Postdoctoral Appointee Argonne National Laboratory Tucson, Arizona
Body of Abstract: The Department of Energy Systems Biology Knowledgebase (KBase) provides computational tools and resources to support researchers in organizing, accessing, analyzing, and sharing data from plants and the microbial communities they host. KBase users create interactive, versioned, and reproducible Jupyter Notebook-based Narratives. A Narrative combines formatted text and figures describing a scientific workflow with App cells that record input parameters and display results from modular analysis tools. Recent improvements to KBase enhance the throughput, findability, and analytical tools of Narratives:
Tools for Bulk Import allow the simultaneous upload of multiple sequencing reads and genomes stored in different data types (SRA, FASTQ, GFF/FASTA, GenBank) to Narratives for use in KBase assembly and annotation Apps.
Narratives with public data can now be assigned DOIs in order to make data findable, accessible, interoperable, and reusable (FAIR), connect KBase analysis with other published records, and track credit for data.
The KBase Sample Set framework collects and links sample metadata to heterogeneous experimental data. KBase can import sample metadata from repositories like NCBI, validate controlled terms with support for ontologies, and provide users with landing pages that summarize sample data linkages and accessibility.
Apps for analysis of Amplicon Matrices and Chemical Abundance Matrices retrieve Sample Set metadata to help identify patterns in omics and environmental data.
Apps for metagenome-assembled genome (MAG) extraction and analysis enable exploration of microbial communities.