Incorporating a collaborative web-based virtual laboratory in an undergraduate bioinformatics course

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<ul><li><p>Article</p><p>Incorporating a CollaborativeWeb-Based Virtual Laboratory in anUndergraduate Bioinformatics Course</p><p>Received for publication, October 6, 2009, and in revised form, October 29, 2009</p><p>DavidWeisman*</p><p>Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125</p><p>Face-to-face bioinformatics courses commonly include a weekly, in-person computer lab to facilitate activelearning, reinforce conceptual material, and teach practical skills. Similarly, fully-online bioinformatics coursesemploy hands-on exercises to achieve these outcomes, although students typically perform this work offsite.Combining a face-to-face lecture course with a web-based virtual laboratory presents new opportunities forcollaborative learning of the conceptual material, and for fostering peer support of technical bioinformaticsquestions. To explore this combination, an in-person lecture-only undergraduate bioinformatics course wasaugmented with a remote web-based laboratory, and tested with a large class. This study hypothesized thatthe collaborative virtual lab would foster active learning and peer support, and tested this hypothesis by con-ducting a student survey near the end of the semester. Respondents broadly reported strong benets from theonline laboratory, and strong benets from peer-provided technical support. In comparison with traditional in-person teaching labs, students preferred the virtual lab by a factor of two. Key aspects of the course architec-ture and design are described to encourage further experimentation in teaching collaborative online bioinfor-matics laboratories.</p><p>Keywords: Collaborative learning, bioinformatics, molecular evolution, online education, virtual laboratory, studentpeer review, web-enhanced, NCBI.</p><p>As bioinformatics has become a standard tool of scienticinquiry, application-oriented bioinformatics courses havebecome routine offerings at the undergraduate level [14].These classes typically integrate a face-to-face lecture witha weekly teaching laboratory, following the traditional para-digm used in courses such as cell biology, genetics, and bio-chemistry. As with wet-lab training, the bioinformatics labo-ratory reinforces the conceptual course content and pro-vides a broadly-applicable practical skill set. Commonly intraining labs, the class divides into small groups that performan exercise, implicitly creating an informal collaborativelearning environment.In distance education bioinformatics courses, the labora-</p><p>tory paradigm has been moved to an online setting [57],taking advantage of web-based learning tools. Whenthoughtfully applied, these technologies can foster a richeducational experience and encourage collaborative learn-ing. However, despite the web-centric nature of bioinfor-matics itself, and despite the wide availability of web-basedlearning environments, face-to-face bioinformatics courseshave retained the traditional on-site teaching laboratory.Combining the strengths of an in-person lecture with aremote web-based laboratory presents a new opportunity toimprove bioinformatics education.</p><p>An upper-level undergraduate, face-to-face, lecture-onlybioinformatics course has been taught at the University ofMassachusetts Boston since 2003. As part of a comprehen-sive course redesign, we hypothesized that students wouldbenet from the addition of a web-enhanced, collaborative,virtual laboratory. To study this hypothesis, the course wasaugmented with a substantive and required online compo-nent, and student opinion data was collected near the end ofthe semester. The experiment had several subcomponents:to test whether collaborative learning was practical in anonline bioinformatics lab, to test whether student groupscould provide peer support for routine questions regardingbioinformatics tools, and to compare the virtual lab with pre-vious experiences in physical labs. This article describes thearchitecture of the course, reports quantitative and qualita-tive student data, and provides suggestions for teaching avirtual laboratory in similar bioinformatics classes.</p><p>COURSE OVERVIEW, CONTENT, ANDMETHODOLOGY</p><p>The bioinformatics course is offered through the UMassBoston Department of Biology and is targeted primarily toupper-level biology undergraduates. The prerequisites are atwo-semester introductory biology sequence, a one-semes-ter genetics course, general chemistry, and college-levelalgebra. The experimental course ran during Spring 2009with one instructor and no teaching assistants. Of the 50 stu-dents initially enrolled, 48 remained after the add/drop date,and of those, ve withdrew. The 43 students who completed</p><p>*To whom correspondence should be addressed. E-mail: David.Weisman@ acm.org</p><p>DOI 10.1002/bmb.20368 This paper is available on line at http://www.bambed.org4</p><p>Q 2010 by The International Union of Biochemistry andMolecular Biology BIOCHEMISTRYANDMOLECULARBIOLOGYEDUCATIONVol. 38, No. 1, pp. 49, 2010</p></li><li><p>the course had majors of BS-Biology (n 37), BS-Biochem-istry (1), MS-Biology (1), BA-Anthropology (1), BA-Psychol-ogy (1), and unknown (2). The class breakdown was eightjuniors, 34 seniors, and one rst-year graduate student.Three strong unifying themes provide a coherent and cen-</p><p>tral framework of the course, and these themes echo andinterplay constantly throughout the semester. First, studentslearn about mechanisms of molecular evolution, and howselection frequently conserves sequence, structure, andfunction. At this point in their education, students have brieyencountered these ideas in their introductory biology andgenetics classes, but most have not internalized that molec-ular-level evolution is a pillar of modern biology. In thisregard, the course is effectively a primer in the theory andpractical consequences of molecular evolution. The secondrecurring theme describes the exponentially-growing volumeof biological sequence data, including its curation, storage,and retrieval. The course stresses the enormity and value ofthis resource, and how sequence data provides a direct win-dow into molecular evolution. The nal theme is the richnessand practical value of cross-linked data, for example, howhuman diseases and drug targets are found in research liter-ature, how research literature links with gene sequences,how gene sequences link with homologues and proteindomains, and how protein domains link with structural data.Using this conceptual framework, the course covers stand-ard introductory bioinformatics topics including PubMed,Online Mendelian Inheritance in Man (OMIM), GenBank,sequence curation and RefSeq, local alignment andsequence database searching, multiple sequence alignment,substitution matrices, phylogeny, gene feature prediction,protein domain architecture, protein modeling and visualiza-tion, and systems biology. Mathematics and computer sci-ence are not emphasized, although the lecture introducesrudiments of probability, statistical inference, and distancemeasure in high-dimensional space, as well as the notions ofcomputational intractability and heuristic algorithms.The virtual laboratory was conducted over Blackboard</p><p>Vista (http://www.blackboard.com/). At the beginning of thesemester, the class of 50 divided into 10 lab groups of vestudents each. A group size of ve was chosen to create acritical mass that fosters meaningful collaboration, whileavoiding the diffuse impersonality of a much larger group. Asis common in wet-lab courses, students chose their owngroups and retained their group membership over the se-mester. Because web-enhanced collaborative learning wasnew to most students, the instructor conveyed strongexpectations of active participation throughout the semester.Both in the syllabus and in lecture, students were informedthat 25% of the nal course grade represented the qualityand quantity of online collaboration, and a detailed gradingrubric was also provided. Collaborations occurred withinBlackboard Vista threaded group discussions; journal andblog software was not employed.Students could read and post messages within their spe-</p><p>cic online group but could not access discussions in othergroups. In addition to their private groups, everyone was alsoenrolled in a single class-wide group that was frequently usedfor clarifying lecture concepts and helping with bioinformaticstools. Instead of privately e-mailing the instructor, studentswere strongly encouraged to use the class-wide group for all</p><p>topics of general interest. Because multiple students oftenhave nearly identical questions, this tactic likely reduced thevolume of redundant instructor e-mails and redundant ofcehour tutoring sessions. A tight feedback loop occurred as theinstructor monitored discussion groups for gaps in compre-hension, and addressed these gaps in the next lecture.Two major course components were conducted within the</p><p>virtual laboratory: weekly laboratory assignments, and sev-eral cycles of peer review of the nal project. As in a tradi-tional class, the weekly laboratory assignments were closelycoupled to the lecture topics. Lab cycles ran Friday-to-Fri-day and had the following steps:</p><p>1. Each student ran a bioinformatics experiment.Depending on the particular assignment, experimentswere identical for all students, or were varied by the in-structor in specic ways, or were varied based on stu-dents nal project topics.</p><p>2. Each student posted initial ndings and interpretedtheir results. Students were required to post by mid-week to facilitate substantive collaboration during theremainder of the week.</p><p>3. The group discussed the ndings and interpreted theresults.</p><p>4. Each student was graded for the experimentalapproach and results, as well as for collaboration inthe online discussion.</p><p>The lab exercises were similar to those used for conven-tional bioinformatics homework, although enhanced to facili-tate group discussions. For example, everyone ran a BLASTfor a single assigned gene, but each student chose analtered set of query parameters. Options included searchingby mRNA or amino-acid sequence, changing the substitu-tion matrix, altering gap penalties, specifying a database,and choosing a search algorithm. Students posted theirresults, and collectively interpreted the relationshipsbetween algorithm parameters and BLAST outputs. Stu-dents observed how various BLAST approaches wereappropriate for specic biological investigations.The virtual laboratory experiments were performed using</p><p>standard web-based bioinformatics tools and databases. Thebulk of the work was performed at NCBI, and students werealso encouraged to nd and explore other tools. Purchase ofbioinformatics software or services was not required. To intro-duce practical use of the tools, in-class demonstrations pro-vided a general overview of the experiment workow; how-ever, detailed, cookbook-style instructions were intentionallynot provided. Instead, students were taught to become self-sufcient in locating and reading bioinformatic tool documen-tation. In addition, students were strongly encouraged to asktheir online peers for help when encountering mechanicalproblems. This peer-support practice was designed toincrease active learning, foster collaboration, and reduce thetechnical support burden of the laboratory instructor.For the nal project, students produced a substantive writ-</p><p>ten report that described bioinformatic analyses of a gene.Students performed research and wrote their reports individ-ually, and each was also required to provide constructivefeedback to the peers in their group. The project began earlyin the semester, giving students an opportunity to experiencea broad-themed bioinformatic study that closely related to</p><p>5</p></li><li><p>the lectures and labs. As a rst step, after learning about</p><p>PubMed, review papers, OMIM, NCBI Bookshelf, and Gen-</p><p>Bank, each student found an interesting gene to study. Many</p><p>chose genes related to human diseases, often from an inter-</p><p>est in a medical career or from rsthand knowledge of</p><p>affected individuals. Several weekly lab assignments directly</p><p>supported the nal project by requiring specic analyses of</p><p>the students chosen gene. Overall, the nal project was</p><p>designed to maximize student engagement and learningthroughout the semester, to connect the major themes andunits of the course, to develop critical thinking and scienticwriting skills, and to assess individual performance.Milestones were required at specic dates, and are shown</p><p>as weeks from the beginning of the semester:</p><p> Week 4: Gene and topic choice, GenBank or Refseqaccession numbers for gene and protein, and briefreview of literature with citations</p><p> Week 11: Paper outline Week 13: Paper draft Week 14: Near-nal version Week 15: Final version to be graded</p><p>Following each checkpoint, students were required toread and provide constructive feedback on their peers post-ings. This peer review process had several goals: to exposestudents to a collaborative review practice common in aca-demia and industry; to raise the groups overall performancelevel; to prevent last minute surprises over project scope andexpectations; and to cross-pollinate ideas within the group.</p><p>RESULTS</p><p>Survey Results</p><p>To quantitatively test the hypothesis that the virtual labora-tory was benecial to learning bioinformatics, students werepolled two weeks before the end of the semester. Figure 1describes the resulting data. The rst group of questionsevaluates the benet of collaborative learning in the virtuallaboratory. Questions A and B measure benets of askingand answering online questions, respectively, and QuestionC measures the benets from passive observation. On thesepoints, the data broadly support the hypothesis that collabo-ration in the virtual lab was benecial. Question D examinedwhether students found their peers to be helpful in a techni-cal support role; the large majority of students found benetfrom this service.Question E asked whether students preferred a traditional</p><p>lab experience to the online lab. Based on the course pre-requisites, students had previously completed at least fourtraditional wet-lab courses. With that background, approxi-mately two-thirds preferred the virtual lab, and of those, thelarge majority strongly preferred the virtual lab. The responseto Question F supports the hypothesis that homework con-ducted within the virtual lab contributed towards learning thecourse conceptual material.As bioinformatics is an interdisciplinary eld and can be</p><p>taught from multiple perspectives, and given that this courseintentionally emphasized a biological perspective, QuestionG tests whether that emphasis successfully integrated bioin-formatics with core biological principles. To examine whetherthis emphasis corresponded with students interests, Ques-</p><p>tion H asked whether more mathematics and computer sci-ence should be taught. Responses to these queries indicatethat the course achieved its goals of presenting bioinfor-matics within a biological framework, and that this particularemphasis meshed with student interests.</p><p>Examples of Student Collaboration</p><p>To illust...</p></li></ul>

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