PAG 2024 Workshops

In preparation for those planning to attend KBase related workshops at PAG, we recommend first creating a free KBase account so you can use the system. This short KBase Quick Start video demonstrates how-to along with a very brief introduction to the platform or follow the step-by-step sign up guide


KBase for Plant Science

Lead: Priya Ranjan

Location: Palm 3-4

Date: Friday, Jan 12 10:30 AM

KBase enables users to analyze, share, and collaborate using data and tools designed to help build increasingly realistic models of biological systems and function in plants and their microbiome. This presentation will include a brief introduction for those new to KBase, and then cover a mix of analyses involving differential gene expression analysis, reconstruction of plant metabolism from a genome, and examining the expression data within metabolic subsystems in a reproducible point-and-click narrative user interface.

Workshop Links & Resources:

Question & Answer document

Empowering Education and Student Research in Systems Biology and Bioinformatics through KBase

Presenter: Bob Cottingham

Location: Pacific H-I (2nd Floor)

Date: Friday, Jan 13 4:00 PM (20 minutes)

The Department of Energy (DOE) Systems Biology Knowledgebase (KBase) is a user-friendly knowledge creation and discovery environment designed for biologists and bioinformaticians. It integrates diverse data and analysis tools from DOE and other public sources into an easy-to-use platform that leverages scalable computing infrastructure to perform sophisticated systems biology analyses without the need for extensive local resources. KBase is a publicly available, and developer-extensible platform that enables scientists to analyze their own data within the context of public data, and fosters collaboration and knowledge sharing.

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 collaborates with instructors and researchers of varying skill and career levels to facilitate effective educational experiences and the transfer of domain knowledge coupled with an understanding of bioinformatic tools and techniques. KBase has been supporting education in three main ways: establishing the KBase Educators program, participating in the Environmental Molecular Sciences Laboratory Summer School, and hosting a variety of topic-based workshops and webinars. Each program targets different segments of the Biological and Environmental Research (BER) community, collectively working toward the common goal of advancing and broadening proficiency in data analysis using KBase. These efforts contribute to the development and expansion of expertise in bioinformatics, fostering a more capable and knowledgeable community of researchers and educators.

POSTER:  A poster will also be available for discussion on this topic: 

PE0842 Empowering Education and Student Research in Systems Biology and Bioinformatics through Kbase

Presenter: Bob Cottingham

Location: Golden State Ballroom/Exhibit Hall

Date: Monday, Jan 15 10:00 – 11:30 AM

BER Plant Genomic Science

Lead: Jeremy Schmutz and Bob Cottingham

Location: Palm 3-4

Date: Monday, Jan 15 6:20 PM

In person – The Department of Energy Biological and Environmental Research (DOE-BER) currently funds both a large-scale user facility for plant genomics at the DOE Joint Genome Institute and a large-scale computational resource for comparative functional genomics and systems biology of microbes, plants and their communities called the DOE Systems Biology Knowledgebase (KBase). The core mission of both of these endeavors is to help scientists carry out experiments and analyses in areas such as improving biofuel development, understanding plant model systems, advancing plant comparative science, and investigating global carbon cycling. In this workshop, we will present current and ongoing developments at the JGI and KBase toward integrative biology and hear from researchers who are applying genomic sequence information to BER-funded activities of plant systems. We will describe how to apply for a project with the JGI Community Science Program and how you can use the KBase system to accelerate your plant genomics research.