Bioinformatics: Learning by Doing (NSF DR-K12 0733255)Andrew Vershon, William Sofer, Jeff Charney, Sue Coletta, Waksman Student Scholars Program, Rutgers University, Piscataway NJ

Abstract

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.

Educational Evaluators: Edys Quellmalz, Mike Timms, Barbara Buckley, Nara Nayar, Mark Loveland WestEd, San Francisco, CADSAP Programmers: Ziv Yirmiyaho, ZV-Ventures LLC

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.

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

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.

Flow Chart for Analysis of DNA Sequences Using DSAP

Students register and take pre-survey

Are the DNA sequences of good quality?

No/No Yes/No Yes/Yes

Submit Analysis Crop ends Crop ends

Determine overlap

Make ContigSearch for similar DNA and protein sequences

(BLASTN, X, P)

Investigate the Gene Function

Submit to WSSP Staff for Review

Student's DNA Sequence Data

Students and their teachers publish their data on Genbank

Students work with sequence analysis programs used by scientists

Students

Teacher

Logins per student

08-09 # of students

09-10 # of students

10-11 # of students

1-5 53 78 322

6-25 154 182 234

26-50 77 134 96

51-75 47 82 23

75-100 24 44 11

>100 15 39 3

Totals 373 559 689

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

Automatic error checking

Clone Clones being worked on

Clones reviewed and need to be

corrected

Number of correct clones

  08-09 09-10 08-09 09-10 08-09 09-10

PC1.09 177 38 201 5 42 444

PC2.09 218 94 155 77 43 300

PC3.09 209 93 91 75 121 235

PC4.09 258 63 133 60 19 213Totals 862 288 580 217 225 1192

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.

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

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).

Links to context-dependent Help pages and Tutorials

Link to Discussion Section for questions

DSAP Interface: