Month: January 2025

Understanding the Research Data Lifecycle: Insights from KBase

Tonight I watched Elisha M. Wood-Charlson, KBase User Engagement Lead, present at the LISA workshop. Wood-Charlson spoke about publishing with KBase and the “research data lifecycle.” The cycle of creating and managing data with FAIR principles in mind. Wood-Charlson noted that 2022 was declared the year of open science and mandates were created to promote […]
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Exploring Microbial Genomics and Lanthanide Mining

Continuing with the LISA workshop, tonight I watched another session. This one was by a postdoc, Andrew Wilson, at Pacific Northwest National Laboratory. They have been working on plasmid and microbe sequencing. The title of the session was “Leveraging Long Reads for Synthetic Biology.” Wilson and team are using Gibson assembly and synthetic biology techniques. […]
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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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Key Insights from LISA Workshop on KBase Narratives

Tonight, I started watching the recording from day 3 of the LISA workshop. This session focused on the narrative for long-read assemblies. John-Marc Chandonia and Lauren Lui, Lawrence Berkeley National Laboratory explained the components of a KBase narrative. Chandonia demonstrated the apps panel, beta and released apps, and finding apps. The configuration of the Filtlong […]
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Understanding Hybrid Assemblies in Genomics Research

Tonight I watched the introduction to day 3 of the LISA workshop. Lauren Liu from Lawrence Berkeley Nation Laboratory spoke about how genomics research can be limited by incomplete genomes. They noted that “genomes are hypotheses about what microbes are doing… but with environmental sequencing we often don’t have complete genomes.” Liu explained that assembly […]
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Insights from KBase LISA: Base Calling in Sequencing

Tonight I started watching the recordings from the KBase LISA workshop. I watched the base calling session by Torben Nielsen from Lawrence Berkeley National Laboratory. Nielsen compared PacBio and Nanopore sequencing. PacBio is sequencing by synthesis with limited length. Base calling is performed by image processing. The native error rate for PacBio is about 15%, […]
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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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Machine Learning in Microbial Community Modeling

Priya Ranjan from Oak Ridge National Laboratory was the next speaker I watched as part of the KBase Microbial Community Modeling Workshop recordings. The title of this session was “Pairwise analysis tools between strains” that would be very useful for us! Rnajan is collaborating with the Plant-Microbe Interfaces (PMI) project and is designing a series […]
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Exploring Community Modeling Simulation Tools in Microbial Research

I am continuing to watch sessions from the KBase Microbial Community Modeling Workshop last year. Chris Henry from Argonne National Laboratory, presented on “Community Modeling Simulation Tools.” Henry and team work with the GROW project. Henry applied ModelSEED2 to build models of GROW MAGs (Genome Resolved Open Watersheds Metagenome Assembled Genomes). The MAGs are incomplete […]
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Exploring ModelSEED2: Key Features and Updates

Tonight I started watching the KBase “Microbial Community Modeling Workshop.” Jose Faria from Argonne National Laboratory began with a session titled “Background on ModelSEED and OMEGGA Apps.” GSP 2024 is the public narrative they described. There is also a preprint with all the details. The ModelSEED2 app is the first significant update in fifteen years, […]
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