Faculty Statements: Impact of GEP on Students

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  • PS - comments regarding problem solving
  • Ind - comments regarding independence
  • App - comments regarding application
  • PI - comments regarding Peer instruction
  • TW - comments regarding Team work/collaboration
  • PR - comments regarding Process of Research
  • Own - comments regarding Ownership
  • BK - comments regarding Bookish knowledge

Table S1: Faculty Statements: Impact of GEP on Students
Impact of GEP on Students Faculty Member/Institution Comment-Codes
Students felt energized about the opportunity to be part of a scientific inquiry. Students developed troubleshooting skills. They sense more responsability of their outcome work since they know it contributes to a nationwide research project in addition to have to demonstrate their work conclusions with hard evidence. They understood more biotechnology as when it is useful and what limitations it has. “Students around the country are given a unique opportunity to learn about gene sequencing by using the same software that the professional technicians use”. “I feel like I have applied much of my knowledge of genetics to the topic of genomics, and learned much more about it during this course. It is a very complex process and requires a great deal of work. This project has given me great insight into the way that genetics and genomics are playing a key role in the science world, especially in the future.” An opportunity “to experience first hand what it is like to work on genome sequencing, and in the process make a contribution to science”. Students experience team work with institutions outside its own. Annotation comment: “I think I gained a lot of confidence in the use of these different internet sites and have a better understanding of what each one does. Overall I think this way a very good learning experience” Consuelo Alvarez, Longwood University PS, Ind, TW, PR,
Own, BK

Students really appreciate working on an authentic research problem and contributing to the body of knowledge.They were both excited and scared to have this responsibility, but realized that the work they did lessened the work someone else would have to do on that gene sequence. They also realized that they need to critically evaluate other people's assertions because more information could change what was even clear to them. Culminating with a poster helps them bring everything together and give them confidence and some closure to the project.

Students are motivated and become more confident in their ability to contribute to the scientific community once they are intimately involved in annotating their gene. They realize the value they are bringing to someone else who is interested in this gene.

Student comments include:

"When I started I couldn't understand how we could help scientists with what we were going to do, but now I see how valuable my work on my gene is to another person."

"I learned that I could contribute to research."

"I first thought that her [teacher] talking about this as a real project was bogus, but now I see that someone else could benefit from the work I did."

Students recommendations for future classes: A. Start poster preparation sooner, B. Start understanding what the protein product does earlier in the semester and C. Have more active learning worksheets to cover the fundamentals as the semester progresses.

Cheryl Bailey, University of Nebraska
Students were excited about the project and participating in novel research.  The realization that their work was a contribution to our over all understanding of a model system enabled to students to take ownership of the project.  Then, when the work was difficult, the students really focused on the problem since they could see the need for the information that they were gathering rather then this simply being a difficult lab exercise for points toward their grade.  Graduating students wanted to know how the project was going to continue and students that would be returning the next semester wanted to stay involved. Additionally, it was clear that the students had a much better understanding of the structure of a eukaryotic gene than they would have received through a lecture based course. Daron Barnard, Worcester State College
After initial reservations and reluctance the students opened up to the idea of working on a challanging project that will result into a meaningful contribution to science. The topic of eukaryotic annotation, for their senior investigative paper (SIP), was new and exciting. Since the first two students finished and presented their SIP successfully, more students have expressed the desire to work along the similar lines for their senior projecs. Satish Bhalla, Johnson C Smith University
This was the first exposure to conducting research for many of my students. They learned that research was challenging, yet rewarding. They learned troubleshooting skills during the process. The feeling of pride that they were contributing to a larger research goal kept them motivated and made them evaluate their data in a more careful manner than they would have in a traditional lab setting. They also gained confidence in their ability to generate good data and in their understanding of genes and how genes work. Overall, I think the GEP project had a positive impact on the students. Vidya Chandrasekaran, St.Mary's College-California

Chitra Chandrasekaran, Texas Wesleyan University
Students learned that the process of conducting research is not a simple path; they have more confidence on their reasoning abilities and are less afraid of making mistakes. Hui-Min Chung, University of West Florida PS, Ind, App, PR

Catherine Coyle-Thompson, California State University - Northridge

Doug Dorer, Hartwick College
Students learned that research does not end in classroom. Research is dynamic and ongoing. Students improved their independent research ability and had better appreciation of real science research. Chunguang Du, Montclair State University
Some students have blossomed under the expectation of doing original research.  This was the first encounter with both the frustrations and rewards of doing research for most of the 20 students in our most recent class.  Students have gone on from the GEP experience to be successful contributors on other research teams. Todd Eckdahl and Jeff Poet, Missouri Western State University
Students have a very positive reaction to this course.  They report positive gains in learning how scientists tackle problems, and develop a much stronger sense of issues related to quality of evidence.  While there are frustrations to start, they learn by doing, and feel a real sense of accomplishment at the end. Sarah Elgin, Washington University Biology Dept

Donald Frohlich, University of St Thomas (Houston)

Anya Goodman, California Polytechnic State University-San Luis Obiospo
1) Knowledge increase:

a) All students learned the basics of comparative genomics, and learned how to read the major reference paper of a protein structure and how to visualize and analyze the protein structure, as well as the connection with its function by completion of the project on disease-related genes.

b) By completion of the gene annotation project, the students learned the basics of comparative genomics, the method of evidence-base gene annotation, as well as how to use online tools and databases such as GeneScan, FlyBase, ClustalW, NCBI BLAST, Genome Browser, and Expasy, etc.

c) Students learned more "vocabulary" (concepts) of genomics and biology from the GEP teaching materials. This facilitates the non-bio major students' self study and communication with biologists.

2.) Increased scientific communication ability - students are exposed to formal scientific writing (both from reading the literature and writing report and power point presentations) which train them to use correct, concise, and clear language

3. The gene annotation project encouraged self study of genetics and genomics and allowed students a purposeful means of investigating the various features of a sequence from DNA to RNA to protein and among species. This is a comprehensive research training helped students to develop their critical thinking and trouble-shooting skills. They learned how to adapt a simple protocol to tackle much harder, individual problems.

4. Due to the availability of web-based servers, students have the ability to work on the project at home. This decreases the demand for equipments compared to other research/lab based class.

5.The project is flexible enough to allow students to participate with diverse and sometimes incomplete backgrounds and still achieve an understanding of gene annotation. In this way they can fill gaps in their knowledge as well go into the depth in the paper that they wish. This impacts a student's sense of the scope of the field and can inspire a new found seriousness.

Yuying Gosser, City College, CUNY BK, Ind, PS, RP, OWn
Students take pride in their projects and are motivated by the fact that they are collaborating on a "real research" project with peers at other institutions. The class typically selects overlapping fosmids to provide a larger context to their individual projects and to illustrate the effectiveness of collaborative work. The notion of working on an open-ended question for which I may not have all the answers is disconcerting at first. However, as they grow into this, the tone of the room changes and students learn to think about the problem, be persistent and when they hit a dead-end, try alternative approaches - students working on overlapping fosmids become good friends! Charles Hauser, St. Edward's University PS,Ind,PI,TW,Own,
Students take ownership of their own project and take pride in what they can contribute to understanding it.

Students feel that they are doing cutting edge molecular biology and joining in the scientific community. It’s good to see them collaborating and helping each other with the projects.

In the short investigational labs at the end of my course, the students said they were confident in using the tools they needed because of what they’d learned in Finishing and Annotation.

Laura Hoopes, Pomona College Ind, PI, Own

Diana Johnson, George Washington University
Students overall have been very enthusiastic about the course, finding it challenging but particularly rewarding because of that. The fact that their results will be used outside the class -- by researchers in the "real world" -- has an impact. I try to choose fosmids which overlap for both finishing and annotation, so that students can collaborate with classmates for some problems they encounter; I think this is a better model for research than the more traditional individualism which typifies assignments in many classes. The open-endedness and flexibility are also good: students learn that sometimes to succeed they need to continue hammering away at a particular difficulty, and at the same time think about alternative approaches. It's all about doing the best you can with the resources available, and sometimes your best answer isn't very satisfying but is still the best possible answer -- this is an important and powerful realization. Chris Jones, Moravian College Ind, PS, PI, PR
My TA/student researcher has taken ownership of this project in a very definitive way, and is learning significant problem solving skills as well as conceptual understanding of gene and genome structure. As we seek to adapt this to a large classroom lab setting, we are particularly concerned with balancing time and learning: will there be sufficinet ownership of the problem(s) if working in small groups?  Should students first work independently and then share progress?  The latter is our planned strategy for this coming spring. 
Marian Kaehler, Luther College Own, App, Ind, TW
I will be implementing during July 2009. Stuart Ketcham, University of the Virgin Islands
Students were initially apprehensive and felt overwhelmed due to the extensive base of knowledge that they were required to know in order to complete the annotation research projects. Being a real research project gave the students a sense of excitement and also compelled them to learn more than they would in a standard lab project. Both of my students said annotation projects were a valuable learning experience where they gained insights into how real research was done. They had the realization that science research is often a collaborative effort, where they are contributing their data to a greater whole. Nighat Kokan, Cardinal Stritch University
Students working on this research project were very enthusiastic. An undergraduate Teaching Assitant was trained and he in turn was able to train several students every semester for a research class in genome annotation.

It takes a while for the new students to get completely familiar with the annotStudents were initially apprehensive and felt overwhelmed due to the extensive base of knowledge that they were required to know in order to complete the annotation research projects. Being a real research project gave the students a sense of excitement and also compelled them to learn more than they would in a standard lab project. Both of my students said annotation projects were a valuable learning experience where they gained insights into how real research was done. They had the realization that science research is often a collaborative effort, where they are contributing their data to a greater whole. ation project, but they are always very enthusiastic and once they grasp the concepts, they are very motivated. I found that it is very important that they understand that their project is part of a larger genome annotation project. Students became more enthusiastic knowing that this was part of a bigger research project and that they were collaborating and being part of this process. Once they understand this, they are more dedicated to their work because they can see the importance of doing a good annotation. When students stumbled during the process, they became very creative and discussed the particular problem with intensity. This created a great environment for learning from peers and ample discussion that led at the end to solutions to that problem. They became very good at troubleshooting and felt the importance of the project and the need for accuracy.

Olga Ruiz Kopp, Utah Valley University
The course has has a variety of impacts on student perception of research, teamwork in research, teaching laboratories and their own creative abilities. Their initial level of frustration with the challenges of bioinformatics was replaced with increasing confidence in their ability to achieve set goals, an increasing excitement with the discovery process, and a recognition of the rigor of scientific research.  It has also revitalized my teaching of of undergraduate laboratories, broadened the involvement of students in research (specifically underrepresented groups in science), and created a paradigm where students can also conduct undergraduate research.  Gary Kuleck, Loyola Marymount University
The students reaction to the course (in all three formats used) was very positive. The fact that they were doing something novel and that the project was theirs was both scary and exciting for them. At first they thought they could not acomplish anything but this changed over time and they became more and more confident and excited about generating results. They learned that you can't always ask someone for the answer and that it was possible that they had to figure out a problem that was unknown to even the instructor. Overall, they felt that this experience was even better in some ways than their experience in the research lab because they could quickly figure out the techniques used to solve the problems and use them to produce results. Sometomes in the lab they felt like it was hard to learn techniques and never seemed to learn enough to solve a problem, only a part of it. Therefore, at least for my students, they felt it was an excellent complement to their experiences in the research lab. Gerard McNeil , York College-City University of New York

Robert Moss, Wofford College
The TMC students definitely had ownership of their project and were quite excited to be a part of a larger project.  They were somewhat surprised by the process of research, in that they mentioned the discrepancy between the information presented in textbooks (often only one brief sentence) and the reality of doing real research with the uncertainty and the amount of time involved for progress.  They felt that their current book knowledge of the genome did not include anything to prepare them for this annotation project.  However, in their curriculum, there was only one course where that type of material would be addressed in any fashion (an optional molecular genetics course), so these particular students would not have been expected to have much background in this area.  The students particularly liked working together, and that they were a part of a larger group of students across the nation.  Because this group did not have the background, and did not have much time each week to work on this project, they did form a good team but were not as successful as peer instructors and did not develop much independence in their work.  They did not feel completely comfortable to move forward without help, but again, this was most likely due to the time constraints and the fact that they did not have sufficient background in their previous coursework to allow them to make great leaps forward in their thinking about annotation and the genome.  They did all say that they had a greater understanding after this research experience, and also that they realised that all research was not as straight forward as they had expected.
Jennifer Leigh Myka, Galen College of Nursing Own, PR, BK, TW, PI, Ind
Our students were very enthusiastic about this course.  They got so involved that they took on more work than we had assigned.  The fact that none of us knew the "right" answer made them feel more like colleagues than students.  One of the students, planning to be a physical therapist, was so excited that she began asking us about career opportunities in this field.  They left the course with greater appreciation for their own abilities and for the frustrations and delight in doing science. Alexis Nagengast, Robert Morris, Widener University

Our first-year students benefitted greatly from the outside-class help of out peer tutor.  We received many wonderful comments about how helpful he was.  We challenged the students a great deal in this course, and having another student to help them made the workload bearable.

By challenging these students to solve the open-ended problem of annotating a section of a genome by working together in teams, we were able to introduce them to how to aproach research work.  The students were clearly challenged, but in the end were successful and we believe better prepared for the course work and research endevors they will encounter in the future.

Paul Overvoorde, Libby Shoop, Macalester College PS, PI, TW, PR
My students were extremely enthusiastic about the project.  They appreciated that they were involved in a real research project and contributing to science.  One student said that the project had increased her self-confidence. Another student said she enjoyed writing her annotation paper because it was on research that she performed, not just another literature review.   I was very pleased to see that the students remained engaged in the project throughout the semester.  Some of the students will be using their annotation project for their senior capstone project.  I hope to also take students to the 2010  Drosophila meeting in Washington, D.C.   Susan Parrish, McDaniel College PR, Ind, Own

Kelynne Reed, Austin College
Students are intrigued by the novelty of the annotation projects at the beginning of the semester. By mid-term, most remain on target, are enthusiastic and continue to work on their projects outside of class hours (a necessity of which they are informed at the beginning of the semester because the course is a one hour per week class).  When they present their projects in power point format at the end of the semester, their exuberance is a delight to behold.  Students are confident and excited about the research that they have performed.  At least three students each year (2 years) have asked if they can continue to work on annotation projects, a pool from which I have chosen a TA for the following year.  Gloria Regisford, Prairie View A&M University
Although the students are frequently overwhelmed at first with all the new concepts and data, they eventually figure out what to do and how to do it.  It is not surprising that the best students do well on the finishing and annotation, but even poor students are able to figure it out and do a good job.  For some students, the light bulb that turns on in their head when they figure out what they should be doing gives them a real sense of accomplishment. Dennis Revie, California Lutheran University PS, PR
This exercise (annotation) was very revealing about the students deep understanding surrounding the crucial topics of genes and gene structure in eukaryotes. Although all of my students were upper-level Biology majors (and most headed for medical school), until they got their hands on actual sequences, they didn't really understand the nuances that they've heard since their first college-level Biology course. Particular trouble spots were revealed about the structure of exons ("Do all exons have to have a start codon? A stop codon?") and splice variants ("What does it mean that part of an exon doesn't code for protein? Why is it that some variants code for the same protein?").  Hence, GEP has instituted a pre-test/post-test to gauge student learning as a result of their GEP experiences. Anne Rosenwald, Georgetown University PS, App, PR, BK
The students were very enthusiastic about this course, beginning the semester before the course was offered. They really embraced the concept and the process. It was clear that they enjoyed working on something that was new and didn’t involve extensive review of basic concepts they had learned in other classes. They also benefited from the sense of teamwork, shared responsibility and shared accomplishment throughout the semester. They all were also thrilled about the potential to be co-authors on a research publication, and enjoyed the opportunity to present their research to the campus community. Many of these students will be attending graduate school or medical school and will benefit greatly from the experiences from this course. Kenneth Saville, Albion College

Stephanie Schroeder, Webster University

I have had a variety of responses from students.  Many have been frustrated by the lack of clear answers and having to find things out for them selves.  Others have been excited by the same features.  Most students really believe that they learned a lot from the course and several have gone on the jobs or graduate programs where the specific skills of annotation and sequence finishing have been useful.  They agree with students from other schools that doing the annotation helped them picture gene structure and get a beter understanding of genetics.  I used some of the other curriculum resources in a genetics lab and the students really liked those exercises.  Two of the students who served as TAs enjoyed the peer tutoring interactions and benefitted greatly form the opportunity to teach others what they knew.
Mary Shaw, New Mexico Highlands University PS, PI, App
For most of the students who took this course, it was their first exposure to true inquiry-based learning.  They enjoyed the discovery aspect of the course and expressed a sense of accomplishment that is only attainable when one is discovering something new.  One student got a job immediately after taking this course during his final year at a company that provides sequencing, finishing and annotation services.  His future employer was pleasantly surprised when I told him of this course during a telephone reference call.  I was met with similarly positive responses from other future employers or graduate school faculty when I told them of other students who took this course.  While they were not hiring, or admitting, individuals to perform these specific tasks, they were impressed that our students were exposed to this sort of discovery-based course. Gary Skuse, Rochester Institute of Technology
At our institution, the GEP annotation project is incorporated into an introductory bioinformatics and genomics course. The course includes predominantly undergraduate biology majors, a few MS degree-seeking students, and occasionally students with a mathematics or computer science background. This course is the first introduction of most of the students to bioinformatics and genomics, and more importantly, to in silico experimentation. We focus on the GEP annotation project to give the students an in-class collaborative research experience and practical experience in genomics and bioinformatics. The annotation project requires students to apply concepts learned in molecular biology, genetics, and biochemistry, integrate their knowledge, and learn science the way it is practiced by biological scientists. Students are challenged to solve a portion of a larger cutting-edge research problem that is being investigated by a broad scientific community. I think they appreciated that fact. The 2013 class was more successful than students in the past in resolving more projects. I was impressed with the effort that they put forth in trying to answer the challenging post quiz questions. I was pleased to observe students applying critical thinking skills.They were taking their time with each question on the post quiz. They did not easily give up. I think they realized that the course had promoted problem solving throughout the semester. The attitudes at the end of the semester were very positive. Students enjoyed the class and one student asked if she could work on additional problems during the summer. One student is working with other faculty members on a next-generation sequencing project to analyze data for viral sequences.
Mary Smith, North Carolina Agricultural & Technical State University PS Ind App PI - TW PR

Chris Smith, San Francisco State University

Impact on Students:

I found a few impacts on both students and faculty:

Investment:  The students were invested in this work.  The amount of effort and personal satisfaction they showed was similar to what is seen at an independent study poster session at graduation.  What they were doing was "their" work, and it was important to them.  There did seem to be a little healthy competition within the course, especially during the finishing.  First to close a gap, first to close all the gaps--these were milestones that warranted a Wooooo! from their classmates, along with a good-natured "I was almost there!" gasp from another student.

Depth of Understanding:  After performing the finishing, the class had a much better understanding of what a specific base call actually means at a position--not all data looks like it does in the textbook.  They even took home a much better understanding of splicing after calling intron after intron.

Impact on Faculty:  After showing other faculty how well my first semester worked with the GEP, a number of faculty are looking into introducing this type of inquiry based teaching into their laboratory courses.  It can be a little scary for both student and faculty not knowing what the outcome of today's lab period "should" be, but that makes the outcome even more rewarding. 

Eric Spana, Duke University Own,PR,BK
This model of teaching, in which students need to use what they have learned in lecture/discussion formats to apply to a research situatiion, makes the entire process of education more meaningful and purposeful to them.  This week, more than six months after their genomics projects ended, some students brought up (unprompted and in another context) how exciting that class was for them.  They really liked the idea that they could contribute meaningful information to scientific research, and took great pride in being young scientists.  I think this type of experience is a powerful way to show students both the excitement and challenges of scientific work.  As in most classes, there was a great deal of difference among students in interest, tolerance of ambiguity, computer skills, focus, and basic knowledge of DNA and protein structure.  This translated into various levels of "success" in terms of completion of their projects.  Some were very frustrated at not having clear-cut, predetermined answers.  However, everyone at the end felt pride of accomplishment and ended up enjoying the process. Mary Spratt, William Woods University

Joyce Stamm, University of Evansville
While it took students awhile to get up to speed on the annotation project, once they got going, they truly embraced their role in this project.  The fact that it is "real research" gave them a powerful motivator to take this work even more seriously than they do their traditional coursework. The students were very excited about the prospects of being co-authors on a publication, and students from my class continue to ask me what the current status is of the project (six months after the course ended). 

I can't say that this particular project is necessarily a more effective motivator than the semester-long projects that we use in many of our upper-level elective courses (all of our courses have lab components).  But being connected with a large university for this project certainly added a sense of importance to the project that I believed served as an important motivator for the students.

Jeff Thompson, Denison University Ind, PR, TW, Own
Watching students go from ‘knowing’ how genes are constructed, to seeing and truly understanding gene structure was amazing. It was also fun to watch students get hooked on genomics as part of a research team that had a broad and clear scientific goal – I wouldn’t be surprised if a few of them move forward with genomics as a career, and I have no doubt that the skills learned during manipulation of genomic databases will serve them well as they move forward in research-based careers in biology as well as other career paths. Matthew Wawersik, College of William and Mary TW, PS, PR, BK
Computer-assisted instructions using annotation as a tool for enhancement of research infrastructure and academic capabilities are hallmarks for implementing the Genetics Educational Partnership (GEP) program at our institution. Problem-solving activities presented through GEP further provide an additional opportunity to strengthen existing undergraduate research performance on model organisms for written reports and class presentations. Barbara Wilson, Jackson State University

Colette Witkowski, Southwest Missouri State University
My students developed an appreciation for some of the current stumbling blocks in genomic annotation-  what are some of the things that we would all like to know about a genome, but can't yet determine.  Some students realized that there are many examples of genes not conforming to the classic textbook example.  More so than in any class I  teach, I get students proclaiming, "now I get it", usually about halfway through the term.  This sense of accomplishment often spurs them to a few days of wildly inspired annotation.  After getting involved in genomic annotation and a real reserach project, some of my students realized that they really liked molecular genetics.
Jim Youngblom, California State University-Stanislaus PS, Ind, BK