KBase Educators Overview

Dow, Ellen

doi:10.25982/1668075

Title: KBase Educators Overview

Dataset
Other Related Research

Abstract

KBase worked with a community of instructors to create a connected workflow that integrates genomics, metagenomics, phylogenetics, and pangenomic concepts in a “choose your own adventure” framework. Each concept is stand alone, while complementing one another as they flow from one topic to another across concepts. The pace of each workflow can be adjusted with the flexibility of modules that are shareable and allow students to copy and interact with data and analyses.

Authors:

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States), US Department of Energy Systems Biology Knowledgebase; KBase

Publication Date:: Tue Dec 31 23:00:00 EST 2019

DOE Contract Number:: AC02-05CH11231

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Subject:: Data science, Education, Training, Genomics, Metagenomics, Phylogenetics, Transcriptomics, Metabolic Modeling

OSTI Identifier:: 1668075

DOI:: https://doi.org/10.25982/1668075

Citation Formats


                    Dow, Ellen. KBase Educators Overview.  United States: N. p., 2019. 
        Web.  doi:10.25982/1668075.

Copy to clipboard


                    Dow, Ellen. KBase Educators Overview.  United States.  doi:https://doi.org/10.25982/1668075

Copy to clipboard


                    Dow, Ellen. 2019.  
"KBase Educators Overview".  United States.  doi:https://doi.org/10.25982/1668075.  https://www.osti.gov/servlets/purl/1668075. Pub date:Tue Dec 31 23:00:00 EST 2019

Copy to clipboard


                    
@article{osti_1668075,

  title        = {KBase Educators Overview},

  author       = {Dow, Ellen},

  abstractNote = {KBase worked with a community of instructors to create a connected workflow that integrates genomics, metagenomics, phylogenetics, and pangenomic concepts in a “choose your own adventure” framework. Each concept is stand alone, while complementing one another as they flow from one topic to another across concepts. The pace of each workflow can be adjusted with the flexibility of modules that are shareable and allow students to copy and interact with data and analyses.},

  doi          = {10.25982/1668075},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Tue Dec 31 23:00:00 EST 2019},

  month        = {Tue Dec 31 23:00:00 EST 2019}

}

Copy to clipboard

Dataset:

View Dataset

DOI: https://doi.org/10.25982/1668075

Save / Share:

Export Metadata

Save to My Library

Similar records in DOE Data Explorer and OSTI.GOV collections:

KBase Educators Handbook

Dataset Dow, Ellen G ; Wood-Charlson, Elisha M

The KBase Educators Handbook is a community resource for educators teaching biology, computational biology, and bioinformatics using KBase. The Handbook includes supporting documentation on how to join and access community-developed resources for teaching with KBase, best practices, and guidelines on how to contribute to the KBase Educators Community.
Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform

Dataset Dow, Ellen ; Wood-Charlson, Elisha ; Biller, Steven ; ...

Over the past year, biology educators and staff at the Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free and easily accessible data science platform that integrates many bioinformatics resources into a graphical user interface built upon reproducible analysis notebooks. KBase held conversations with college and high school instructors to understand how KBase could potentially support their educational goals. These conversations morphed into a working group of biological and data science instructors that adapted the KBase platform to their curriculum needs, specifically around concepts in Genomics, Metagenomics,more »« less
KBase Narrative - Mse_Genome_Assembly

Dataset Rastegar, Kiarash

Upon investigating the gut microbiome of mice for microbes related to Polycystic Ovary Syndrome (PCOS), our team found 2 metagenomes that could not be classified using alignment based methods. To further investigate microbial species from these samples, we used common MAGs workflow to create draft genomes which were then later taxonomically classified using GTDB-tk app.
KBase Narrative - natrialba

Dataset Rodge, Seema

The genome sequence revealed PHB synthase gene in Natrialba swarupiae. The genome-scale metabolic model was built based on the ModelSEED pipeline using the Build Metabolic Model App in KBase.
KBase Narrative - Metabolic_reconstruction_ETDI_mangrove

Dataset Laux, Marcele ; Ciapina, Luciane Prioli ; Carvalho, Fabiola Marques ; ...

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

Similar Records