Month: December 2024

Explore MetaPathPredict and OMEGGA: Tools for Bioinformatics

Tonight I watched another KBase Science Session: Data integration to support (or refute) predictions. “Integrating data to predict functions for gaps in metabolic models” was the title of Bill Nelson’s session. Nelson is from the Pacific Northwest National Laboratory. The work was part of two PNNL SFA projects: a soil microbiome project and a persistence […]
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KBase Pipeline for Protein Function Prediction

Continuing with the KBase Science Session: Data integration to support (or refute) predictions, tonight I watched Chris Henry from Argonne National Laboratory present on “Predicting Protein function using structure nd sequence similarity in KBase.” Henry and team built a pipeline in KBase to analyze structure and sequence similarity data. Henry noted that KBase has a […]
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Unlocking Knowledge Extraction with KBase

I didn’t know KBase could be used for knowledge extraction from literature! Tonight I watched the session by Shinjae Yoo from Brookhaven National Laboratory titled “Knowledge extraction from literature.” This was part of the KBase Science Session: Data integration to support (or refute) predictions I started watching yesterday. The primary focus of this study was […]
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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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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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