Genomic Science Program PI Meeting 2023

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

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

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: https://lbnl.zoom.us/meeting/register/tJcpduCorj0oE91UyaqLacDZZKiumUPbyZ5Q

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. 

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 Nebraska–Lincoln; 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

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