Bioinformatics:  Learning by Doing (NSF DR-K12 0733255)
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Bioinformatics: Learning by Doing (NSF DR-K12 0733255). Andrew Vershon, William Sofer, Jeff Charney, Sue Coletta, Waksman Student Scholars Program, Rutgers University, Piscataway NJ. Flow Chart for Analysis of DNA Sequences Using DSAP.

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Bioinformatics: Learning by Doing (NSF DR-K12 0733255)

Andrew Vershon, William Sofer, Jeff Charney, Sue Coletta, Waksman Student Scholars Program, Rutgers University, Piscataway NJ

Flow Chart for Analysis of DNA Sequences Using DSAP

Progress Report: DSAP was launched in the middle of the 08-09 academic year. The new program significantly reduced the time for students to perform the analysis and for staff to review the student’s answers. Comments from the students, teachers, staff, and the project evaluators were used to direct over 200 revisions and improvements in the program. During the fourth year, additional revisions and expansion of DSAP are being made, including enhanced reporting and assessment capabilities and a peer review system. Within the first three months of the 10-11 academic year, over 689 students from 47 schools from NJ, PA, MD, DC, TN and TX are already using DSAP.


Student's DNA Sequence Data

Bioinformatics: Learning by Doing is a full-scale project to develop a state-of-the art web based tool that will make it possible for high school students to conduct authentic research in bioinformatics, publish their findings in GenBank (a national repository that carries all of the DNA sequence data in the world), and make real contributions to the scientific knowledge base. This tool, known as DSAP: the DNA Sequence Analysis Program, is an online, multifaceted, interactive, learning and teaching tool that incorporates embedded assessments. These help guide instruction and provide users with feedback about their understandings of molecular biology and bioinformatics. By using DSAP, students become knowledgeable about the emerging field of bioinformatics, which draws upon mathematics, biology and computer science, and molecular biology, the foundation of all biological sciences. The tools and resources that are being developed are web-based and therefore almost all public schools or libraries that provide computer and Internet access will be able to use the program. Thus, regardless of socioeconomic background and/or geographic location, all students will be able to participate in original research and contribute to scientific investigations. DSAP provides students, teachers, and university scientists with opportunities to directly collaborate with each other on a genuine research project.

Students register and take pre-survey

Are the DNA sequences of good quality?




Students work with sequence analysis programs used by scientists

Submit Analysis

Crop ends

Crop ends

Determine overlap

Search for similar DNA and protein sequences (BLASTN, X, P)

Make Contig

Before the students start the analysis of their unknown DNA sequences they learn and practice how to do the analysis on four Practice Clones (PC) that are progressively graded in terms of difficulty. The number of PCs that have been analyzed correctly have significantly increased over the last year.

Investigate the Gene Function

Submit to WSSP Staff for Review

Students and their teachers publish their data on Genbank

Student Research Project: The students are conducting research to sequence and analyze genes from the aquatic plant Wolffia australiana. Students first isolate DNA clones that contain fragments of the Wolffia genome. After the students determine the size of these DNA fragments through wet lab experiments, the students then analyze the sequences using DSAP at their high schools.


DSAP Interface:


Links to context-dependent Help pages and Tutorials

Link to Discussion Section for questions

Analysis of the completion rate of PCs of students in classes (266 students) and clubs (192 students) show similar trends as the analysis becomes more difficult. As expected, classes have a higher completion rates than voluntary clubs (54% vs. 33% for completing all four clones).

DSAP contains six components:

1] a student DNA sequence analysis scaffolding program,

2] a set of practice example DNA sequences that are used as instructional tools,

3] a series of tutorials and help modules to guide students through their DNA sequence analysis,

4] an administrative program so that teachers can view student work and communicate with their students,

5] staff administrative tools to monitor student and teacher work and provide feedback,

6] an embedded assessment tool that also contains pre/post evaluation instruments

The number of unknown clones completed by the students have risen over 3-fold after the introduction of the revised DSAP.

Automatic error checking

*10-11 numbers are only for the first 3 months of the academic year.

Educational Evaluators: Edys Quellmalz, Mike Timms, Barbara Buckley, Nara Nayar, Mark Loveland WestEd, San Francisco, CA

DSAP Programmers: Ziv Yirmiyaho, ZV-Ventures LLC