Genomic Science Program PI Meeting 2024

Leads: Hyun, Bill, Jason, Patrik, Chris

With the goal of improving the overall accuracy and precision of microbial annotations, developers from several SFAs teamed up with KBase to update ModelSEED tools for building improved metabolic models in KBase. In this workshop, participants will use KBase to build models from multiple input annotation sources, leveraging tools co-developed with the LLNL µBiospheres SFA. The workshop will also cover the new Snekmer annotation tool developed by the PNNL Persistence Control SFA, and demonstrate tools for using models derived from annotations to simulate phenotype data (based on experimental isolate phenotype data in KBase contributed by the PMI and ENIGMA SFAs). Finally, the workshop will demonstrate the OMEGGA tool developed by the PNNL Soil Microbiome SFA to enable the fitting of metabolic models to phenotype data to propose novel annotations.

In-person: White Oak (A and B)

This session will be hybrid, with space for ~30 people in-person. Please sign up via Zoom registration: https://lbnl.zoom.us/meeting/register/tJEodu2srDwtHdTBG14D4fYP_opWmWMa99RL 

Leads: Lauren, Ben, Elisha

In early Dec 2023, ENIGMA and KBase partnered to deliver a Long-read Isolate Sequencing and Assembly workshop (LISA workshop). Details at https://sites.google.com/lbl.gov/lisaworkshop. This GSP session will walk through the LISA workshop structure, outline the wet lab and computational procedures used to generate and analyze long-read isolate sequence data, and emphasize the ease and importance of sharing data among the BER research community, while still getting credit for your contributions. If you are interested in long-read sequencing and how to generate data that are comparable across BER-relevant research, join us for an interactive walk-through on how to do long-read sequencing, analysis, and publishing. 

In-person: White Oak (A and B)

This session will be hybrid, with space for ~30 people in-person. Please sign up via Zoom registration: https://lbnl.zoom.us/meeting/register/tJItcuugrTkjGNzL7D-CXMMTJAioxxcvoHm- 

Room D

2:30pm   Adam Arkin (LBNL)
Coping with Data: Towards Community-Driven Data Representation and Organization to Drive Biological Data Science

3:15pm   Moderator – Lee Ann McCue (PNNL); Panelists: Kerstin Kleese van Dam (BNL), Shantenu Jha (BNL), Adam Arkin (LBNL), Nikos Kyrpides (JGI), Kjiersten Fagnan (JGI)
Panel Discussion: Challenges of Data Integration Across BER Data Systems

White Oak (A and B)

Session Moderator – Ramana Madupu

Much of biological science knowledge is based on prediction – algorithmic assessment of taxonomy and function, determined by parameters based on current knowledge. But how certain are we that those parameters are accurate across the tree of life, across ecosystems, and across time. By exploring and integrating multiple lines of evidence (i.e., multi-omics data, experimental validation, mechanistic modeling, machine learning, etc), we can build a story that supports or refutes our predictions. This session will feature examples of research questions and tools integrating data with the goal of building trust in our assertion of the world around us.

3:45pm   Welcome – Why bother with data integration, and why does my data matter?

3:50pm   Dale Pelletier (ORNL)
Measuring microbial phenotypes for improving genome-based predictions

4:05pm   Shinjae Yoo (BNL)
Knowledge extraction from literature

4:20pm   Break

4:30pm   Chris Henry (ANL)
Predicting protein function using structure and sequence similarity in KBase

4:15pm   Bill Nelson (PNNL)
Integrating data to predict functions for gaps in metabolic models

5:00pm   Paramvir Dehal (LBNL)
Leveraging LLMs to synthesize and develop new questions

5:15pm   Elisha Wood-Charlson (LBNL)
Getting credit for contributions in a big data world 

5:30pm   End of session

Plant-Microbe Interfaces SFA

Leads: Ranjan, Ulas, Gianna, Chris

This session will demonstrate new workflows envisioned for analyzing microbial communities in KBase using tools currently under development. We will show how to build community metabolic models, highlighting new tools for performing community-level flux balance analysis with examples of successful analyses of species interactions from multiple microbiome systems. We will demonstrate the CommScores tool being co-developed with the PMI SFA for predicting likely pairwise interactions among all the genomes in an input set. We will also demonstrate new apps that enable seamless prediction of ecophysiological traits of bacteria and archaea from KBase genomes (microTrait) and their representation in a coherent dynamic energy budget-based trait-based modeling framework (DEBmicroTrait).

In-person: White Oak A and B

This session will be hybrid, with space for ~30 people in-person. Please sign up via Zoom registration: https://lbnl.zoom.us/meeting/register/tJUocuihqjwoGtQqVd117fQmJlAuLL__fDuI

Microbes Persist SFA

Leads: Jeff, Elisha, AJ, Kathleen

The ability to conduct quantitative stable isotope probing (qSIP) has become more accessible to the BER community through the efforts of the LLNL’s Microbes Persist SFA to streamline and share qSIP data analysis steps in KBase. This workshop will demonstrate how the SFA and KBase teams are envisioning the upload and validation of sample and qSIP fraction tables, and subsequent qSIP analysis and comparison features in KBase. If you already do qSIP, or are thinking about including qSIP in your future research plans, please join this workshop and give us feedback on the integration and user experience of these features.

In-person: White Oak A and B

This session will be hybrid, with space for ~30 people in-person. Please sign up via zoom registration: https://lbnl.zoom.us/meeting/register/tJYocOqgqT8tGdfoKJZBeE9vkVmIknHrVNsX 

Room D

Moderators – Na Ji (University of California, Berkeley), Chris Henry (ANL), and Hugh O’Neill (ORNL)

In a roundtable discussion attendees will identify scientific opportunities for ECR principal investigators that support bioenergy and environmental research within BER and identify key biological questions and novel methods for exploring bioenergy and environmental research.