Faculty Statements: Lessons Learned During Implementation

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  • CS - # of students
  • Org - "SA" for stand alone course , "LS" for a section of a larger course, or "IS" independent study. 
  • HA columns - Estimated number of total hours spent on all GEP related activities including lecture, lab, discussion, in annotation;
  • HF - Estimated number of total hours spent on all GEP related activities including lecture, lab, discussion, in finishing

Table S2: Faculty Statements: Lessons Learned During Implementation
Lessons Learned During Implementation Faculty Member/Institution CS Org HA HF

Students learned about new software tools like Consed and all options of Blast. They used these tools and thus understood their utility and applications.
Students’ work tends to become tedious and repetitive.
At the end of the semester, students felt more confident with the all aspects related to finishing/annotation projects than when they came into the class.
Although some projects were not totally completed, students did not see that as a failure.
Students approaches to computer research work is much different and sometimes opposite to bench research work.
Students developed skills to troubleshooting their own projects although some are unenthusiastic to take decisions and search on their own.Team work is highly encouraged along the semester.

Consuelo Alvarez, Longwood University 4 SA 42 42
2 IS 42 0
A. Basic concepts of e-value, score, six-reading frames, genes, intron/exon boundaries, etc., was best introduced in an active learning environment. I used process-oriented guided inquiry learning (POGIL) with students in groups. This facilitated further interactions among students when they were working on their genes. I need to generate more activities for group work on Drosophila chromosomes and evolutionary trees.

B. We found that having a word file of the genomic sequence including some surrounding sequence of the gene of interest serves as a visual aid. This sequence file allows the following notations that provide students with a reference sequence to go back to. Notations included: highlight exons in bold type, introns in lighter text, put a line through all other sequences, highlight ATG in green, highlight stop codon in red, color nucleotides at both ends of exons that contribute to a codon.

C. We found that using a small program called "Gene runner" allowed students to easily search genomic sequence in the context of 6-reading frames.

Cheryl Bailey, University of Nebraska

Implementing a GEP annotation project as independent study, I found that it was very important to have students working together.  The first semester, I had a single student working on annotation. In a subsequent project, I had two students working together on an annotation project and found the students were able to do more of the work on their own as they discussed their findings and difficulties with each other.  When it was a single person, the experience was a little isolating and easier for the student to get stuck in a rut.  The single student also was unable to really participate in and observe the collaborative nature of science.
Daron Barnard, Worcester State College

Students easily pick up on the software tools like BLAST. It is the interpretation that is challanging.

We used portions of the GEP material for 2-3 weeks in the Bioinformatics class. Encouraged by the results and support from GEP, we will be starting a Genomics class in the coming academic year. We also plan to start a student/teacher partnership research program on annotation, in collaboration with a near by research center.

Satish Bhalla, Johnson C Smith University 12



The things I learnt from  my implementation last Fall :

1) It is necessary for students to see the big picture about the relevance of the project. Also, they need to understand that the tools used in the annotation project can be used on other genomes and they are learning useful skills.

2) The students need to take ownership of their project. The students put in a lot of effort into annotating the fosmids and completing their projects, much more than in a regular lab project. I had two people working as a team on each fosmid. My hope was that I could use the data from one person on the team to that of the other as a control. This check did not work because they worked in pairs most of the way and did not independently annotate the fosmid. However, the team setup did help them with trouble shooting.  Next time, I will set it up so they work on the first gene as a pair and then each one independently annotates the fragment, so we can compare their annotations.

3) It was difficult to do this project with 16 students and no TA. However, it made the students teach each other - which helped me figure out their weaknesses and address them. It also helped them learn problem solving skills and understand the concepts better.

4) Since the course was not described in the books as a genomics/ bioinformatics lab, there were a couple of students who were disappointed that they only got to do a computer lab throughout the semester. They enjoyed the annotation part and the visit to JGI, but I am not sure the finishing demo helped them. Next time, I am planning to intersperse the annotation labs with gene expression or SNP mapping labs to give them some more wet lab experience.

Vidya Chandrasekaran, St.Mary's College-California

Chitra Chandrasekaran, Texas Wesleyan University

Providing students practices that focus on one issue at a time helped them connect dots. Having students taking turns to lead open discussions is a good way to track students’ progress. Hui-Min Chung, University of West Florida 7

Catherine Coyle-Thompson, California State University - Northridge

Doug Dorer, Hartwick College

Basic computer skills are neccesary for the students to have. I installed Consed into my unix workstation and students as client can login to my workstation for accessing the Consed software. It is always a challenge for the first of a couple weeks to setup student's client computers. After the system setup, students took lead and worked on their projects with some help of TA and myself. However, students often had difficulties for closing the gaps. Chunguang Du, Montclair State University

Students find the work both frustrating and rewarding.  Team-teaching the course with one faculty member from biology and one from mathematics has presented opportunities to model interdisciplinary communication and different perspectives has been well-received by both students and administration.  Having an established end-of-experience poster session has encouraged students to think not only about their finding but also about how to effectively communicate their findings to a more general audience.
Todd Eckdahl and Jeff Poet, Missouri Western State University

Students need ownership of their work; this can come not only from experimental work (finishing), but also from computer-based work (annotation).  While collaboration can be effective (working with a partner on Chimp Chunks was a good introduction to annotation), I therefore prefer to assign each student their own project that they are responsible for, whether a fosmid or a gene (will depend on the time available).  While this is research - and one cannot grade in any specific way based on outcomes - one can assign letter grades based on graded training excercises and the final paper/presentation; here we look for reasoning from evidence.  Teaching in this mode - "live with the data bases" - is challenging, as both software and data bases change constantly; but the positive response of the students makes it worth while!  The quality of the data generated has been very good.  Genomics seems to be a very good area for student-scientist partnership. Sarah Elgin, Washington University Biology Dept

Donald Frohlich, University of St Thomas (Houston)

Anya Goodman, California Polytechnic State University-San Luis Obiospo

1. Since 2003, we have offered 12 bioinformatics workshops ( winter, 3 days, summer, 3-4-6 weeks), the attendees were composed of approximately 45% to 55% engineering students. This indicates that the engineering students are interested in the research topics in genome science. However, they have no time to complete the pre-requisites to take the research oriented genomics and bioinformatics course. We can conclude that expanding genomics education to engineering and non-biomajor students is to meet a demand and a challenge of current science education.

2. Because we are trying to offer the genomics education course to engineering students, and freshmen and sophomores, we found it is necessary to start from Central dogma, and introduce protein structure visualization and homology modeling. By finishing the first project on protein structure modeling, the students became familiar with many vocabulary of biology, and the tool BLAST, CLUSTALW, as well as literature reading. This prepared the students for taking on the next project on gene annotation.

3. Gene annotation project provided a focus to our bioinformatics course. Students, ranging from sophomore, to Freshman, and to High Schools, are exposed to a research field early in their education. This course prepared students in many aspects for further engaging in research, from literature reading to informatics technology, from rigorous checking of the coordinates to broad similarity searching and from summary of results to writing a complete research report.

4. The web-based teaching materials can be adapted to provide instruction to different levels of college students, from freshman to senior. Level of difficulties and amount of course materials can be adjusted accordingly. Therefore, the class can be given to a wide range of students from many different disciplines.

5. The students can really be the best teachers to each other for troubleshooting tips and efficient procedure advice.

6. Although group work may be helpful for larger projects, individual work on one full contig or fosmid helps to have a more cohesive understanding of the whole project, from beginning to finish.

7. In explaining the annotation procedure, such as identifying the splicing signature using Genome browser, it is important not to skip steps the first time and be sure that everyone is following by getting frequent feedback at key junctures. 'Pictures are worth a thousand words'. Visuals emphasize and explain things much more quickly than longwinded sentences.

Yuying Gosser, City College, CUNY

Students are typically enthusiastic in tackling both annotation and finishing projects and embrace the ‘ownership’ aspects of the projects. The labs offer an open and collaborative atmosphere, which students appreciate. Students are very willing to demonstrate to the class how they solved a challenging aspect of their finishing or annotation project - a trait I do not normally find in more traditional courses. The annotation projects anchor concepts of eukaryotic genes and splicing students experienced in molecular biology – a common refrain is, “oh that’s what was meant by ….”. Capping the course off with poster presentations at a university-wide colloquium has encouraged students to think critically about their data and how to effectively communicate their findings to their peers.

Charles Hauser, St. Edward's University 9
Students approach both annotation and finishing with enthusiasm, even though parts of it can seem repetitive to the professor.

More practice with the restriction enzyme pattern matching would be helpful.

Students felt that finishing first would have worked; they didn’t find the Consed software as difficult as I anticipated.

If I resist telling them exactly what to do and tell them instead which of the practice exercises covered the concept they’re struggling with, they develop that independence they need to carry out a research project. And they work together more. What one understands puzzles another, very often.

Laura Hoopes, Pomona College

Diana Johnson, George Washington University

1. Computer setup is still problematic. A number of idiosyncratic issues (peculiar to our IT situation) cost us a week or two this year. Run through procedures as much as possible with the actual setup before classes begin (if this is possible; I'm dependent on our IT people for setup).

2. I'm still struggling with how best to bring students up to speed with the computer side of things; some students have essentially no facility with anything beyond word processing, chats, and downloading files while others have taken basic programming courses.

3. I need to more rigorously vet practice materials from GEP; they are excellent, but don't always align well with what we've covered in class and this causes some confusion for students.

4. I need to supervise students more closely; all deny having (many) problems once the mechanics of finishing and annotation are mastered, but then some complain in evaluations of not having enough guidance. Finding the right balance continues to be a challenge.

Chris Jones, Moravian College 6
We - my student researcher and myself - worked independently on a second cosmid, following the workshop, to reinforce the process of annotation.  It was very helpful to have deadlines with specific targets for completing the work.  We will be adapting the GEP curriculum for a 3-4 week annotation and gene fine structure unit to be integrated into our Genetics course, a sophomore/junior majors course.  First run will be spring of 2010.  (Numbers listed are expected outcomes for that course.)
Marian Kaehler, Luther College 60
I will be implementing during July 2009.
Stuart Ketcham, University of the Virgin Islands

Only annotation projects were implemented in the lab portion of a genetics course and continued as independent projects in another course. Implementation of GEP projects in the classroom was definitely challenging for the first time, but subsequent implementations should become easier for the instructor. Students should be “warned” of the challenging nature of the projects and also be reminded that in the end it would be an extremely rewarding experience.

If adjoining contigs are being annotated, the instructor and students should examine their data as a group to ascertain any overlapping regions and genes on different contigs. This would eliminate duplication of effort by different students in the class.

Emphasize to students the value of recording their data and programs used in collecting data from different databases. The students should keep a record of their work in a Word document and save multiple copies of their work /data.

Nighat Kokan, Cardinal Stritch University 12
Students need to understand the importance of the project and the impact the project has. This makes students more enthusiastic about their annotations. After each group of annotated genes is done, students must give their reports and upload the data. For students that become involved in the project more than one semester, t is important that they keep record of the history of the genes they have annotated. Peer learning is very important for students to develop confidence in their annotation. Olga Ruiz Kopp, Utah Valley University

Annotation focus: I have found, after 3 years of implementation, that students get excited by seeing a big picture (e.g. genic structure in a larger chromosome region) and then being taught how to examine the data to build a gene model, followed by a global analysis of synteny, etc. While students adapt well to the work of annotation after the initial learning curve, their follow-through to completion is enhanced by a team effort. I usually have all students work on their original fosmid, then submit their efforts to a ‘global’ effort of annotation of contiguous fosmids with all students participating. Some of the students get particularly excited about seeing the structure of genes in a larger region and even documenting chromosomal rearrangements. Even though the gene model and annotation are the publishable bits, having students present their analysis at conferences is especially exciting and motivating to most.
Gary Kuleck, Loyola Marymount University

Spring 2008 Independent Study

The semester went really well although I had only three students which made implementation and monitoring progress easy. I think with more students as I will have this coming semester, some organized method of monitoring student progress will be important for both finishing and annotation. I think students presenting their progress to the class periodically would be a great way to do this. It would help the instructor follow the progress and identify groups needing help and would help other students identify and solve problems in their own fosmids. Encouraging interactions between students was a great benefit. At first I though it would be better if they worked more independently but I found they learned how to problem solve much better between themselves and got more out of it. This should be strongly encouraged.

It was amazing to learn how little students really knew about gene structure. They came in thinking they knew it all but quickly realized how much they did not know. It was a great lesson learned for them. It was also amazing how quickly the student became comforable with the applications and soon were better at consed then me. Overall, the experience for them was terrific in learning concepts, learning how to solve problems, and in their confidence in their ability to do complete something novel.

Spring 2009 Bioinformatics

This was the second run at running a GEP course and this time I implemented it as Btec 352, Bioinformatics. I had 6 students, all juniors, and 5/6 previously had taken an upper-level genetics course. The one that did not have this course I expected to struggle and this turned out to be true. Since I needed a grade for this course, I instituted homework assignments, paper summaries, weekly progress reports, papers, and presentations in a more formal fashion in this course. For the independent Study, I was more lax at having them pass in anything during the semester and based the grade more on completion of the projects (with a paper submission for both finishing and annotation and a presentation). We did less of the homework together and I think this was the part of the course that the students struggled with the most and needed to either interact with other students better and or with me. However, the weekly progress reports were both written and submitted to the instructor and presented orally once a week. This was very useful for a number of reasons , including keeping the instructor informed or progress and problems that one might encounter. This was also very helpful to the other students and generated a lot of class discussion. I found there was direct correlation between how well they did in genetics and how well they did in this course so I can use this as a good predictor in the future. Although students can complete the course without a genetics course, they have a lot more trouble and rely on the TA too much. Overall, the curriculum worked very well in this stand alone format.

Bio 490 Independent Study (Fall semesters)
I have also had students working in my research lab do an annotation projerct during fall semesters. We work in between wet experiments and during free time during the semester. Students can easily finish a fosmid project suring this time and it provides the student added exposure to genomics and enhances their research experience.

Gerard McNeil , York College-City University of New York

Basic concepts of eukaryotic gene structure, BLAST comparisons, reading frames, intron/exon boundaries, became “second nature” to most of the students, due to the active learning environment. I believe they have a much better understanding of genes than other bio majors do.

Although the exercises were quite good, students ended up just following the instructions, and didn’t really learn very much from them, until they dove into their own sequences. Most of the students were rather frustrated at first, as I couldn’t give them a “cookbook” approach to handling their sequences. But most got over that.  I would re-write the exercises to be more "open-ended" as well.

I did not give students anything except the raw sequences to start with; requiring them to develop their own gene models with gene modeling software. Unfortunately, NSCAN failed to work properly over the web. Next time, I’ll give them the NSCAN models from the GEP.

Using a small program called "Gene runner" or another called “Six Pack” at http://gander.wustl.edu/cgi-bin/emboss/sixpack allowed students to easily view genomic sequence in the context of 6-reading frames. This turned out to be very important.

If adjoining contigs are being annotated, it’s important that the students examine their data as a group to ascertain any overlapping regions; they didn’t do this until their presentations in my class.

Doing this course for the first time with 16 students and no T.A. was challenging. I was running around the lab, with 3-4 hands in the air at any given time asking for help! Next time, I’ll have students working in pairs to support each other.

Robert Moss, Wofford College

My TMC students worked together on an annotation project.  The biggest challenges faced had to do with the fact that we could not coordinate to meet more than 2 hours once per week.  The students would just start to get going on their annotation, and then would have to leave for other courses.  They also wanted to work on the project in between our meetings, but they did not have sufficient computer power available elsewhere on campus.  They did feel that they were a part of a "real" research project, and this was something new to these students, particularly as the school was undergraduate only and only a small number of students were able to participate in research projects with faculty.  Even though the curriculum projects available seemed to be very useful from my perspective, the students seemed to want to learn with the raw data, and not a pre-designed assignment.  This was frustrating in that they hit challenges that were more difficult for me to help them through since they didn't have the background yet, but seemed to give them the excitement of working with data that no one else had worked with before - their enthusiasm was worth the confusion of them jumping right into the project. 

My original idea had been for each student to work on a separate annotation project, but they decided that they preferred to work together on one data set at a time.  This made my job a bit easier, as I could move from computer to computer to help each student get to the same point as they made progress. 

With the requirements for participating in the annotation project being sufficient internet and computer resources, the GEP annotation project was perfect for a school with limited research opportunities for students.  And again, the students really felt that they were a part of the scientific community by working on the GEP project.

Jennifer Leigh Myka, Galen College of Nursing 4

Students enjoyed working on a real research project and were excited by the prospect of a publication. We started by annotating erecta and then progressed to mojavensis. Although mojavensis was more challenging, the students had gained confidence in annotating erecta and were able to apply the skills learned in erecta to mojavensis. They were able to easily alter the parameters of BLAST and had confidence in their conclusion that smaller-sized exons were present or missing in mojavensis. At the end of the semester, students commented that they would have liked to start by jumping into the annotation without the background introductory lectures because they learned more by actually working with the sequence. I don't know if this would have made the class easier or frustrated them. We did run out of time to completely annotate mojavensis so starting hands-on annotation earlier with less time devoted to erecta may have helped.

We did not do enough formal intermittent checks on their progress and this made checking the final submission of the gene reports difficult. In the future, I would like to require weekly short student presentations of their progress in addition to the more formal presentation at the end. We also had web browser compatibility issues with Gene Checker and I would try to make sure everyone was using the same version of a web browser to help with this.

Alexis Nagengast, Robert Morris, Widener University

We tried GEP annotation as a major portion of a first-year course on genomics and bioinformatics.  The students had a great deal to learn to be able to understand how to analyze their portions of the genome, but they were able to make great strides.  As a first trial, the course was reasonably successful and we learned that it is possible to introduce students to genomics early in the curriculum.  The students were able to work together in teams of three and successfully annotate one gene by the end of the course.

  We also learned that we would likely free up a bit more time than we used for the annotation part of the course.  While we spent time going over BLAST and describing how to conduct analysis, we found that the first-year students needed to spend even more time than we planned learning about what they were seing on th reference genome and how they should interpret what they saw on the genome browser.  We ended up spending a great deal of out-ofclass office hours sorting this out for them.

We also learned that a smaller group of students for a course like this with first-years likely would have been better.

Our trained peer tutor was invaluable for this course.

Paul Overvoorde, Libby Shoop, Macalester College 26
Student involvement in a real research project inspired scientific curiosity and excitement. They gained an in-depth understanding of eukaryotic gene structure that they had not been able to acquire through lecture alone. They also gained practical experience using web-based bioinformatics tools that could be helpful in other classes or in the future. Furthermore, students had to think critically to solve complex problems. Since I had students work in pairs, they had to learn to successfully collaborate with others.

As far as practical teaching lessons: I found it useful to walk students through the annotation procedure before diving into their actual projects. First, I gave a lecture on the overall goals of the GEP project and I had the students read the GEP Science article. This seemed to get the students excited about the project. Next time I teach the course I will have the students read the Lopatto et al.,2008 article as well (although I did discuss the overall conclusions in my introductory lecture). The introduction was followed by a lab lecture on the BLAST algorithm followed by a BLAST exercise. Next, I had a lab lecture outlining step by step (with relevant screen shots) the protocol for annotation. I had students follow along on their computers as we went through a sample gene annotation. Then the students had to complete an annotation exercise on their own. I also created an "Annotation Help Sheet" that outlined the relevant websites and the overall steps used during annotation, which the students seemed to appreciate. The next class they were assigned their annotation project.

Next year I will add another week or two to the annotation project (this year I had ~7, including the introductory lectures). We managed to submit our projects, but the last couple of weeks were hectic.

Susan Parrish, McDaniel College 7 LS 24 0
For semester long annotation project:  Rather than a single report at the end of the semester, I think it is important to have checkpoints along the way.  In my next implementation, I will have students present annotation updates every few weeks to the rest of the class. Kelynne Reed, Austin College 5 LS 27 0
Students work better in groups, than individually, on the annotation projects.  Although the projects became tedious and repetitive for them, the tasks were made easier because they had quick and easy access to each other and to the TA.  Having an undergraduate as a TA, one of their peers, is a great asset.  Providing assignments with due dates also helped tremendously.
Gloria Regisford, Prairie View A&M University

We have been interlacing annotation and finishing.  We start with finishing, and in the "off weeK" when we are waiting for sequences, we start the annotation.  This has worked out very well, as it gives more time for annotation.  The hard part for students is the first couple of annotation sessions, as they have to switch their thinking back and forth.  By interlacing, we can spend more time getting them into the learning curve.

Annotation seems to be more difficult for students.  Although some catch on immediately, others spend weeks being intellectually lost.  They are too focused on the details and not the goals, and have a hard time understanding that they are the ones that have to determine a gene model and not the computer programs.  Although I keep telling them that they have to resolve the inconsistent results, next time I'll spend more time on problem solving sessions to get them to rely more on their interpretations instead of the computer programs.

Dennis Revie, California Lutheran University 14
The GEP annotation project was implemented into a junior/senior level Cell Biology course at Georgetown University. The students involved are mostly upper level biology or biochemistry majors. After I explain the scientific goals of the project as a whole (efforts to understand the chromatin structure of the dot chromosome across evolution) and the technical goals (efforts to understand the organization of the dot chromosome by annotation), the students see an example of a completed annotation project. Then, working in groups of 2, the students dive in. The first week is usually difficult for them because they’re trying to get an idea of the scope of the problem and become familiar with the tools available. After that, things proceed smoothly until it’s time to check their models with Gene Model Checker. At this point, they realize that attention to detail is crucial because they’re often forced to revise their models. Although frustration levels can be high at this stage, correct resolution of problems results in a concomitant feeling of achievement. In all, students find this to be a valuable exercise despite the frustrations because they appreciate being part of a real research effort and they feel pride in achieving successful completion of the project.
Anne Rosenwald, Georgetown University

  This was an ideal course from both the perspective of the faculty member and the students. Faculty are often confronted with a conflict between how much content to include in a course versus how much focus should be placed on the process of learning. Students often yearn for a clear connection between what they are studying and why it is important. This course allowed students to tap into knowledge from previous courses and to integrate this knowledge with new analytical skills to solve a real problem. The roles of the faculty member included those of facilitator, technical support, behind-the-scenes problem solver and, perhaps most importantly a co-learner of the tools and skills involved in solving the problem. This was truly a collaborative effort between the students and the professor, rather than a simple didactic dispensation of information from the professor. In fact there were many instances where the professor relied completely on students who had solved a particular problem to teach other students how to solve similar problems.

The atmosphere of the class was that of a problem solving team. It was reminiscent of a small start-up company or some other similarly dynamic and creative group. The course was divided into a one hour session and a four hour session per week. While this wasn’t an ideal division of time, the one hour session was long enough to discuss the underlying biology of the DNA sequencing problem being addressed. It also often served as a ‘problem identification’ day, with the intervening day used by the professor to fix any computer issues and the following session being used to solve the problems identified. This process of just identifying and clearly describing a problem, separate from trying to actually solve the problem, was an excellent learning experience. The students, while often impatient and anxious to know the answer, got an excellent sense of how the problem solving process actually works. Specifically, that problem solving occurs in steps: Identify the problem, suggest various causes of the problem, attempt appropriate solutions to the problem, repeat as necessary, seek outside help when needed.

At the end of the semester the entire class prepared a poster (you can see the poster here)to be presented at our annual undergraduate research symposium. This process was also an excellent learning experience. Certain students stepped up as leaders of the process, gathered information from others in the class and collated this information into a poster. All students were present at the poster session.

In conclusion, this course had all the hallmarks of a ‘capstone experience,’ in which students integrate past knowledge with new skills and information to solve a real-life problem.

Kenneth Saville, Albion College

Stephanie Schroeder, Webster University

I have taught the annotation portion of the course one time as a stand alone course.  We have done both annotation and finishing as either an independent research project or as the research portion of our Senior project course.  One of the hardest things to do is to keep the independent resaerch or senior project students on track.  Since it is not a "real" course with set meeting times and scheduled exams it tends to be last on the list for too many students.  Time management is a difficult issue as is finding a time when the students with different schedules can meet.  Even with these problems the annotation and finishing have tured out to be good student projects especially for students who are not able to do wet lab work for a variety of reasons.  Having a student who is good with the computers is really important for a person like me who is not good at solving computer problems.  Mary Shaw, New Mexico Highlands University 9, 6

The GEP material is used in a stand-alone course at RIT.  Since many of the students were either senior undergraduates or graduate students in Bioinformatics they were reasonable familiar with fundamental computer skills and biology.  Once they became comfortable with the software used in the course, i.e. the UC Santa Cruz Genome Browser and Consed, they were able to enjoy the discovery inherent in their work.  For most of them, this course was the first time they actually did "research" in which the answers to their questions were not predetermined.  It was interesting to observe even the best students encounter, and resolve, unexpected biological problems.  For example, they realized that even related species of Drosophila could be very different genetically, all while they acknowledged the limitations of the of the tools they had access to.

During each of the three times this course has been taught to date, students at first could not understand why we devoted so much time each work to the course.  However, once they became involved with finishing and, especially, annotation they realized the amount of time that was necessary to overcome some of the intrinsic genetic challenges they faced exceeded their expectations.

Gary Skuse, Rochester Institute of Technology

The annotation project was integrated into an existing genomics and bioinformatics course. After attempting to teach the annotation course for the past 5 years, there were a number of changes that made this year's offereing much more successful.  Having a trained TA in the course is critical for working effectively with different groups of students and keeping everyone on task.  The GEP tools are excellent and improvements over the years has enhanced the instructional capability in the course. The workbook is fantastic and saves students a lot of time and prohibits student frustration with annotating the same exons over and over again. Traditionally, students  in my course do most of the work in the classroom.  I think that I will encourage more effort outside of the classroom so that we can go beyond the annotation. The GEP resources are making much easier to plan a more effective course. I really appreciate the course is student-centered and it encourages students to think and integrate knowledge from different sources and at the same time become familiar with the tools of genmics and bioinformatics.     


Mary Smith, North Carolina Agricultural & Technical State University 12



Chris Smith, San Francisco State University

Lessons Learned:

Infrastructure:  The computers were easily able to handle the workload, but the wireless network traffic was terribly slow at times when downloading or uploading to our server space--using USB drives may work better for data storage.  We had problems with uploading primer sequences, and it seems that we were the only ones who had that issue.  We had to email the primer names & sequences to GEP and they took care of everything.  Other than that, all the software/hardware/network issues were easily solved within a few minutes.

Scheduling:  For finishing, we actually had too much time on our hands.  The course was set up for Monday and Wednesday from 1:15 to 5:15, and we typically only had an hour or so of finishing to do on Mondays.  Wednesdays were a long day, though (add new reads, solve issues, call new reads).  I stopped trying to lecture on Wednesdays and double lectured Mondays toward the end of finishing.  For annotation, the schedule was a much simpler and reproducable from day to day.

Content:  The course worked very well.  Every student was completely invested in their finishing and annotation projects.  After a day or two to get familiar with consed, each student was focused on solving their unique problems.  They helped each other, tested hypotheses, and ultimately identified solutions.  It was quite novel to them to actually accomplish something useful in a course.  The intro to consed materials that they used helped quite a bit.  They struggled with annotation at first until I walked through annotating a gene with them.  After that, they went after it.  Once they knew what they were doing, they could have easily done the annotation as homework (and a couple did).

Eric Spana, Duke University 8
It is important to have good IT support. We could not have worked through the problems of using Consed on PCs without the superb, patient help of the Wash U staff. Integrating the Annotation and Finishing projects into a required ongoing class provided both opportunities and challenges--but I probably wouldn't do both types of projects again as part of another course the first time through for me!  However, the model of the project was that of a research team, and students became caught up in working on real research and being part of a larger project. Exercises to help learn individual computer programs, and weekly journal reports of individual/team progress helped keep everyone on track. Another time I will have even more structured exercises and short tests along the way. They were amazed by the information provided by the computer programs, and seemed to be surprised that they could learn to manipulate these sophisticated programs and use them to provide useful information. They were particularly excited about contributing new information that might be published. Mary Spratt, William Woods University

Joyce Stamm, University of Evansville

I found that it was important revisit the overall purpose of the project multiple times during the eight weeks in which we were doing annotation. Some students appeared to lose sight of the over-arching purpose and goals after the initial presentation on the project, which led to confusion during the latter stages. I had asked students to do some self-selecting/designing of follow-up "experiments" on their fosmid sequence after completing the basic gene identification/exon-intron mapping. This was very challenging for some students, because they had lost a sense of what we were trying to learn from the annotation, and had a difficult time figuring out what sorts of questions they could ask. Regardless, I think it is important to encourage the students to pursue other ways to analyze the sequence data, since the basic gene mapping can get a bit tedious and repetitive after several weeks.
Jeff Thompson, Denison University 15

1. Relevance and ownership of annotation projects is critical. It is extremely important to take time to explain the goal behind the GEP and the rationale for annotating the dot chromosome, as well as to set up a mechanism that allows students to feel as if they have some input as to what genes they will choose to annotate.

2. Explaining annotation as a series of hypothesis-driven in silico experiments ensures that students understand that their annotation projects are more than just computer exercises. To do this, I have found that a clear explanation of the rationale behind annotation steps is useful. In this explanation, it is important to stress that the first steps are performed in order to generate a hypothetical gene model for a predicted protein is based on the best sequence match to a ‘known’ gene. From here, I suggest explaining that all subsequent steps in annotation are a series of independent in silico experiments where students test their hypothesis/gene model by attempting to assemble a similar gene from finished sequence through multiple BLAST ‘experiments’ against individual exons of the ‘known’ gene ortholog.

3. Don’t rush into annotation experiments. Before students can feel comfortable as independent annotators, I have found that one should first work as a group in which the students get a clear overview of the initial steps they should follow during annotation. These steps and databases used to perform them should be spelled out explicitly. This should be immediately followed by a sample annotation of a known gene in which the students walk through each step on the computer with you. After this, an assignment in which students work as individuals or in pairs to fully annotate a simple gene feature, helps them practice and build confidence in the annotation process. Once they have taken these steps, most students are ready to start annotating predicted gene features alone or in pairs.

4. Let students learn from each other. Allowing the students to work in pairs is extremely beneficial. A final oral annotation report allows students to visualize the structural diversity of different genes. Intermittent annotation ‘status reports’ in which students share their research progress helps them overcome annotation challenges and learn new annotation strategies.

5. Combination of wet lab and in silico lab was a successful mix (but also a challenge to fit things into one semester). Note that my course was a stand-alone lab class where annotation only was performed for 6 weeks. Annotation projects were performed in between two 3-4 week wet lab modules in which students learned DNA cloning & sequencing techniques and obtained experience with practical uses of a fully annotated genome.

Matthew Wawersik, College of William and Mary 8 SA 16.5 0
An online tutorial session available with the Genomics Educational Partnership (GEP) program provides sufficient step-by-step modules for students through all phases of annotation. In our initial assessment, students tend to work most efficiently in a peer-to-peer learning format following initial guidance and instruction by GEP faculty and TA mentors. Barbara Wilson, Jackson State University

Colette Witkowski, Southwest Missouri State University

Students are initially confounded by the difficulty of annotation. After a while, they (at least some of them) learn how to attack the problem. I spent a fair amount of time at the beginning of the term telling my students to be patient and to keep plugging along.  A couple of good introductory exercises are invaluable.  Once students figure out how to annotate, some of them really get charged up to finish their project.
Jim Youngblom, California State University-Stanislaus 24