Softwares

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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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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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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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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