biology

Long-Read Sequencing: Solving Genetic Diagnostics Challenges

Sebastian Lunk from the Victorian Clinical Genetics Services (VCGS) in Australia spoke at London Calling 2025 on “Long-read sequencing and adaptive sampling solve complex diagnostic conundrums.” VCGS is a not-for-profit subsidiary of Murdoch Children’s Hospital with forty years of clinical genetic service delivery and 20,000 diagnostic tests performed annually. With 330 staff, they have the […]
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Plant Genome Assembly Insights from ONT Workshop

Tonight I watched the Oxford Nanopore Technologies (ONT) PAG Industry Workshop session titled “A single-platform solution for plant de novo genome assembly.” Jeannie Mounger, a field applications scientist with ONT, was the presenter. They noted that for plant genome assembly there are several considerations. Plant genome size varies greatly: from Mb to Gb. Polyploidy varies […]
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Exploring Student Knowledge in Biofilm Development

Drs. Sharleen Flowers and Stephanie Gardner presented at JMBE Live! on September 29, 2023. Rachel Horak moderated the session. The title of the session was “Here Is the Biology, Now What is the Mechanism? Investigating Biology Undergraduates’ Mechanistic Reasoning within the Context of Biofilm Development.” Gardner spoke about the challenges of understanding complex biological systems. […]
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Revamping the Central Dogma: Teaching with Chromogenic Proteins

Tonight I watched another JMBE Live session with Greg Phillips from the University of Georgia and Nancy Boury from Iowa State University. Stanley Maloy, Editor in Chief of JMBE, was the moderator. Maloy spoke about how this Curriculum article revisits the Central Dogma. Boury and Phillips were together for several years at Iowa State. The […]
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Exploring N50 and Genome Assembly Techniques in KBase

Tonight I continued watching the LISA workshop videos. Lauren Lui from Laurence Berkley National Lab explained the apps available on KBase for long-read only and hybrid assemblies. Using a KBase narrative, Lui shared a Spades short-read-only assembly with 30~ contigs. They described the N50 as a metric for comparing genome assemblies. To calculate N50, contigs […]
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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 […]
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Enhancing Genome Predictions through Data Integration

I started another KBase session because I want to continue learning and be prepared for courses. This semester I want to share genomes and narratives. Tonight, I started watching the KBase Science Session: Data integration to support (or refute) predictions. Elisha Wood-Charlson from the Lawrence Berkeley National Laboratory was the first speaker and presented a […]
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