Metagenomics

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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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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KBase: Enhancing Credit Systems for Researchers

The last presentation of the KBase Science Session: Data integration to support (or refute) predictions was by Elisha Wood-Charlson from Lawrence Berkeley National Laboratory. Wood-Charlson’s presentation was titled “Getting credit for contributions in a big data world.” The message emphasized that science is a creative and collaborative pursuit. 2023 was declared the “Year of Open […]
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Introduction to KBase: Empowering Research in Systems Biology

Tonight I started another KBase video. This was the September 18, 2024 “Introduction to KBase” webinar. Ben Allen from Oak Ridge National Laboratory was the presenter along with Ellen Dow and the KBase team. Allen described KBase as “a community-driven research platform for systems biology” and it has the tag line “empowering researchers by integrating […]
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KBase and the Research Data Lifecycle

The ISME19 workshop day 2 concluded with Ellen Dow speaking about “Publishing with KBase.” Dow spoke about how KBase fits into the “research data lifecycle” by helping integrate data, customize analyses, share with collaborators, access tools, and publish results. This is one part of the creating and managing FAIR data that KBase emphasizes. Dow noted […]
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Enhancing Microbiome Data Collection with NMDC Tools

I’m still watching day 2 of the ISME19 workshop “From Reads to Function.” This session included Iyanu Oduwole, Emile Skoog, and Kent Pham. They introduced NMDC and Sample Metadata. The National Microbiome Data Collaborative (NMDC). Iyanu Oduwole is a Genome Science and Technology Ph.D. candidate at Bredesen Center UTORII. Emilie Skoog is a postdoctoral researcher […]
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Understanding DRAM and Genome Analysis at ISME19

I continue watching the ISME19 KBase workshop: “From Reads to Function, Day 2.” Jared Ellenbogen presented next. They spoke about “DRAM and genome-resolved inference.” Ellenbogen spoke about analyzing the fifteen genomes studied during the workshop with DRAM. The outputs of DRAM were described: a heat map with every row corresponding to a different genome or […]
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Insights into dRep and DRAM Tools for MAGs

Tonight I started watching day 2 of the ISME19 workshop “From Reads to Function.” Mikayla Borton from Colorado State University presented on “DRAM and genome-resolved inference.” Borton started with dereplication of bins/MAGs. After that step, MAGs are annotated with DRAM. The tool used to dereplicate metagenome assembled genomes (MAGs) is dRep. Borton explained that the […]
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