Nanopore CURES FMN Space
Overview
This pilot project will lay the groundwork for integrating Nanopore DNA sequencing technology into undergraduate course-based research experiences.
CUREs that engage students in generating and analyzing DNA sequence are well-positioned for adoption by faculty across the curriculum. However, there are barriers to developing DNA sequencing CUREs. Although the price of DNA sequencing has reduced dramatically, most CURE sequencing projects are not large enough to achieve price reductions offered to bulk consumers. Furthermore, most non-Research I institutions do not have in-house DNA sequencing or high-powered computing capabilities. Instructors at primarily undergraduate institutions (PUIs) lack necessary bioinformatics skills to analyze DNA sequences, and those working at minority-serving institutions (MSIs) are disproportionately disadvantaged. Finally, DNA sequencing curricula should apply evidence-based design principles to maximize the potential to meet
desired learning objectives.
We propose to break down the barriers to DNA sequencing CUREs by developing technical, logistical, and pedagogical support for Oxford Nanopore sequencing. This technology has reached a level of maturity that can enable impactful CUREs at relatively low cost. A hand-held Oxford Nanopore MinION device generates up to 50 billion DNA bases—the equivalent of 16 human genomes—in 72 hours for less than $1500. Nanopore startup costs are 30–50 times less than other high-throughput sequencing platforms. Nanopore’s mobility, ability to generate long reads (>1 million bases), and increasing accuracy has resulted in its adoption for de novo genome assembly, detection of DNA modifications, RNA sequencing, and metagenomics. Consequently, faculty can focus on a single common platform to support a variety of student research questions. For the first time, Nanopore sequencing makes it practical and affordable for students at PUIs to use the same tools and methods to analyze DNA sequence as elite researchers at multi-milliondollar genome centers.
This Level-1 multi-institutional IUSE (Institutional and Community Transformation) project draws together a diverse team of investigators to develop and test infrastructure to support genome science at three MSIs: New York City College of Technology, Spelman College, and University of Puerto Rico-Río Piedras. The project relies on the DNA sequencing expertise of Cold Spring Harbor Laboratory’s Genome Center and the experience of its DNA Learning Center in developing educational cyberinfrastructure, training undergraduate faculty in bioinformatics, and supporting CURES. The project has three objectives:
I: Develop a Nanopore biochemistry and bioinformatics workflow.
II. Develop demonstration projects and pilot the Nanopore workflow with students.
III. Evaluate the project and characterize barriers to faculty adoption of Nanopore technology.
The achievement of these objectives will lay the groundwork for nationwide dissemination.
Funded by the National Science Foundation (DUE:2216349)
FALL 2024 SESSION DATES TO BE POSTED SOON
Keep in mind, that:
- Faculty joining the discussion should plan to attend all sessions on the dates above.
- Discussion will center on teaching, and not specifically how to use Nanopore (although this will be part of our efforts).
- Faculty can be anywhere on their journey to using Nanopore (complete novice or advanced user).
What will we do during these sessions?
- Work through our teaching and class curricula to identify learning outcomes that Nanopore sequencing can enhance or enable
- Identify concepts and prior knowledge students will need
- Develop concept inventories and assessments
- Learn from colleagues and guest speakers as they develop and share materials
- Get motivation and encouragement as we work through challenges
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Jennifer Katcher @ on
Hello - I'd like to be included in this group. I am interested in using Nanopore technology in a CURE at Pima Community College - a 2 yr HSI. I'd like to collaborate to create resources and best practices for using Nanopores with introductory undergraduate students. Thank you!
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Debora J O'Reilly @ on
Hello - I'd like to be included in this group. I am interested in using Nanopore technology in a High School setting. I have begun some lessons on next gen sequencing but really could use help developing lessons. I'd like to collaborate to create resources and best practices for using Nanopores with introductory students. Thank you!
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Narayan Prasad Kandel @ on
Hello - I'd like to be included in this group. I am interested in using Nanopore technology in some biology courses/research here at University of the Southwest, Hobbs, NM. I'd like to collaborate to create resources and best practices of nanopore technology for undergraduate students in this Minority Serving institution. Thank you.
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Christof Stumpf @ on
I'd love to join this group. I teach at a 4-year college and have started research with students using nanopore technology. I would like to eventually introduce this approach in several courses.
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Daniel Kainer @ on
Hello,
I would very much like to be included in this group. I direct a community college-based Biotechnology program and we are at the beginning stages of integrating nanopore into our curriculum. This group seems like an outstanding forum to share best practices and I would be most grateful to gain access to what I am sure will become a fascinating discussion.
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Lory Z Santiago-Vazquez @ on
I am a biology/biotech faculty at the U of Houston-Clear Lake, and HSI. I have tasked myself with developing a Bioinformatics/Biotech Biology specialization and this course would be perfect for it. I would also incoporate it in my own research lab.
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Melanie Melendrez-Vallard @ on
I would love to be included in on this group. We are actively using nanopore at Anoka Ramsey Community College for 16S amplicon sequencing for identification for one of our classes but would really love to expand how we use it in the classroom with students. However, I am teaching during the times above - but I would be interested in future opportunities! I will be creating a sediment metagenomics CURE with nanopore for my majors class as well and would be happy to collaborate.
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monica trujillo @ on
I am a Professor of Biology at Queensborough Community College. I would like to include Nanopore sequencing into my General Microbiology class (BI 461). I am interested in joining this group.
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Melanie Van Stry @ on
Hello. I would like to join this group. I am using Nanopore sequencing for metagenomics in General Biology and Undergraduate research courses at Lane College, an HBCU in Jackson, TN.
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Monia Haselhorst @ on
Hello,
I just saw this FMN and would like to join. Is it too late? I am a faculty member at Colorado Mountain College in Leadville, CO. We just launched a BS in Ecosystem Science & Stewardship, where we want to incorporate field sequencing into our curriculum.
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Chitra Chandrasekaran @ on
I just saw the posting on LinkedIn and I am very interested in joining. Specifically, I am really interested in learning how to use and teach RNAseq using Nanopore technology in the context of a CURE that I am currently developing. Unfortunately, I teach during the meeting times listed above. Would there be another opportunity to join and/or participate in this group?
Thank you!
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Lory Z Santiago-Vazquez @ on
Hello, did the training start? September 18 is gone but I did not get a notice. Perhaps there is no space left. Please let me know. Thanks. Lory
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Hui-Min Chung @ on
I have used Nanopore tech for the microbiome projects in the genetics lab courses at UWF; I am also part of the SEA-PHAGES program. I would like to share my experiences and like to explore more (such as metagenomics and small genome sequencing) and learn with the community. I just submit the application through another page. Thank you for considering my application.
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Tammy Laberge @ on
I would like to be a member of this group if it is not too late. I am currently a faculty member at Miami-Dade College and am trying to use metagenomics in my biotechnology classes. Thank you!
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Trevor Duarte @ on
Hello, I would like to be included in this group if it is not too late. I am currently using the 16s barcoding kit and minion to analyze soil samples with 1st and 2nd semester general biology students at a 2 year HSI.
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Frank Emanuele @ on
Hello, I would like to be included in this group as I have been using Nanopore MinION in undergraduate research and as a CURE in introductory Biology courses at a HSI Cochise Community College for many years with my students without much support in learning protocols and the best tried in true methods. Unfortunately, because of costs and learning curve we have had less opportunity to use these excellent tools. My students and I are looking forward to working with you to help progress and make it easier to implement the hands on methods of sequencing and introducing students to bioinformatics. We understood early on that this technology puts in reach the cutting edge methods of bioinformatics in the reach of our students instilling the confidence they need to enter into fields involving genomics/bioinformatics. Thank you for the opportunity to collaborate.
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Maria B. Lazebnik @ on
I would like to join this group. I teach at Bentley University. Given your expertise and leadership in DNA sequencing and synthetic biology education, I am reaching out to explore the possibility of collaborating with Cold Spring Harbor Laboratory. I am specifically interested in receiving training and guidance on using the Oxford Nanopore DNA sequencer and designing experiments for my students.
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