ABLE 2013 Mini Workshops – Association for Biology Laboratory Education

Mini Workshops were 45-minute, drop-in sessions on Friday, June 28, 2013 covering topics ranging from wet lab techniques to discussions on pedagogical research and practice. Browse titles and abstracts below, sorted by time of presentation.

8:30 a.m. – 9:20 a.m., Mini-workshop Concurrent Sessions I

Do the right thing – teaching responsible conduct in science (Kuei-Chiu Chen, Weill Cornell Medical College in Qatar, Qatar; Laurel Hester, Laurel Hester, Keuka College, NY, U.S.A.)

As teaching students to conduct authentic science becomes one of the major foci in biology education, there is a need for institutions to prepare students for conducting science responsibly. In this mini workshop we will use three to five separate fictional stories to cover some of the most common violations of ethical behavior in science. The instructor introduces the background and characters involved in each story. The characters then start their dialogue that often leads to a dilemma. The instructor then presents questions and conducts a poll using student response system (i.e “clicker”). A short discussion follows with students expressing their comments on the story. The instructor then concludes by describing the common professional practice for the specific situations in the play. The plays require little training of the actors, which could be played by other instructors, teaching assistants or volunteer students, and may be performed in a lecture hall setting or in a lab.

Sources of grade variability in multi-section lab courses: Should we seek legitimate correction factors to mitigate detectable variations in student grades? (Saewan Koh and Mark Wolansky, University of Alberta, Alberta, Canada)

Grades amongst groups in large multiple section lab courses can be highly variable. The spread amongst lab sections in our own courses were at times +/- 4.5%. This spread is of concern since we strive for fairness in how students are evaluated. More importantly students themselves expect this to be true. We examined grades from two large multiple section lab courses (819 students and 358 students) to identify the sources of variation in student’s final lab grades. TA, lab section, room assignment, day of lab, time of lab and home program of individual students were used in a linear mixed effects model to determine which variables were important in determining a student’s final lab grade. Some of the sources of variation we detected such as room assignment can be controlled for administratively while best practices in TA training can reduce TA bias and thus a portion of the overall differences in scores amongst sections. Surprisingly, we discovered other significant sources of variation that were self-selected by the students and so out of reach of any mitigation process that we would be able to perform. In this mini workshop we will present the results from our analyses and then open the floor to discuss potential strategies to reduce grade variation. For each source of variation we will also discuss whether or not mathematical corrections should be applied to mitigate its effect on overall grades if it were possible. We ask when if ever would these corrections be appropriate.

The Pros and Cons of Electronic Laboratory Notebook Use in Undergraduate Courses (Debra Mauzy-Melitz, University of California Irvine, CA, U.S.A.)

Notebooks are an important component of any laboratory experience, but the logistics of grading laboratory notebooks can be a problem. Electronic lab notebooks provide a solution while serendipitously increasing student interest. Students with electronic lab notebooks share easier with lab partners for better assignment completion, while simplifying progress monitoring and grading. Online notebook use develops skills translatable to many careers requiring online data management systems. Electronic laboratory notebooks have been used successfully for multiple quarters in a large upper division laboratory course with multiple sections. Students overwhelmingly prefer the electronic notebook to paper. Electronic notebooks facilitate creativity by allowing inclusion of multimedia, links, safety data, protocols and other metadata. Students are found to be more reflective, get more quality practice in writing. Electronic notebooks provided real time and any time monitoring of student progress, without ever removing access from the student, TA or instructor. Grading is easier due to being always accessible, more effective searching and much better legibility. Electronic notebooks are not easily lost. TA comments can be as easily reviewed allowing better class management. This session will describe the successes and challenges of managing and implementing electronic notebooks. Available free electronic laboratory notebook programs will be reviewed. At the end of the session, participants will record their results and reflections in an electronic laboratory notebook.

Good Reason to Hate Broccoli! (Dani Meyers and Suzie Jekel, Colorado Academy, CO, U.S.A.)

What is it about eating we love? Tasting something!! For some there is no taste. That is where we begin our study. Utilizing the Denver Museum of Nature and Science (DMNS), a lab kit from Carolina Biological and simple taste experiments we have interwoven a study on why some folks can taste a bitter compound and others can’t. Starting with a simple question of whether or not you like broccoli (which can be for many reasons), leading to the actual sequence of the taster gene from your cheek cell. During this workshop we will be able to see if you can taste the bitter compound, show you the sequence for the gene, run you through the basic process of acquiring a gel for this sequence and introduce you to the Genetics of Taste study being done at DMNS. We have been quite fortunate to have our students participate in research being done at DMNS. They are currently conducting a long term study on the Genetics of Taste. Through our contact with them, students have been able to enroll in the study and talk to scientists about their research. Students have gained an appreciation for the intricacies of research and have learned first hand how to sequence their own genes.

Regional ABLE Meeting Preparation. Tips for a RABLE of your own! (Joe Newsome, San Diego State University, CA, U.S.A.)

If you’ve ever wondered about hosting a regional ABLE conference, this workshop is for you! Participants will learn the critical steps and timing issues to properly prepare for a successful RABLE. The workshop will begin with a review of the San Diego 2013 RABLE preparations, including obstacles and successes. Participants will exchange ideas about the best distribution of RABLE meetings with regard to timing and geography. Each participant will receive a sample budget, schedule, and proposal. You will also receive sample letters you can modify to send to your local institutions to raise interest among fellow lab instructors and coordinators. You will see the internet-based resources you’ll need for your own RABLE. You will also access your own web-based resources in a hands-on exercise to get started with your planning.

A Recitation Program to Improve Student Success in Majors and Non-Majors Introductory Biology Courses (Donna L. Pattison, University of Houston, TX, U.S.A.)

Undergraduate teaching assistants were selected to team teach recitation sessions for either a majors or non-majors Introductory Biology course as part of a Comprehensive Student Success Program grant through the Texas Higher Education Coordinating Board. The recitation sessions complement our large enrollment lecture courses. Curriculum for recitations is designed to provide reinforcement and practice of concepts covered in the lecture part of the course. The activities are intended to be completed in groups of four. Hands-on activities are incorporated as often as possible. The activities are also designed to teach and reinforce good study skills and habits. The recitations are open to any student enrolled in the course but any student who scores below a 70% on the first course exam is required to attend one session per week for the remainder of the semester. Teaching assistants meet once a week with the course instructor and project co-director to discuss the activity for the upcoming week and issues that have arisen in the classroom or lecture hall. The teaching assistants also meet every other week with the co-director for training in educational pedagogy. Topics have included developing positive classroom dynamics, discussion skills and quality questioning, the value of cooperative learning, the psychology of learning and development, how memory occurs, cultural competence in the classroom, motivating students, the value of repetition and elaboration, reading for college, and working with students in crises. Conference participants will participate in a mock TA training session on our Lac operon recitation activity.

The Great Larva Race: Using Fruit Fly Larval Speed to Study Quantitative Genetics (Ann Yezerski, King’s College, PA, U.S.A.)

Recently, ABLE member Kathy Nolan presented a mini-workshop about measuring the speed of the larval stage of the commonly used fruit fly, Drosophila melanogaster. Based on these techniques, I designed a semester-long module that uses this trait to study quantitative genetics. Students begin by measuring the average larval speed from a genetically variable line of Drosophila melanogaster, and then select for both fast and slow larval speed over several generations of flies. Halfway through the semester, the high- and low-speed lines are crossed and the progeny’s speed is quantified. The class data is used to calculate heritability and response to selection. The final exercise is an end-of-semester race amongst each lab group’s fastest line to determine a winner of extra credit. This module can serve as a more interesting alternative to classic quantitative genetics studies such using bristle hair counts or modern computer simulations. The results of the inaugural semester of this module did suggest genetic heritability of the trait as well as identified improvements and variations of the exercise.

Action Potentials Are Child’s Play (Rick Wiedenmann, New Mexico State University-Carlsbad, NM, U.S.A.)

Action potentials are difficult for most students to comprehend. Ion channels open and close in sequence. Sodium and Potassium ions move across membranes in opposite directions. With all of the details to learn students can easily lose sight of the overall concept of depolarization as electrical impulses travel down neurons. This workshop will show how to demonstrate depolarization/repolarization both kinesthetically and visually using a simple folk toy that has amused children and adults for over one hundred years. Workshop participants will build their own “depolarization toys” and be provided handouts with printed instructions to take home.>

11:00 a.m. – 11:50 a.m., Mini-workshop Concurrent Sessions II

Use of radioactive material in undergraduate laboratory exercises (Mike Adams, Eastern Connecticut State University, CT, U.S.A.)

We have had a departmental radiation license for over 25 years, and have used this to develop a variety of laboratory exercises undergraduates. We introduce students to working with radioactivity at the sophomore level, with a simple uptake and incorporation experiment using 35S. This is expanded in upper level courses to include examination of protein synthesis in the presence of antibiotics, induction of heat shock proteins, hormone assays, use of pulse-chase techniques and autoradiography. Examples of specific exercises will be presented, with results and analyses, as well as information on what is involved in applying for a license, along with the required reporting and safety regulations.

Incorporating Evolutionary Medicine into an Introductory Lab Program (Donna Bozzone, Saint Michael’s College, VT, U.S.A.)

Since “nothing makes sense except in the light of evolution” we designed a lab unit that would connect our students’ seemingly inherent (and unlimited!) interest in medicine and health care to evolutionary biology. In this multi-week unit, students design and implement experiments that test an aspect of the anti-microbial hypothesis. This hypothesis states that humans eat spices because this behavior is an adaptation that reduces infection and illness. Students explore the capacity of spices, extracted in different ways, and in various combinations to affect the growth of various microbes. Students present their results to the class and integrate their findings with relevant published literature. Although this unit is an component of our majors’ introductory course, this lab project would also be suitable for courses in microbiology, evoutionary biology, and non-majors’ biology, with appropriate modifications.

Podcasts in the General Biology Laboratory — Not Just a Communication Tool (John O. Drummond, Lafayette College, PA, U.S.A.)

Podcasting for the general biology laboratory can be used not only as a communication tool, but an educational tool as well. At Lafayette College, we have been using both audio and video podcasts in general biology for over 5 years now. We use weekly audio podcasts to recap from the previous week and for reminders and general information about lab for the current week. Video podcasts have been used to demonstrate techniques and have also been used as “review sessions.” Podcasts allow the students to digest the information in small pieces and replay the information again and again. Students report viewing the podcasts mostly on their personal computers, but also on their smartphones and tablets. Feedback from students has been overwhelmingly positive. Some have included the podcasts as the most important factor for their success in the course. In this session, we will discuss the theory behind podcasting and review sample podcasts used at Lafayette and other institutions. We will demonstrate how to create both video and audio podcasts using Audacity (a free and easy to use audio recorder and editor), PowerPoint, and Keynote. Where to post podcasts for student use will vary from institution to institution. We will review what has been done at Lafayette and discuss options for your institution. There will be time set aside at the end of the session to help you practice making your own short podcast and to discuss how you might use podcasts in your setting.

Tools to Document Phenological Color Changes in Trees (Rosemary H Ford, Washington College, MD, U.S.A.)

Throughout the academic year campus trees undergo silent changes from bud break in the spring to leaf abscission in the fall; major events that typically are unnoticed by students. While phenological transitions could be monitored at either season, I have students document changes in selected deciduous trees throughout the fall semester. Among the activities included in their study are two that involve analysis of the color changes occurring within their assigned trees. To identify where and when major changes occur within a tree, students produce weekly digital images of their trees. These are analyzed using ImageJ, a free software program that can separate colors into three channels (red, green, and blue) and then quantify those colors. On a smaller scale color changes and their locations within individual leaves on selected branches are analyzed weekly; the Globe Plant Color Guide is used to identify colors. At the end of this project students have an understanding of how the green down process differs among species and within a single tree. This workshop will allow participants to use ImageJ for analyzing colors within a tree and the Plant Color Guide for leaf analysis.

Design-Based Virtual Biology: Finally Something That Works (Ashley Gess, Virginia Western Community College, VA, U.S.A.)

“Teach Biology online”, “Make Biology more accessible”. These kinds of requests are plaguing science educators. Oftentimes, as a result, rigor is compromised and the affective part of learning that is provided by a face to face laboratory experience goes by the wayside. Some people are choosing to use a separately purchased lab kit, requiring a lot of extra cost to the student. This session will walk attendees through the creation of a virtual design-based course (using an integrative STEM model) that uses wet lab to drive the content presentation. Students complete the lab at home with minimal cost and meet synchronously (but still at a distance) as lab groups to discuss conclusions and decide the method/design for the next lab experiment. The example BIO 101 course culminates with student lab groups designing and building a device used to harvest and recycle Carbon Dioxide. Student groups then present the device live online. Preliminary pretest/posttest data indicate that student success rate is higher for this virtual course and that learning is at a higher level that comparative face-to-face or hybrid courses.

An Excellent DNA Model (Bob Ketcham, University of Delaware, DE, U.S.A.)

3D Molecular Design, a company based in Milwaukee, WI, USA, produces and sells a kit that allows students to assemble a large-scale model of DNA. Twelve nucleotide pairs are included in each kit, and when fully assembled these make a DNA model that stands twelve inches high. The phosphate group, the sugar, and the nucleotides all disassemble as separate pieces. They reconnect using hefty lock and key fittings or magnets. Atoms are color coded. The double helix with its major and minor grooves is obvious. The model is very satisfying to use. Workshop attendees will have ample opportunity to explore with the model.

The Pros and Cons of Electronic Laboratory Notebook Use in Undergraduate Courses (Debra Mauzy-Melitz, University of California Irvine, CA, U.S.A.)

Applying a versatile rubric for authentic research assignments: An easier and more reliable way to give feedback to students? (Doug Graber Neufeld, Eastern Mennonite University, VA, U.S.A.)

This workshop will introduce a versatile rubric bank that was developed to assess three non-content aspects of authentic research assignments: higher order cognitive skills, the understanding of the nature of science and scientific inquiry, and the establishment of oral and written communication skills. This rubric was developed to facilitate grading of a variety of assignment types, at different developmental levels, and for different science courses. The rubric was designed to speed assessment of assignments while providing more consistent and specific feedback to students. Workshop participants will practice the application of this rubric on samples of student research posters, and compare ratings as an exercise in encouraging the reliability of rubric use among multiple raters. Discussion of the pros and cons of rubric use will help to define the situations in which rubrics are appropriate, and will work towards clarifying what educators feel are the most important items for assessment in order to develop students as scientists.>

1:30 p.m. – 2:20 p.m., Mini-workshop Concurrent Sessions III

Vision and Change? Challenges and Opportunities for ABLE (Lawrence S. Blumer, Morehouse College, GA, U.S.A.; Christopher W. Beck, Emory University, GA, U.S.A.)

This workshop will begin with a guided discussion on how we each became scientists and an identification of the skill development we most value in our students. Increasing the adoption of inquiry-based laboratory work in undergraduate courses is an explicit recommendation of the AAAS/NSF/NIH/HHMI Vision and Change report of 2011. Regular ABLE members know that this focus on undergraduate laboratory learning and teaching has been the mission of our organization for the past 34 years. ABLE resources, both our annual meetings and our publications, may readily be used to foster the transformation in learning and teaching recommended in the Vision and Change report. The annual ABLE proceedings, Tested Studies for Laboratory Teaching, provide ready to use teaching protocols that can be provided to colleagues as best practice models to use, modify, and emulate. How we proceed to foster the changes recommended by the Vision and Change report, in laboratory education and in lecture courses will be explored. We also will lead a discussion on overcoming barriers to change.

Teaching experimental design using labs that “don’t work” (Emily Boone, University of Richmond, VA, U.S.A.)

There is nothing that a lab instructor dreads more than a lab that “doesn’t work”. As instructors, we are continually tweaking our lab exercises to make them “work” for our students. Have you ever considered that a so-called “failed” lab might teach them more than whatever concept the original lab was designed to teach in the first place? What if instead of fixing them ourselves we allowed our students to troubleshoot them? In this workshop we will examine how you can take a lab that you may have otherwise discarded because it “doesn’t work” and transform it into a lab on experimental design for your students. We will use an ecology lab as an example but this concept can be applied to a variety of different specialty areas in biology. So dig out those old forgotten labs and see how you can transform them into a whole different learning experience.

Podcasts in the General Biology Laboratory — Not Just a Communication Tool (John O. Drummond, Lafayette College, PA, U.S.A.)

Design-Based Virtual Biology: Finally Something That Works (Ashley Gess, Virginia Western Community College, VA, U.S.A.)

Using Excel Simulations to Explore Thermodynamics (Robert J. Kosinski, Clemson University, SC, U.S.A.)

Microsoft Excel is available to virtually all students, and it can be used to rapidly create simple simulations. In this exercise, used in Clemson introductory biology, students learn simulation skills by modeling the equilibrium reaction between dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) in glycolysis. First, they create a two-compartment model with constant, literature-based transfer coefficients. They determine that starting concentrations have no effect on the final equilibrium concentrations. These concentrations are determined only by the ratio of transfer coefficients, reflecting relative molecular stability. Then they add the effect of temperature to their model. The third simulation uses a more complex spreadsheet downloaded from a course Web site. This model allows students to vary standard delta G of the reaction as well as initial concentrations. Students are asked to make predictions of how the simulation will turn out for a variety of starting conditions and standard delta Gs, and then test their predictions with the model. This exercise is used as part of a laboratory on respiration in freshman biology, and can be rapidly completed by most students. We had previously used Excel to model buffering, and in the second semester course we return to Excel simulation for an exercise on weight regulation.

CACAO: Linking evidence-based functional annotations to education (Brenley Kathleen McIntosh, Texas A&M University, TX, U.S.A.)

A significant obstacle to analysis of gene function on genomic scales is the lack of experimentally supported functional information available in forms amenable to data mining and comparative analysis. The Gene Ontology (GO) provides a system for organizing this information, but capturing the experimental literature is overwhelming, even for genome databases with professional biocurators curating information from well-studied model organisms. Thus, efforts to enlist the broader scientific community in increasing the coverage and specificity of literature-based functional annotations have been attempted. Such community annotation initiatives often suffer from low throughput due to lack of participation. Here, we describe the CACAO (Community Assessment of Community Annotation with Ontologies), which provides an incentive to join the community annotation efforts by linking functional annotation to education. Teams of students at campuses around the world compete over multiple rounds to add, review and refine functional annotations that comply with the standards of the GO Consortium. During each round, teams have one week to find scientific papers, analyze experiments and add functional annotations to our website, GONUTS (http://gowiki.tamu.edu) and are given points for each complete annotation. During the second week of a round, teams review and challenge other teams’ annotations, performing peer review of the student’s understanding of the experiments cited as well as an opportunity to steal points for identifying and correcting errors. The CACAO competition has now been incorporated into molecular biology, chemistry, bacteriology, genetics and cell biology courses at twenty-two campuses and has created thousands of functional annotations for hundreds of species. Thus, CACAO provides a solution to the problem of community participation. A large fraction of the annotations are suitable for incorporation in the corpus of annotations deposited with the GO consortium and are being propagated to major database resources such as UniProt via EcoliWiki. We will describe the competition, how we assess of the quality of the annotations and how we deal with the large numbers of annotations created by the competition.

Applying a versatile rubric for authentic research assignments: An easier and more reliable way to give feedback to students? (Doug Graber Neufeld, Eastern Mennonite University, VA, U.S.A.)

How ‘Salmon in Trees’ leads to greater student engagement and learning in First Year Biology (Susan Purdy, Thompson Rivers University, British Columbia, Canada)

Educational research in the STEM (Science, technology, engineering and math) disciplines has shown that students learn more when class time is given over to active learning and where students have the opportunity to spend time actively engaged with the subject matter. This includes opportunities for students to solve problems together in small groups by working cooperatively and collaboratively. The impediments to implementing such practices in large first year lecture classes are often great, but luckily there are opportunities to do so in our first year laboratories. Here students are scheduled to spend three hours a week in smaller groups already and the nature of labs is that they are intended to be places for active learning. In 2012 we implemented a new team-based project as part of our first year biology labs based on the ‘Heifer in a Tank’ project that was developed at the University of Alberta in the Agriculture Science program. For this project students work in small groups to answer a ‘quirky’ biological question with one component being to develop a video. We called our project ‘Salmon in a Tree’ after the first question on a list of questions that students could choose to work on. Students work in teams of four to five people to find the solution to their question. Integrated into the project are many of the core competencies that we feel are important for biology undergraduate students to learn. In this workshop I will present an overview of the project as well as a discussion of some of the evidence-based research on collaborative learning, and then ask participants in the workshop to share their experiences with team based learning and we can develop a list of ‘best practices.’>

3:00 p.m. – 3:50 p.m., Mini-workshop Concurrent Sessions IV

Gene Rummy: A Card Game about Mendelian Genetics (Katrin Becker, Mount Royal University, Alberta, Canada)

Many people struggle with the fundamental concepts underlying Mendelian genetics. As soon as we involve more than two traits things get complicated. The classic examples are fine, but additional resources can be helpful. Besides, playing with blood isn’t all it’s cracked up to be, and rabbits are cuter. Here’s a visual way to learn the jargon and the basic principles of Mendelian inheritance while playing a fast-paced card game using rabbit coat color genetics. Coat color in rabbits demonstrates dominance/recessive traits, differences in pheno- vs genotypes, epistasis, and multiple alleles – all of which blend together to form the color we see. Gene Rummy is a variation of Gin Rummy. Players can try their hand at breeding rabbits – without the mess, smell, or expense. This workshop is a demonstration of our prototype card game and participants will have an opportunity to examine the cards, see how the games are played, and try a few hands themselves. Two variants exist: “Families”: attempt to form families from the rabbits in their hands by choosing a sire and dam and the babies that this mating could produce. 2) “Production”: pick a rabbit from the “Gene Pool” and try to find two parents who could produce it. Join us.

Teaching experimental design using labs that “don’t work” (Emily Boone, University of Richmond, VA, U.S.A.)

Digital Coyote: examining geographical variation using a virtual museum collection (Declan J. McCabe, Saint Michael’s College, VT, U.S.A.)

Measuring geographical variation requires access to museum specimens from diverse and far flung locations. To provide such access to more teachers, we have built a virtual museum collection of calibrated photographs of coyote (Canis latrans) skulls. Hosted by Wikieducator, Digital Coyote is an open educational resource that provides access to 70 specimens from 22 locations ranging from Texas to Alaska, and from New Brunswick to Washington State. In this laboratory activity, students use ImageJ or printed images to take measurements from northeastern and northwestern specimens. Recently-published mtDNA sequences confirm that northeastern coyotes have hybridized with wolves. Students can test the hypothesis that skulls from the northeastern coyote population are larger than their northwestern conspecifics. The topic is well supported by a rich literature and provides an entry point to the species concept, hybridization, conservation genetics, and wildlife management. Although not specifically addressed during the workshop, the collection can be used to test Bergmann’s rule and other hypotheses. A planned expansion of the collection to include domestic dog skulls will facilitate comparisons between artificially and naturally selected populations. This activity demonstrates the applicability of museum collections to hypothesis-driven science.

Lucy in the Sky with Diamonds: comparing and contrasting hominids and other primates (Kathleen Nolan, St. Francis College, NY, U.S.A.)

The Australopithecan “Lucy” was discovered while the song in the title, written by the Beetles, was playing on the radio in the background. In this workshop participants will learn about three activities that can be used to supplement a laboratory session on vertebrates: 1. Draw and color in bones that are “missing” on a poster of a Lucy skeleton (by comparison with a human skeleton) 2. Discuss sexual dimorphism in primates, make a graph from height and weight data of males and females of various primate species and explore how these differences may have helped the primates survive. 3. Calculate and compare size and volume of various skull models and discuss the implications of this. We will break up into three groups so that each person can try one, then the whole group will share their results. This hands-on exercise has been received well by both a Baruch College Honors class and a St. Francis College nursing and a biology majors’ class, and has been lauded as a way to help the students grasp differences among hominids and primates.

Journaling and Botany: Documenting Learning with Words and Pictures (Christine Petersen, Thompson Rivers University, British Columbia, Canada)

Nowadays it seems science and art are very separate but in the past it was common for science and art to be done together (DaVinci). There has been a push to reconnect art and science. Ainsworth et al. (2011) found that drawing increased the students’ engagement, reasoning abilities and communication skills. Baldwin and Crawford (2010) examined the role of journaling which included drawing in a science lab and the student’s perception of their learning. They found overall students felt the illustrated journal had a positive impact on their learning; they became more aware of the plants morphology, the drawing process itself taught the students to “see” and understand the plants in a new ways, and they became more aware of their own learning. Drawing plants in particular helps overcome “Plant Blindness” (Wandersee and Schussler 1999). In this workshop we will examine the use of illustrated journals in botany class. Participants will be asked to draw a little too! This invaluable approach can be adapted for other science classes.

Using the statistical software “R” in Biology Courses (Mark A. Sarvary, Cornell University, NY, U.S.A.)

“R” is a comprehensive, programming, graphical and statistical software that will provide significant help with the statistical analysis needed for the research projects conducted in biology labs. It became one of the most popular statistical software in the biological sciences in the past few years. “R” is an implementation of the statistical programming language “S,” which was developed at Bell Laboratories. In every semester, nearly 400 students learn how to use “R” in our introductory biology course at Cornell University. In this workshop I will explain how to teach the basics of this statistical software to students who are not familiar with programing or did not take statistics before. The attendees can have a hands-on experience to learn how students can apply this software to analyze the data collected from their laboratory exercises. After a one-semester biology lab our students do not only walk away with laboratory skills, but by using “R”, they improve their statistical, mathematical and analytical skills as well. This new addition to our labs has been very successful, and the feedback from the students, TAs and other faculty has been overwhelmingly positive. “R” is a freeware, and compatible with Unix, Apple and Windows operating systems. The freeware can be downloaded from http://www.r-project.org/. In addition, I will also teach attendees how to use Rstudio (http://www.rstu d io.com/) that organizes graphs, scripts and variables in a user friendly way.

An introduction to gene annotation using the resources of the Genomics Education Partmership (Ken Saville, Albion College, MI, U.S.A.; Gerry McNeil, York College, NY, U.S.A.)

The Genomics Education Partnership (GEP) is a national, collaborative, scientific and educational project involving hundreds of undergraduate students in the investigation of a ‘real’ research problem in genomics. A major goal of the GEP is to annotate the genomes of several Drosophila species, using the genome of D. melanogaster as a reference. In particular, the GEP is focused on genomic regions in other species that correspond to chromosome four (also referred to as the dot chromosome) of D. melanogaster. The scientific interest is based on observations that the dot chromosome shows a mixture of heterochromatic and euchromatic properties. The research approach entails generating finished DNA sequence from the fourth (dot) chromosome of various species of Drosophila, annotating these sequences, and making comparisons among species to discern patterns of genome organization related to the control of gene expression. Students become deeply involved in investigating existing (and often competing) evidence for gene models within a region of DNA using a variety of web-based tools. Students exhibit strong learning gains typically associated with more traditional lab-based research experiences. This project is centered at Washington University in St. Louis (www.gep.wustl.edu) and has been used in a variety of educational settings, involving over a thousand undergraduate students at over 50 diverse institutions, mostly primarily undergraduate colleges. The intent of this mini-workshop is introduce the tools and resources of the GEP using a relatively simple gene annotation example, and to inform other interested educators of how to become involved in this innovative and rewarding educational effort.