KBase

Exploring Gene Linkages with Random Walk Tools

What a long day! Tonight I continued watching the session on Exploring Plant Gene Linkages using Random Walk with Restart Tools. The apps were described and how the Random Walk with Restart tools can be used to explore networks. The output can be the top one hundred genes visualized in a network. The starting seed […]

January 15, 2025
By Carlos C. Goller
KBase, Reflections

Using Random Walk with Restart in GWAS: Insights from KBase

I continued watching the KBase session “Exploring Plant Gene Linkages using Random Walk with Restart Tools.” Kyle Sullivan, a scientist from Oak Ridge National Labs, is working on these apps. The webinar was recorded January 31, 2024. The team developed a series of tools and a narrative. In the example KBase narrative they simulated a […]

Understanding Random Walk with Restart in Plant Genetics

Tonight I started watching the KBase session “Exploring Plant Gene Linkages using Random Walk with Restart Tools.” Kyle Sullivan, a scientist from Oak Ridge National Labs, is working on these apps. The webinar was recorded January 31, 2024. The team developed a series of tools and a narrative. The genome wide association studies (GWAS) and […]

January 13, 2025
By Carlos C. Goller
KBase, Reflections

Exploring KBase Educators: Key Features and Tools

I continued watching the KBase Educators Orientation from December 2024. Ellen Dow from KBase provided an overview of the narratives in the KBase Educators Org. Dow shared how students, for example, can import data from other narratives. This is a feature I did not know about! RAST and Prokka are two annotation tools available. Dow […]

January 12, 2025
By Carlos C. Goller
KBase, Metagenomics, Reflections, sequencing, Softwares

How to Join and Utilize KBase Educators Group

Tonight I started watching the KBase Educators Orientation meeting from December 2024. Ellen Dow facilitated the session and shared resources from the KBase Educators group and handbook. Dow explained the structure of KBase narratives and how to join the KBase Educators group. The Educators Org has several narratives that can be copied. There are a […]

January 11, 2025
By Carlos C. Goller
KBase, Reflections, sequencing, Softwares

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 […]

January 10, 2025
By Carlos C. Goller
KBase, Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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. […]

January 9, 2025
By Carlos C. Goller
KBase, Reflections, sequencing, Softwares

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 […]

January 8, 2025
By Carlos C. Goller
KBase, Metacognition, Oxford Nanopore Technologies, Reflections, sequencing

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 […]

January 7, 2025
By Carlos C. Goller
KBase, Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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 […]