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Higher Education

Genomics in Education: Gene Annotation and Comparison

The iPlant Collaborative has developed DNA Subway as a platform for genome annotation and comparison in educational settings and beyond. DNA Subway presents complex bioinformatics and visualization tools in an intuitive and appealing interface. This collaborative workspace allows students to edit gene models and compare genes from key plant species such as Arabidopsis, maize, Mimulus, poplar, and rice. Annotating and comparing genome sequences gives students a concrete understanding of gene structure and function far beyond the concepts conveyed in a textbook. “Riding” different lines, students can predict and annotate genes in up to 100,000 base pairs of DNA (Red Line), and prospect entire plant genomes for specific genes (Yellow Line). Additional lines are being developed to analyze next-generation sequencing data, and to construct and work with phylogenetic trees.

DNA Subway includes a video tour to orient beginners, a user manual and sample data sets so it can be used by anyone. In addition, educator training workshops on DNA Subway are scheduled at locations around the country.

Orphan Data Collaborations

DNA Subway iPlant’s Orphan Data project supports distributed research by connecting plant scientists who have under-utilized datasets with faculty and students who wish to work with “real” data. An online “marketplace” will index projects with descriptions of the data available and suggestions for how they can be used for class or independent research projects. The site will also include networking tools to allow collaborators to coalesce around datasets. Additional information is available in a flyer. Contact Jason Williams to inquire about participating in this project.

DNA Barcoding of Chloroplast Gene Sequences

iPlant’s chloroplast barcoding project complements the Plant Tree of Life Grand Challenge project by providing cyberinfrastructure support for college and advanced high school students to participate in plant DNA barcoding research. A streamlined workflow will allow students to identify and classify plants for which they have sequenced short, standardized DNA barcoding regions -- such as the rbcL and matK genes. Finished sequence data will be posted to an iPlant website that provides tools to gauge sequence quality and visualize trace files. Students will use their sequences as a starting point in a study of plant phylogenetics or diversity using alignment and tree-drawing tools on the DNA Subway. Validated data can be readily submitted to research databases, such as the Barcode of Life Database at the University of Guelph. Additional information is available in a flyer. Contact Jason Williams to inquire about participating in this project.

Other Workshops and Courses of Interest

The iPlant Collaborative aims to provide a centralized directory of upcoming courses, and workshops the reader may find of interest. If you have a course workshop you'd like to have listed on iPlant's website, please contact the webmaster.

Teaching Resources

Instructional materials for Modeling C3 and C4 photosynthesis, and Water Transport. Content is aimed at university faculty, undergraduate and graduate students.

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Precollege

DNA Subway

DNA Subway is a bioinformatics workspace that makes high-level genome analysis broadly available to educators and students (undergraduates and advanced high school students). "Riding" different lines in the DNA Subway, users can predict and annotate genes in up to 100,000 base pairs of DNA (Red Line), and prospect entire plant genomes for specific genes (Yellow Line). Additional lines are being developed to analyze next-generation sequencing transcriptome data, and to construct and work with phylogenetic trees.

Teaching Resources

Curriculum Modules and Teacher Resources - Lesson plans, modules, posters and presentations aimed at high school biology, mathematics, AP and IB classes, developed by iPlant Collaborative Teacher Fellows, graduate students and University faculty.

Past