KBase

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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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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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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Exploring Metagenomic Tools: Kaiju, GOTTCHA2, and More

Tonight I continued watching the recording for the ISME19 workshop “From Reads to Function” corresponding to the last part of Day 1. Ben Allen from KBase described completeness and contamination of bins/MAGs. The next step in the workflow is taxonomic assessment and classification. First, one option is to classify taxonomy of metagenomic reads with Kaiju. […]
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Understanding Metagenomics Workflows in KBase

I continued watching the ISME19 Workshop “From Reads to Function” day 1 sessions. Next, Ben Allen from KBase spoke about “Metagenomics in KBase.” Allen went over metagenomics workflows in KBase. They explained that the workflow is based on the Chivian et al. (2023) Nature Protocols publication. Allen shared a graph with the NCBI Sequencing Read […]
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