Educator Training

We offer up-to-date teacher training through biology workshops and development for teachers in genetics and biotechnology. With federal and private foundation funding, we offer these free workshops to high school and college educators, especially those in the areas of genetics, biology, genomics, and bioinformatics.

DNA Barcoding and Metabarcoding for CURES Workshops

Funded by the NSF Improving Undergraduate STEM Education Initiative

The Cold Spring Harbor Laboratory DNA Learning Center (DNALC), in collaboration with New York City College of Technology (City Tech), Bowie State University (BSU), and James Madison University (JMU), is offering two five-day workshops on DNA barcoding or metabarcoding in course-based undergraduate research experiences (CUREs). Applicants to these free workshops should be undergraduate teaching faculty with a sincere desire to involve students in authentic research projects, especially in CUREs for students in introductory courses.


DNA Barcoding Workshop

Bowie State University, Bowie, MD
June 15-19, 2020

Just as the unique pattern of bars in a universal product code (UPC) identifies each consumer product, a “DNA barcode” is a unique pattern of DNA sequence that identifies each living thing. DNA barcoding provides a powerful way for biology faculty to lead CUREs, which have been shown to increase student retention and success when provided early in undergraduate programs. Barcoding integrates ideas from molecular biology, genetics, bioinformatics, ecology, and biodiversity—while at the same time providing the flexibility to address a variety of student-driven questions. Barcoding can be mastered in a relatively short time, allowing students to generate new data and reach a satisfying research endpoint within a single course. Furthermore, undergraduate students often have limited patience for bioinformatics, and DNA barcoding provides a wet-lab or field-based “hook” to increase engagement. Bioinformatics analysis of DNA barcodes generated via Sanger sequencing are conducted in the user-friendly DNA Subway Blue Line, an open-access, browser-based pipeline.

DNA Metabarcoding Workshop

CUNY City Tech, Brooklyn, NY
June 22-26, 2020

Rather than analyzing one DNA barcode at a time, metabarcoding leverages next generation sequencing (NGS) to analyze thousands of DNA barcodes from complex mixtures of DNA—representing microbes (microbiomes) or environmental DNA (eDNA). Moving from DNA barcoding to metabarcoding perfectly embodies the conceptual transition from single gene to massively parallel genome analysis, introducing students to NGS analysis and data science. A single lane of an NGS machine can accommodate hundreds of student metabarcoding samples. Similar to DNA barcoding, metabarcoding draws on techniques from molecular biology, genetics, bioinformatics, ecology, and biodiversity. Bioinformatics analysis of metabarcoding NGS data are conducted in the recently developed DNA Subway Purple Line, a browser-based pipeline incorporating QIIME2, a research-grade metabarcoding platform.

 


Workshop participants learn all the biochemical and bioinformatics techniques required to implement DNA barcoding or metabarcoding, including the use of the DNALC’s sequence analysis tools. Workshop seminars introduce key concepts (“big ideas”), CURE development, management and evaluation, data science, methods to work with diverse student populations, workforce development, and details about the project. Seminars include insights from project Co-PIs, including DNALC’s experts; faculty leading JMU’s curriculum, which engages 800 students and 20 instructors in DNA barcoding each semester; and City Tech and Bowie State faculty who lead DNA barcoding and metabarcoding with diverse student populations. The competencies required for bioinformatics, genome science, and biological data sciences are also presented.

Faculty who complete the workshops receive travel support, a stipend, and have year-round mentoring and support from project Co-PIs as they implement barcoding CUREs. Those implementing CUREs receive free reagents and DNA sequencing for student research. DNA barcoding workshop participants from the previous year are eligible to attend metabarcoding workshops—any remaining spots will be filled competitively. Select faculty will be invited to mentor other faculty, building a network of educators implementing DNA barcoding CUREs.

Faculty are asked to participate in a series of evaluation activities throughout the project, beginning with workshop evaluation. Faculty who go on to implement CUREs are enrolled in additional evaluation activities centered on their experiences as well as those of their students. Select schools will be asked to participate in additional longitudinal evaluation of students.

  • DNA Barcoding Workshop at Bowie State University, Bowie, MD, June 15-19, 2020
  • DNA Metabarcoding Workshop at CUNY City Tech, Brooklyn, NY, June 22-26, 2020
  • Audience: Undergraduate Faculty

Apply

Maize Annotation Jamboree

The NSF-funded MaizeCODE and Gramene host maize genome annotation jamborees for PUI faculty.

Maize is one of the most important crops in the world. Its genome sequence is the foundational resource for improving yield and adapting maize to environmental and biological challenges. Even though the fourth-generation maize genome assembly is supported by abundant RNA-based evidence, many gene models still need to be examined and corrected by a human being – that is, hand annotated! The NSF-funded MaizeCODE and Gramene projects have developed a system to identify genes in need of curation. Our objective is to train faculty to use simple genome annotation tools and to lead maize annotation projects as course-based undergraduate research experiences (CUREs). In this way, students can contribute to the improvement of the maize genome. At the same time, gene annotation is the best way for students to learn about gene and genome structure and function.

Learn More

  • Upcoming: March 10-12, 2020 [Registration closed] at Maize Genetics Conference, Kailua-Kona, Hawai'i
  • Additional Maize Genome Annotation Jamboree dates tbd

PAST EVENT

Webinar:
Metabarcoding and Microbiomes in the Classroom
QIIME2 with DNA Subway

Held Wednesday, February 26, 2020
12:00 PM Eastern/9:00 AM Pacific

Research into microbial diversity and microbiomes has transformed the way we understand the environment, agriculture, and human health. Now, DNA Subway makes it easier to explore this unseen diversity in the classroom using the latest research tools in a simple interface.

The newest release of DNA Subway Purple Line is a streamlined, classroom-friendly version of the popular QIIME2 microbiome bioinformatics software. Purple Line supports large datasets (your own or provided examples) and guides educators and students through real analyses while simplifying complex tasks such as metadata validation and generation of interactive visualizations. Experienced QIIME users can export Purple Line outputs to use in custom analyses.

This one-hour webinar covered Purple Line basics (topics below) to get started with Purple Line in the classroom, integration into course-based research (CUREs), and ways to generate your own data. We also highlighted future faculty DNA Barcoding and Metabarcoding for CURES Workshops (above).

Webinar included:

  • Uploading sequence data to CyVerse Data Store/Purple Line
  • Creating and validating QIIME2 metadata
  • Running a metabarcoding analysis on Purple Line
  • Basic descriptions of QIIME2 plots and figures
  • Future training opportunities
  • Question and answer session

This webinar was open to everyone. Our focus was on applications of DNA Subway including microbiome, metabarcoding, and environmental DNA (eDNA) in undergraduate education. DNA Subway is an educational bioinformatics platform developed by CyVerse. Get a Free CyVerse account at www.cyverse.org.

 

Presented by the DNALC and CyVerse

Sites of Major DNALC Faculty Workshops, 1985-present

This map shows the locations of the DNALC's faculty workshops taught over more that thirty years.

Open the map key map key to show/hide the years in groups of three. Click the check boxes to show or hide the years. Click the dots for information on host institution, year, and instructional level of participating faculty. Map can be opened full screen in a separate browser window by clicking the full screen icon at the upper-right.