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Cold Spring Harbor Laboratory
Outcomes, Challenges, and Resources
Outcomes
- Developed problem-driven modules to integrate bioinformatics research routines into the teaching of biology. Developed Gene Boy (http://www.dnai.org/geneboy/), an intuitive, appealing, algorithm-driven bioinformatics tool for basic DNA analysis, gene prediction and sequence searches.
- Taught 16 week-long Vector Bioinformatics Workshops at 13 different AIRI member institutes, NCBI, the Contra Costa County School District, and Rockefeller University. Through these workshops, 322 biology educators learned the basics of sequence and genome analysis and how to integrate bioinformatics applications in their own teaching.
Taught 133 Gateway teachers in the use of the mobile computer laboratory VectorNet and the DNALC's web site Gene Almanac.
Disseminated Vector Bioinformatics curriculum through seven workshops at five different conferences with a total of 284 participants.
Conducted follow-up surveys with the 2001 Vector Bioinformatics Workshop participants and learned that over 80% of respondents had integrated workshop materials in their own teaching. By comparing participants' expectations surveyed at the end of the workshops with the results of the follow-up surveys it became apparent that teacher predictions of future behaviors are, in fact, useful indicators of their actual behavior.
- Dispatched the mobile computer laboratory VectorNet to 24 different high schools in the NYC area where a total of 1,993 students utilized the system during 2000-2003. An additional 12,657 students was reached through 2001 workshop participants who reported to have taught these students what they had learned in the workshop.
Challenges
- Math and biology: The amount and types of data generated by genome sequencing projects are transforming biology into a much more quantitative science. Traditionally, however, biology attracted students because it was less math-based than chemistry and physics. Thus, while the new biology presents great opportunities for an increased integration of math into the biology curriculum, it will require sensible (and sensitive) ways of preparing teachers and students for this shift. Solving biological problems using engaging bioinformatics tools such as Gene Boy (http://www.dnai.org/geneboy/) and studying meaningful content such as our bioinformatics modules and DNA Interactive (http://www.dnai.org/) present great ways to help students (and teachers) bridge this gap.
- Computer skills: Teachers' computer skills are predominantly geared towards writing text documents and emails, and browsing the Internet. Bioinformatics analysis routines require familiarity with a different set of skills and teachers need to be provided with the opportunity to acquire and practice these skills. Students have usually much less problems with this. The DNALC's new bioinformatics tool Gene Boy helped to minimize teachers' problems by providing a simple platform, integrating sequences with a variety of analysis routines.
Resources
- Gene Boy (http://www.dnai.org/geneboy/)
Gene Boy is a fun, intuitive, web-based tool to explore the characteristics of DNA sequences. Shaped like a well-known computer game console, Gene Boy integrates DNA sequences and bioinformatics tools for the analysis of sequences. Gene Boy can be used to discover the differences between random DNA, DNA in genes, and the DNA between genes (intergenic DNA). It can identify open reading frames (ORFs) and search the WWW for sequences that are related to an input sequence.
- DNA Interactive (http://www.dnai.org/)
DNAi is a multimedia resource commemorating the 50th anniversary of the discovery of the DNA Double Helix by Jim Watson and Francis Crick in 1953. This web site provides teachers with remarkable teaching resources and tools. Video captions of interviews with scientists explain their discoveries and facts from basic DNA structure to bioinformatics. Central to DNAi is Lesson Builder, which allows teachers to build their own presentations using any of the animations, images, videos, quizzes, and captions that form the content of DNAi. These presentations can then be saved and made available to students. Visit DNAi at http://www.dnai.org/.
- DNA Science (2nd. Edition) By David A. Micklos, Dolan DNA Learning Center, Cold Spring Harbor Laboratory; Greg A. Freyer, Columbia University, New York
Second edition of a successful textbook in which a highly illustrated, narrative text is combined with easy-to-use laboratory protocols. It contains a fully up-to-date collection of 12 rigorously tested and reliable lab experiments in molecular biology, developed and tested at the DNALC. As in the first edition, the laboratories are completely supported by quality-assured products from the Carolina Biological Supply Company, from bulk reagents, to useable reagent systems, to single-use kits, thus satisfying a broad range of teaching applications at a number of educational levels. In this second edition, the first eight chapters have been completely revised, extensively rewritten, and updated. The new coverage extends to the completion of the draft sequence of the human genome and the enormous impact these and other sequence data are having on medicine, research, and our view of human evolution. All sections on the concepts and techniques of molecular biology have been updated to reflect the current state of laboratory research.
- Bioinformatics in the Classroom (http://www.dnalc.org/bioinformatics/)
Currently the web site for the bioinformatics teacher workshops, this site will become the gateway to teach our new bioinformatics modules. These modules pose biological questions which are solved using bioinformatics tools, most prominently Gene Boy (http://www.dnai.org/geneboy/).
The availability of sequence data for entire genomes is fueling tremendous research efforts to understand the information DNA sequences encode. Scientists have begun to identify genes, define the proteins they produce, and understand how these proteins function. To achieve these goals, biologists are integrating computer-based tools into their research routines. This new field, called bioinformatics, allows scientists to make sense of the huge amount of sequence data and to "mine" genomes for meaning.
Students have the unprecedented opportunity to work with the same computer tools and data that genome scientists use. The computer-based modules that can be accessed through this web site integrate enticing content with hands-on computer exercises. Using bioinformatics tools, students analyze human, plant, bacterial, and viral genomes; compare DNA sequences across species; study the evolution of modern humans; understand how variations in DNA sequence contribute to disease; view three-dimensional structures of proteins; and learn about new strategies for developing therapeutic drugs.
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