Delftia

January 5, 2025
By Carlos C. Goller
Delftia, KBase, Metagenomics, Reflections, sequencing, Softwares

DEBmicroTrait: Innovations in Trait-Based Microbial Modeling

Gianna Marschmann from Lawrence Berkeley National Laboratory presented at the KBase Microbial Community Modeling workshop. The title of the session was: DEBmicroTrait: Trait-based Microbial Community Modeling in KBase Overview.” Marschmann is a postdoc with Ulas Karaoz. Genome-informed trait-based modeling takes multidimensional data. Marschmann noted that they can reduce dimensionality and model traits. The parameter distributions […]

January 22, 2023
By Carlos C. Goller
Delftia, Molecular Biology Education Research, Oxford Nanopore Technologies, Reflections, sequencing, Softwares, Undergraduate Research

New Oxford Nanopore Technologies

I am now watching videos from the Oxford Nanopore Technologies (ONT) YouTube playlist that includes sessions from the NCM 2022. I want to learn more about what others are doing with Nanopore and how to use automation and pipelines more efficiently. The first session I watched tonight was on “End-to-End human genome nanopore sequencing and […]

January 20, 2023
By Carlos C. Goller
Delftia, Presentations & Talks, Reflections, sequencing, Softwares, Undergraduate Research, Website, Why, Workshop

Alignments and Assemblies

We began working with the VolTRAX2 today. I’m excited to use it for library preps along with the Miroculus Miro. Tonight I watched the NCM 2022 Masterclass session by Matt Attreed on “How to generate and call variants.” Attreed is a technical applications scientist (bioinformatics) with Oxford Nanopore Technologies. They began by providing an introduction […]

January 18, 2023
By Carlos C. Goller
Delftia, Oxford Nanopore Technologies, Presentations & Talks, Reflections, sequencing, Softwares, Undergraduate Research, Workshop

Flongles and Several MinIONs and PromethIONs

Austin Compton is a Technical Applications Specialist at Oxford Nanopore Technologies and presented a masterclass at NCM 2022. We’ve used the MinION but I don’t know as much about the PromethION and Flongle. Compton shared a slide that indicated that the Flongle flow cells have 126 pores, MinION flow cells have 512, and PromethION flow […]

January 17, 2023
By Carlos C. Goller
Delftia, Oxford Nanopore Technologies, Presentations & Talks, Reflections, Softwares, Undergraduate Research, Website, Workshop

A Collection of Library Prep Options for Nanopore

Yan Yang from the Oxford Nanopore Technologies Technical Services North America West Coast Team, presented the NCM 2022 Masterclass “How to select the right library preparation workflow for your experiment.” Yang explained how Nanopore DNA/RNA sequencing works as the nucleic acid is passed through a nanopore and electrical signals are interpreted into sequence data. Yang […]

December 27, 2022
By Carlos C. Goller
Academic Development, Books, Constructivism, DBER and SoTL, Delftia, Discussions, Diversity, Information Literacy, Instructor Behaviors, Pedagogy, Reflections, Service Learning, UDL, Why

Swabs and Microbes in the Second Grade Classroom

The JMBE Live session I watched tonight was entitled “Microscopic Communities: Interdisciplinary Exploration of Microbes in the Classroom” and presented by Dr. Jennifer Surtees and Dr. Sandra K. Small from the University of Buffalo. They are both part of the Genome, Environment and Microbiome (GEM) program that aims to integrate research, education, and engagement. GEM […]

October 14, 2022
By Carlos C. Goller
Academic Development, Constructivism, Delftia, Reflections, Undergraduate Research, Why

Plate Readers for Diauxic Growth Determination

“Student-Led, Instructor-Supported Investigations into Diauxic Growth” was the title of the ASMCUE 2022 recorded session I watched tonight. Drs. Matthew B. Crook and Matthew J. Domek from Weber State University presented this ten-minute video. They defined the diauxic growth curve as a fundamental growth curve associated with the growth of Escherichia coli. A challenge is […]

October 12, 2022
By Carlos C. Goller
Academic Development, annotation, Articles, Constructivism, Delftia, Diversity, Information Literacy, Pedagogy, Reflections

Perusall and the Golden Age of Microbiology

Gwendowlyn S. Knapp spoke about “Reading of Original Microbiology and Virology Literature Using the Online Platform Perusall” at ASMCUE 2022. This was a ten-minute recorded session. Knapp is an Assistant Professor of Biology at Illinois College. Knapp began by talking about milestones in “the Golden Age of Microbiology” and the cool experiments people have performed. […]

October 6, 2022
By Carlos C. Goller
Academic Development, Case Studies, Delftia, Diversity, Guest Speakers

Case Studies with Significant Examples

Emily Rotich from South College in Nashville TN and Jennifer Thomas from Belmont University also in Nashville presented a recorded ASMCUE 2022 session entitled “Improving Student Performance Using Significant Examples to Explain Concepts.” They started by explaining how many professional disciplines use case studies and help students build on prior knowledge and a scenario. The […]

January 23, 2022
By Carlos C. Goller
Accessibility and UDL, Books, Constructivism, Course Design, Delftia, Diversity, Mobile Learning, Online Learning, Open Pedagogy, OpenEd, Publishing, Reflections, Softwares, Website, Why

Google Sites for Accessible and Mobile-Friendly OER

While the snow is quickly melting, it may freeze again tonight… and Wake County Public School System has canceled classes. I am no longer sure what day of the week it is with snow days and disruptions! Tonight, I watched another forty-minute Open Ed 2021 session entitled “Using Google Sites to Create Accessible and Mobile […]