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
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.
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.
Student's DNA Sequence Data
Progress Report: DSAP was launched in the middle of the 08-
Students register and take pre-survey
Are the DNA sequences of good quality?
No/No
Students work with sequence analysis
programs used by scientists
Submit Analysis
Yes/No
Yes/Yes
Crop ends
Crop ends
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.
Logins per
student
Determine overlap
Search for similar DNA
and protein sequences
(BLASTN, X, P)
Make Contig
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
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
Clone
Students
Students and their teachers
publish their data on Genbank
Teacher
DSAP Interface:
Links to context-dependent
Help pages and Tutorials
Link to Discussion Section for questions
Clones being
worked on
Clones reviewed
and need to be
corrected
08-09
09-10
201
5
PC1.09
08-09
177
09-10
38
PC2.09
PC3.09
218
209
94
93
155
91
PC4.09
Totals
258
862
63
288
133
580
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).
Number of correct
clones
08-09
42
09-10
444
77
75
43
121
300
235
60
217
19
225
213
1192
Percentage Completion of Practice
Clones in WSSP Schools 09-10
120
Club
100
Class
80
Percent
Abstract
60
40
20
0
PC1
PC2
PC3
PC4
Practice clones
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
Automatic
error
checking
The number of unknown clones
completed by the students have
risen over 3-fold after the
introduction of the revised
DSAP.
*10-11 numbers are only for the first
3 months of the academic year.
Analysis of Unknown Clones
800
Incomplete
Number of clones
DSAP contains six components:
700
Completed
600
500
400
300
200
100
0
AY 07-08
AY 08-09
AY 09-10
AY 10-11*
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