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Microarray Spot Synthesizer
The Microarray Spot Synthesizer, developed at Davidson College, is an electronic resource that permits faculty to generate simulated DNA microarray data for use in their teaching. The Spot Synthesizer is not intended to produce real data; its purpose is to enable teachers to help students improve their ability to work efficiently with experimental data by giving them practice with known outcomes. With this Web-based tool, educators can quickly generate intensity data in the form of images of spots with known gene expression ratios. The Spot Synthesizer requires only a Web browser, a program (such as Excel) that can produce tab-delimited text files, and access to the Internet to produce tiff files and a gene list. The Web application will produce paired tiff files that students can use to measure predictable ratios, and one merged JPG file for verification. To analyze the tiff files, students can use the free, research-quality software program MAGIC Tool (see related links). In addition to producing spots with constant pixel values, the spot synthesizer can also generate spots with random variation or with one of six predetermined patterns. Students can experiment with various algorithms for quantifying spots and can determine whether the shape of the spot affects the outcome. Educators can use this tool to test student competence and/or can use it as a training set with expected ratios. Make Microarray Data with Known Ratios, a Letter to the Editor in the fall 2007 issue of CBE Life Sciences Education, explains the purpose and operation of the Spot Synthesizer. It is available online (see related links).
Program Director: Verna Miller Case, Ph.D.
Award Years: 1988, 1996, 2004, 2008
Summary: Davidson College is a private baccalaureate institution in Davidson, North Carolina. Its HHMI-funded initiatives include:
- The use of multiple strategies to engage students in the biomedical sciences, including the creation of a community of mentors and peers to carry students beyond the gateway year;
- An intensive summer laboratory “bridge” experience for rising high school seniors from underrepresented groups that prepares them for the challenges of college introductory biology courses by teaching them basic laboratory techniques and scientific methodology; and
- Support for the collaborative Genomic Consortium for Active Teaching (GCAT), which has helped produce new cadres of student researchers, primarily by introducing powerful DNA microarray methodology into the undergraduate curriculum at more than 160 institutions in the United States and Canada.