Genomic Science Program PI Meeting 2023

Genomic Science Program PI Meeting 2023

Find where and how to connect with the KBase team and collaborators!

Monday - April 17th

Monday - April 17th

Plenary Session 2

2:50-3:10pm ET: Community-driven predictive biology with KBase
Adam Arkin, LBNL

Poster Session 1

F-133: ENIGMA Long Read Sequencing and Assembly for Microbial Genomes: KBase Integration for Assembly and LISA Workshop
Lauren Lui, LBNL

G-163: NLP for Synthetic Biology: Providing Generalizable Literature Mining Through KBase
Shinjae Yoo, BNL (presented by V. Mutalik, LBNL)

J-217: Learning and Training in KBase
Ben Allen and Ellen Dow, ORNL and LBNL

J-221: The KBase Knowledge Engine: Ecosystem Classification Prototype
Paramvir Dehal, LBNL

J-229:Integration of Enzyme Function Initiative Tools in the KBase Platform
Chris Henry, ANL

J-235: Plant-Microbe Interfaces KBase: Design and – omics exploration of synthetic community
Priya Ranjan, ORNL

KBase User Working Groups
Tuesday - April 18th

Tuesday - April 18th

KBase Training Session

10:00- 12:00pm ET
KBase Training Session at GSP 2023: This session will introduce users to the KBase platform and showcase popular protocols for multi-omics analysis in KBase. Attendees will learn how to import data and use KBase apps for processing NGS reads, assembly, annotation, feature analysis, and taxonomy. We will also introduce users to KBase’s microbiome analysis workflows, from metagenome assembly and genome extraction to functional annotation and taxonomic prediction. Learn how KBase users perform powerful comparative analysis of their multi-omics data within an online platform that hosts a variety of public data and supports publishing and collaboration. This session is a great opportunity for new and experienced KBase users to learn about new features and developments to advance your research, and to ask questions and get support from KBase staff.

Registration required:

In preparation for those planning to attend the KBase training session, 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

Register required to join!
Breakout Session 2: BER Science Across Facilities

3:30-6:00pm ET 

Cross-site Syntheses with Quantitative Stable Isotope Probing
Speaker: Bruce Hungate, Northern Arizona University; PI: Jennifer Pett-Ridge
Microbes Persist: Systems Biology of the Soil Microbiome

From Microbial Isolates to Metagenomes and Back: Long Read Sequencing for Predictive Microbiology
Speaker: Lauren Lui, LBNL; PI: Paul Adams
ENIGMA: Ecosystems and Networks Integrated with Genes and Molecular Assemblies

Terabase Scale Metagenome Coassembly with MetaHipMer
Speaker: Robert Riley, LBNL; PI: Nigel Mouncey
Joint Genome Institute User Facility; JGI-KBase Co-development

Putting Microorganisms on the Map: Continental Scale Context for Microbial
Speaker: Mikayla A Borton, Colorado State University; PI: Kelly Wrighton
Microbial Genomes Across the World’s Rivers Community Science Project at JGI to create GROW (Genome Resolved Open Watershed) Database Genomes Sampled from North American watersheds
Microbial ecoSystems Laboratory 

Expanding functional annotation coverage for genomic data
Speaker: William B Nelson, PNNL; PI: Robert Egbert
Persistence Control of Engineered Functions in Complex Soil Microbiomes

From Annotation Uncertainty to Modeling Confidence: Probabilistic Annotation and Ensemble Metabolic Modeling in KBase
Speaker: Patrik D’Haeseleer, LLNL; PI: Rhona Stuart
A Systems Biology Approach to Interactions and Resource Allocation in Bioenergy-Relevant Microbial Communities

Integrating Tools in KBase for Automated Fitting of Metabolic Models to Multi-omics and Growth Phenotype Data
Speaker: Hyun-Seob Song, University of NebraskaLincoln; PI: Kirsten S. Hofmockel
Phenotypic Response of the Soil Microbiome to Environmental Perturbations

Moving from Single Species to Exploration of Synthetic Community Development in Plant-Microbe Interfaces in KBase
Speaker: Priya Ranjan, ORNL; PI: Mitchel J. Doktycz
Plant-Microbe Interfaces

Visit our collaboration pages for more on Science Focus Areas and User Working Groups.
Poster Session 2

F-130: Microbes Persist: Towards Quantitative Theory-Based Predictions Of Soil Microbial Fitness, Interaction And Function In KBase
Jeffrey Kimbrel, LLNL

J-222: Probabilistic Annotation and Ensemble Metabolic Modeling in KBase
Patrik D’haeseleer, LLNL

J-228: Crosslinking KBase and the RCSB-PDB to Support Protein Function Discovery
Chris Henry, ANL

J-234: Improved Protein Annotation in KBase Using Machine Learning, Multi-Omics Data Integration, and Structural Prediction
Bill Nelson, PNNL

J-236: OMEGGA: A computationally efficient omics- guided global gapfilling algorithm for phenotype- consistent metabolic network reconstruction
Hyun Song, University of Nebraska–Lincoln

J-238: KBase Science and Infrastructure Updates (2022-2023)
Elisha Wood-Charlson, LBNL

KBase User Working Groups

Resources and Helpful Links

KBase 1-on-1 Consultation and Help (by appointment)

KBase offers one-on-one consultation support throughout the GSP meeting, as an opportunity to meet with KBase staff to discuss specific questions regarding how you would use KBase in your research. Appointments are available in-person and virtually during the GSP poster sessions. Email to request an appointment.

Data Management Plans & Promoting Inclusive and Equitable Research Plans

Resources for developing DMPs and DOE-required PIER Plans that include collaborations with KBase.

Scan to find KBase resources for DMPs and PIER Plans!

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