Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Learning and Training with KBase

Authors:

Ellen G. Dow1 ([email protected]), Benjamin Allen3* ([email protected]), Jason Baumohl1, Kathleen Beilsmith2, David Dakota Blair4, John-Marc Chandonia1, Dylan Chivian1, Zachary Crockett3, Meghan Drake3, Janaka N. Edirisinghe2, José P. Faria2, Jason Fillman1, Tianhao Gu2, A. J. Ireland1, Marcin P. Joachimiak1, Sean Jungbluth1, Roy Kamimura1, Keith Keller1, Dan Klos2, Miriam Land3, Filipe Lui2, Erik Pearson1, Gavin Price1, Priya Ranjan3, William Riehl1, Boris Sadkhin2, Samuel Seaver2, Alan Seleman2, Gwyneth Terry1, Sumin Wang1, Pamela Weisenhorn2, Ziming Yang4, Shinjae Yoo4, Qizhi Zhang2; Shane Canon1, Paramvir S. Dehal1, Elisha Wood-Charlson1*, Robert Cottingham3, Chris Henry2, and Adam P. Arkin1

Institutions:

1Lawrence Berkeley National Laboratory; 2Argonne National Laboratory; 3Oak Ridge National Laboratory; and 4Brookhaven National Laboratory

URLs:

Goals

The Department of Energy Systems Biology Knowledgebase (KBase) is a knowledge creation and discovery environment designed for both biologists and bioinformaticians. KBase integrates a large variety of data and analysis tools, from DOE and other public services, into an easy-to-use platform that leverages scalable computing infrastructure to perform sophisticated systems biology analyses. KBase is a publicly available and developer extensible platform that enables scientists to analyze their own data within the context of public data and share their findings across the system.

Abstract

The KBase user interface (UI) enables instructors to work with students to conduct hands-on data science research and analysis without the need for programming skills or computational resources. The KBase team works with instructors and researchers of varying skill and career levels to ensure the transfer of domain knowledge is accompanied by an understanding of bioinformatic tools and techniques. KBase supports learning and training through the KBase Educators Community and by hosting workshops and webinars on community-focused topics. The variety of programming targets different cross-sections of the BER research community, with the overall goal to improve and expand the next generation of data analysis using KBase.

KBase Educators

The KBase Educators program (https://www.kbase.us/kbase-educators/) consists of biological and data science instructors ranging from high school to graduate level that have adapted the KBase platform to their curriculum needs by developing modular, adaptable, and customizable instructional units using KBase Narratives. These instructional modules contain teaching resources, data analysis tools, and mark-down utility to tailor instructions and learning goals. Each module can be adapted for independent class concepts across Genomics, Metagenomics, Phylogenetics, Pangenomics, Metabolic Modeling, and Transcriptomics. The KBase Educators Organization provides access to resources in KBase, and a KBase Users Slack channel provides access to a community network of peers, supported by community-driven guidelines, instructional templates, and KBase staff.

Educators from community colleges, primarily undergraduate institutions, and doctoral research institutions make up the KBase Educators Community. There is also representation of diverse student populations from Minority-Serving Institutions, including Hispanic-Serving, Asian American and Native American Pacific Islander-Serving, Alaskan Native-Serving or Native Hawaiian-Serving, Native American-Serving Nontribal, Historically Black Colleges or Universities, and Predominantly Black Institutions. Program growth and expansion will continue, as the community identifies additional areas that are important to support educators and their students.

Come see how KBase can support Promoting Inclusive and Equitable Research (PIER) Plans and develop connections with new collaborators for Reaching a New Energy Sciences Workforce (RENEW) and Funding for Accelerated, Inclusive Research (FAIR).

Outreach

The KBase team hosts outreach and training events to support research groups, educators, and collaborators advance their research. Training events include workshops and webinars to demonstrate use of the platform and showcase popular workflows. Workshops are used to reach specific institutions to facilitate collaboration with researchers and students. Webinars reach a broader audience through web-based training to introduce new features, showcase workflows, and host speakers including KBase staff, community developers, and subject matter experts.

Webinars are posted on the KBase YouTube channel (https://www.youtube.com/DOEKBase) for anyone to revisit and view after the event and often include public Narratives for users to test out new tools and workflows.

Through each of these approaches, KBase empowers skilled researchers and inspires the next generation of biologists and data scientists by providing a platform that seamlessly enables users to integrate conceptual knowledge with sophisticated systems biology investigative tools.

Funding Information

This work is supported as part of the Biological and Environmental Research (BER) Program’s Genomic Science program. The DOE Systems Biology Knowledgebase (KBase) is funded by the U.S. Department of Energy, Office of Science, BER Program under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886.