overall ratings of materials and ratings of materials by students for learning particular concepts are reported as response frequencies. In addition, student comments will be noted. We have not yet graded the undergraduate drawings with explanation assessments administered in common to each group. Besides testing for significant growth and comparing Treatment and Control groups within each setting where appropriate, we will analyze the responses in terms of conceptual achievement according to the 35-item rubric with a .90 inter-rator reliability (Batiza et al., CBE-Life Sciences Education, 2013) used earlier to analyze the teacher responses.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: As described above, our previous work provides causal evidence through a randomized, controlled trial of large, significant, immediate and long-lasting (year later) effects of a new way to learn about biological energy transfer. These effects on knowledge and self-efficacy were reported for 19 regular biology Treatment Group teachers who attended a two-week workshop about CR and PS vs. 20 Control teachers (Batiza et al., 2013). A paper regarding significant effects on their students is in preparation. Preliminary analysis of the UW-Madison honors biology trial shows no significant difference in achievement by the Treatment and Control groups, but it must be noted that ALL STUDENTS used SUN study guides and therefore were exposed to SUN concepts. The major difference was the use of SUN manipulatives by the Treatment group for half of each of two 50-minute discussion sections. Nonetheless, the Treatment group scored significantly higher that the Controls in terms of confidence in their knowledge (T 27.65 +/- 4.26 vs. C 25.00 +/- 5.26 out of a possible 32). The small MSOE trial, which had only 14 students in a Treatment Group, showed a significant gain in self-efficacy pre-to-post. Preliminary analysis of the evaluations of the SUN materials by students indicated that students valued the materials for learning concepts predicted by their expected affordances. For example 70% of students indicated that the nested trays with movable components were useful for understanding the path of electrons in photosynthesis. 75% of the MSOE students rated the hydrogen fuel cell and animations as 'Extremely' or 'Very' useful. 54-62% of the MSOE students and UW-Madison students put the mechanical ATP synthase into these categories. The majority of students in Treatment groups at both schools also found that the SUN mitochondrial and chloroplast eBooks and the nested trays configured as these organelles to be more useful than not.

Describe any unexpected challenges you encountered and your methods for dealing with them: Once the TAs in the UW-Madison trial were trained in use of the SUN materials, we felt that it would be impossible for them to provide a ‘business as usual’ condition for the controls. Therefore we decided to test only the manipulatives in this trial; however, that is not a fair test of the entire SUN Project. In the upcoming large biochemistry trial, only half of the teaching assistants will be trained with the SUN materials. One of the PIs who found herself overcommitted resigned; although we will miss her participation, we were able to replace her with a distinguished professor at her institution. We aborted one trial because we felt that exposure to the pre-test would unfairly advantage study participants when they encountered these same questions on the final. When we implement that trial with a comparable group this year, we will administer the pretest to all students in the course. Another trial suggested that the post assessment needs to be a high stakes test and so in future trials all post tests will be either part of a quiz, unit test or final exam.

Describe your completed dissemination activities and your plans for continuing dissemination: Professor Carol Hirschmugl of the UW-Milwaukee physics department and Dr. Ann Batiza, the PI of this project, gave a 'Science Bag' presentation on 'Fuel Cells, Cellular Fuels: What Powers Life?' at UW-Milwaukee for ~1000 members of the public. The presentation included the SUN materials and the SUN Mitochondrial and Chloroplast eBooks as well as a 6-foot mechanical ATP synthase into which kids from 5-15 threw tennis-ball 'proton' fuel. The alpha/beta subunits were opened and closed by a rotating central shaft to simulate ATP production. At the NSF-PI meeting, Dr. Ann Batiza of MSOE and Professor Bo Zhang from the Educational Psychology Department at UW-Milwaukee gave a workshop on materials development and also presented a poster from the entire research group. At the 2013 National Association for Science Teachers, Ann Batiza co-presented a workshop for 28 teachers with Pat Deibert of MSOE on use of the SUN materials and eBooks at the high school level. In addition, Professor David Goodsell of Scripps Research Institute has presented the SUN Chloroplast eBook at three national or international meetings.

Acknowledgements: Acknowledgements: We thank then MSOE undergraduate Heather Bobrowitz for earlier development of the microbial fuel cell. Other undergraduate and graduate research assistants who have provided technical and clerical support for this project include Elise Pinkerton and Lindsey White. This material is based upon work supported by the Institute of Education Sciences under award number R305B070443 and by the National Science Foundation under award number DUE-1044898. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the Institute for Education Sciences nor the National Science Foundation.

Innovations in Using Digital Approaches to Teach biology

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Title of Abstract: Innovations in Using Digital Approaches to Teach biology

Name of Author: Graham Walker
Author Company or Institution: Massachusetts Institute of Technology
Author Title: Amer. Cancer Society Prof./HHMI Prof.
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Biotechnology, Cell Biology, General Biology, Genetics
Course Levels: Introductory Course(s)
Approaches: Mixed Approach
Keywords: genetics, biochemistry, cell biology, software, on-line

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The Department of Biology plays an integral role in undergraduate education at MIT. Introductory Biology is a required course for MIT students. Furthermore, so many other science and engineering departments are currently studying biological systems and materials that non-majors now outnumber biology majors in our core biology courses. To improve the effectiveness of our teaching to this large interdisciplinary set of students, we have followed a multi-year, multi-faceted strategy that embodies many of the key principles laid out in the Vision and Change report. This work has led to the Biology Department’s current effort to engage the passion of our faculty and students, both on campus and around the world, by exploiting the potential of digital approaches to improve learning through innovative uses of technology and technology-enabled pedagogies. Most recently, we have concentrated on improving conceptual understanding and student engagement in the learning process. To this end, we performed a comprehensive analysis of the concepts taught in our various Introductory Biology versions, which resulted in their organization into a hierarchical, cross-referenced framework (Khodor et al., Cell Biol. Educ. 2004). In turn, this focused our attention on core concepts that are difficult for students to understand and led us to explore innovative strategies for inquiry-based learning. This effort led to a collaboration between the MIT-HHMI Education Group and MIT’s Office of Educational Innovation and Technology that resulted in the development and implementation of freely available, internationally used visualization and simulation software programs and accompanying curricula: StarBiochem (https://star.mit.edu/biochem/), StarGenetics (https://star.mit.edu/genetics/) and StarCellBio.

Describe the methods and strategies that you are using: StarBiochem is a molecular 3-D visualizer designed specifically for education to enable the visualization and manipulation of any Protein Data Bank structure. In addition, StarBiochem includes examples of macromolecules and their subunits to aid in their identification. Through StarBiochem, students discover structure-function relationships through exploratory and guided activities. Usage of protein 3-D viewers has been shown to increase student’s understanding of protein structure and function, one of the core concepts for biological literacy in the Vision and Change report. StarGenetics is a customizable genetics virtual laboratory that simulates the inheritance of Mendelian and non-Mendelian traits. In StarGenetics, students perform crosses with model organisms, such as Mendel’s peas, fruit flies, and yeast, as well as non-model organisms such as cows. The goal of StarGenetics is to enhance procedural knowledge by allowing students to design and conduct their own genetic experiments, one of the core competencies in the Vision and Change report. StarGenetics is used extensively in MIT’s undergraduate Genetics course (7.03). StarCellBio is a cell and molecular biology experiment simulator that uses simulated and real data to provide realistic experimental results. During its first funding year, we developed a StarCellBio prototype, enhanced its usability and functionality, and began implementing an assessment plan. StarCellBio was used for the first time in MIT’s Cell Biology course (7.06) this past spring. Our OpenCourseWare Scholar Course ‘Fundamentals of Biology’ (https://ocw.mit.edu/courses/biology/7-01sc-fundamentals-of-biology-fall-2011/), a non-interactive online course for self-study, helped prepared us for the development of online courses. This past spring, the Biology Department’s first MITx course, 7.00x, a freely available on-line introductory biology course was taught by Professor Eric Lander.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Self-reported student data within MIT’s introductory biology courses indicates that StarBiochem increase student’s understanding of protein structure and function, one of the core concepts for biological literacy in the Vision and Change report. In survey results, 7.03 students indicated that StarGenetics problems were more effective than traditional problems in teaching genetics experimental design and analysis. Evaluation of the effectiveness of StarCellBio is in progress.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Support of the STAR tools within MIT courses has allowed the Biology Department to more easily extend the adoption of our tools nationally through curriculum development and outreach workshops. In turn, this has led to recognition of our work by outside funding agencies: Howard Hughes Medical Institute (Institutional grant to MIT and Professorship grant to G.C.W.), Davis Educational Foundation, and NSF (TUES grant). This outside support has greatly facilitated our efforts and, in turn, has stimulated further institutional recognition and support within MIT. Recently, we expanded outreach internationally. Through the MIT-Haiti Initiative, we have led workshops in Haiti for Haitian faculty on the use of innovative biology tools to enhance student understanding of core biology concepts. Translation of the tools’ user interfaces and associated curricula into Haitian Creole has opened the door to the translation of these programs into other languages, which will make these tools more accessible internationally.

Describe any unexpected challenges you encountered and your methods for dealing with them: Many technical challenges were overcome.

Describe your completed dissemination activities and your plans for continuing dissemination: StarBiochem and StarGenetics are already freely available. 7.00x was freely available on-line, as will be future MITx courses.

Acknowledgements: This work was supported by HHMI, the Davis Educational Foundation, and NSF 1122616.

Visual Analytics in Biology Curriculum Network

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Title of Abstract: Visual Analytics in Biology Curriculum Network

Name of Author: Raphael Isokpehi
Author Company or Institution: Jackson State University
PULSE Fellow: No
Applicable Courses: Bioinformatics, Biotechnology, Evolutionary Biology, General Biology
Course Levels: Across the Curriculum, Faculty Development, 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: Visual Analytics, Data-Rich Biology, Teaching with Data, Data Visualization

Name, Title, and Institution of Author(s): Shaneka S. Simmons, Jackson State Universtiy Jian Chen, University of Maryland, Baltimore County Edu Suarez-Martine, University of Puerto Rico at Ponce Robert Dottin, Hunter College of the City University of New York

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The Biology of the 21st Century (the New Biology) already generates massive amounts of data on biological systems from cellular molecules to ecosystems. It demands new skills and knowledge for teachers and learners of biology to make biological inferences from large datasets (such as genome sequences and long-term ecological measurements) that are now essential for evidence-based learning. The primary mission of the Visual Analytics in Biology Curriculum Network (VABCN; www.vabcn.org) is to contribute to the national efforts to change the way the core concepts for biology literacy and practice are taught and learned. According to the Final Report of the July 2009 National Conference titled “VISION AND CHANGE IN UNDERGRADUATE BIOLOGY EDUCATION: A CALL TO ACTION”, the core concepts for biological literacy and practice are (i) evolution; (ii) structure and function; (iii) information flow, exchange, and storage; and (iv) systems. To transform undergraduate biology education these concepts need to be mastered using a set of core competencies. Incorporating visual analytics, the science of analytical reasoning facilitated by interactive visual interfaces, in the biology curriculum will improve the ability of biology learners to develop competencies to understand (master) the core concepts for biological literacy. The overall goal of the Visual Analytics in Biology Curriculum Network (VABCN) is to facilitate and promote the collaboration of researchers, educators, and students who are developing approaches for incorporating visual analytics into biology undergraduate education. The intended outcomes of the VABCN are to (1) Develop and expand a network of scholars for improvement in undergraduate biology education; (2) Produce, assess and disseminate course resources designed to improve biological literacy; (3) Promote a globally engaged network of faculty and students; and (4) Provide effective communications and collaboration tools.

Describe the methods and strategies that you are using: Many interactive visual interfaces that are key to teaching, learning and assessment are now available through diverse computing devices including desktop computers, laptops, notebooks, tablets and smartphones. The three main strategies for implementing the Visual Analytics in Biology Curriculum Network (VABCN) are: (1) Web Portal to Visual Analytics for Undergraduate Biology Education; (2) Development of Visual Analytics Enhanced Biology Course Resources; and (3) Webinars and Classroom Guest Speakers. A visual analytics enhanced biology course resource incorporates the use of interactive visual interfaces and software that facilitate visual analytics tasks on the selected biological datasets. The course resources will be mapped to the categories that are aligned to the core concepts and core competencies as described in the 2011 Vision and Change Report. Other categories are student audience, scientific domain and nature of research.

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 planning phase (April 2011 to March 2012) of the VABCN enabled us to develop frameworks for the design of evaluation studies: e.g. pre- and post-assessment materials; comparisons between implementations at different sites; and comparative assessments of course resource implementation with and without the visual analytic component. Additional frameworks are students’ pre and post knowledge and skills in different aspects of scientific inquiry. The proposed project will allow members to further develop these assessment strategies and share them.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The Preparing Faculty Working Group (Theme III: Ways to Bring About Change: Change Agents) during the 2009 Vision and Change meeting recognized the need “To develop and grow communities of scholars (students, postdocs, faculty, and administrators) who are committed to creating, using, assessing, and disseminating effective practices in teaching and learning” (https://live-visionandchange.pantheonsite.io/working-group-descriptions/). The planning phase of the VABCN enabled the formation of a Steering Committee consisting of 33 scholars from 13 diverse institutions. The full implementation of the VABCN will provide activities to improve and expand a network of scholars interested in improving the approaches to teaching and learning biology in a data intensive world. Our measurable aim is to reach at least 100 unique participants per year in the VABCN activities. Integrated analysis and visualization can allow learners and teachers of biology to analyze data of interest, display relevant parts, and concurrent ways to interact with the data for deeper understanding. Science education research suggests that activities are most effective when they are designed to interactively engage students.

Describe any unexpected challenges you encountered and your methods for dealing with them: In the planning (incubator) phase of the VABCN we identified that heterogeneous virtual communities take time to develop the bonds, sharing of expertise, shared understanding and vocabulary needed for productive development of visual analytic course materials. More time than a year is needed to develop at once solid collaborative dynamics, high quality instructional materials integrating innovative visual analytics, implementation of the materials, and assessment instruments. It is likely that investment in these longer start-up times for a first module will make it possible for a group to produce additional instructional materials very efficiently and effectively. Thus efforts are in progress to secure grant funding and other funding sources to continue the activities of the VABCN.

Describe your completed dissemination activities and your plans for continuing dissemination: The principal product from the network activities will be a system of course resources on visual analytics for mastering core concepts for biological literacy. The VABCN will facilitate the production, assessment and dissemination of biology course resources that incorporate visual analytics. During the planning phase, members of the network produced, assessed and disseminated prototype course resources on diversity of life targeted at biology courses offered to freshmen and sophomores (https://www.vabcn.org/). We will promote, encourage and support the use of best practices for student-centered course resource development as recommended by the Vision and Change Report. Therefore, an expected outcome of this VABCN activity is that the developed course resources will have well-articulated learning outcomes to align assessments with learning activities. As an international network with participants in different geographical locations, the VABCN will maximize the use of cyber-based collaboration strategies and promote the use of videoconferencing to accomplish collaborations. As part of our international public dissemination of the results of the planning activities of the VABCN, we have worked with International Innovation Magazine to prepare an article on the importance of visual analytics in biology curriculum in language accessible to the public. The full digital edition of the May 2012 International Innovation can be found at: https://www.research-europe.com/. Since the VABCN is responsive to the Vision and Change effort, we will establish a VABCN group on the PULSE (Partnership for Undergraduate Life Sciences Education) website (https://www.pulsecommunity.org/). In particular, we will provide VABCN information materials to the PULSE Vision and Change Ambassadors, a group dedicated to meeting with biology and life science departments to encourage them to adopt the principles and recommendations of the “Vision and Change” report.

Acknowledgements: The incubator phase of the Visual Analytics in Biology Curriculum Network was jointly funded by the Directorate for Biological Sciences, Division of Biological Infrastructure and the Directorate for Education and Human Resources, Division of Undergraduate Education of the National Science Foundation as part of their Vision and Change in Undergraduate Biology Education efforts. Award: NSF-DBI-1062057

Group Research: Experiment in Efficiency of Delivery

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Title of Abstract: Group Research: Experiment in Efficiency of Delivery

Name of Author: Louise Temple
Author Company or Institution: James Madison University
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Evolutionary Biology, Genetics
Course Levels: Upper Division Course(s)
Approaches: Mixed Approach
Keywords: Undergraduate research Efficient delivery Multiple students Single mentor

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: With the overwhelming documentation of undergraduate research as a transformative experience, biology educators are being challenged to offer research to more students. The goal of this project is to offer original research opportunities to more undergraduates by developing experimental questions that can be addressed by small groups of students mentored by one faculty. Since 2008, we have offered a research class to freshman involving bacteriophage discovery and genomics, originally sponsored by HHMI and now continuing with institutional support. This program has been extremely successful, so much so that there is enormous pressure on faculty to host more upper-level students in their research labs. One solution to this fortuitous problem is to continue a more advanced research project with groups of 6 to12 students mentored by one faculty member. We have dubbed this class 'Superphage'. The intended outcomes of the project are twofold: (1) students will derive the benefits of an undergraduate research experience similar to that offered by a one-on-one mentoring situation, and (2) different models will reveal the best possible way to offer this opportunity to more students.

Describe the methods and strategies that you are using: The SuperPhage course has been offered for four semesters and involved 25 students. Half of these enrolled for two semesters, which is the limit, and the other half for one semester. Four different models have been tried: (1) 16 students working in groups trained and supervised by the faculty mentor, (2) 12 students working in small groups of 3-4 with an assigned student leaders, (3) 11 students working at designated times all together for several hours a week, and (4) 5 students working somewhat independently on the same project. In every case, the research questions have derived from the freshman Viral Discovery course, building directly on biological discoveries and data generated by the first year students, as well as an additional project that utilizes the skills learned in the course and applied to a different question. Regardless of the model, the groups have met more or less regularly for journal club, which has consisted of primary data literature reading and discussions, as well as reports on individual results and issues.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Every semester, the students have answered questionnaires and been involved in discussions about the effectiveness of the course for them, what they would change about how the course is run, and what they would change about their own behavior. In addition a recent survey was given which included the attitude assessment questions from the Classroom Undergraduate Research Experiences (CURE) survey. It is our intention to track the students for the next few years, as closely as possible, in their career tracks.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The major question, 'Do students benefit from group (as opposed to individual) research experiences'? seems clear from the early outcomes. All student report that they strongly benefited from this experience. There are several other measurable outcomes, including that all these students have continued beyond the group experience into individual, independent projects, and high numbers of them obtain summer research opportunities outside our school. One additional, explicit goal of this project is to address the challenge of publication of undergraduate research results. In this regard, a second outcome has been the preparation of two manuscripts that are student driven, one accepted for publication in the journal, Virology, and the other likely to be ready for submission by the end of the summer. The strategies used in designing research with the expressed goal of publication have been documented and student feedback recorded. Our initial observation with regard to the different models described above is that different groups of students will be differently successful due not only to the model but also to their personalities, motivation, and preparation. One incontrovertible conclusion is that regular journal clubs are extremely valuable, giving students a strong background for the particular project and the skills needed to read primary literature, and fostering ideas that directly impact their approaches to their research. An additional outcome is new collaborations within our institution and with another university, which have already resulted in external funding and promise higher success rate in dissemination of the work.

Describe any unexpected challenges you encountered and your methods for dealing with them: The challenge of this model is to ensure that the members of the group receive the benefits that have been shown so profoundly in the one-on-one, mentor - mentee model. The CURE attitudinal question results are not completely analyzed at this writing, but initial observations indicate this model provides equal or better self-evaluation than other high research classes, including intense summer experiences. A second challenge for the model is faculty effort. Regardless of which of the four models is used, a large effort is required of a single faculty mentor. Because the students are signed up for academic credit under a single rubric, the faculty member receives teaching credit for this 'course'. Financial support for the projects is also a challenge, which in our case has been met largely by departmental support and some external funding from the state of Virginia.

Describe your completed dissemination activities and your plans for continuing dissemination: The science produced by the students has been disseminated in several regional and national meetings. This write-up is the first effort to disseminate what we have learned from the faculty and educational standpoints, about this model.

Acknowledgements: Several faculty members in the Viral Discovery and Biotechnology programs have assisted in this project, either by helping students directly or by teaching coverage to allow a single professor to mentor students using this model. These include Drs. Steve Cresawn, Stephanie Stockwell, Ron Raab, Crystal Scott, and Bob McKown. The Department of Integrated Science & Technology and Dr. George Coffman have been very supportive from financial and lab support perspectives.