Register for workshops when registering for the Annual Meeting. Workshop fees range from $25-$100.
NMDC Hands-On Workshop:
Overview of the NMDC and Tutorial on the Submission Portal, NMDC EDGE and the Data Portal.
Monday, September 30
04:00-06:00PM
This workshop will integrate live demonstrations and hands-on activities to provide an overview of the National Microbiome Data Collaborative (NMDC), and will cover themes of microbiome data stewardship, FAIR data, and microbiome data standards. This workshop will introduce attendees to new features incorporated into the 3 NMDC Products: the NMDC Submission Portal, the NMDC Data Portal, and NMDC EDGE (a platform for running the NMDC standardized bioinformatics workflows).
Host: Emiley Eloe-Fadrosh: NMDC Project Lead
Co-hosts: Rebecca Maher, Zachary Murcham, Daniela Betancurt-Anzola
Analyzing & Publishing Microbial Genomes and Community Metagenomes with KBase
Thursday, October 3
01:30-3:30PM
This workshop will provide an overview of the Department of Energy Systems Biology Knowledgebase (KBase) through both live demonstration and hands-on practice using the KBase platform. Participants will learn how to import data, develop customized analysis workflows, and publish their research Narratives. Participants will be able to build a workflow using KBase apps that process next-generation sequencing reads, assemble, bin, annotate, and perform feature analysis and taxonomic classifications on metagenomic data. The hosts will also demonstrate how to use KBase Narrative templates for data publications for American Society for Microbiology’s Microbiology Resource Announcements. New and experienced KBase users alike will have the opportunity to familiarize themselves with recently added features, best practices to get credit for sharing data, and connect with the KBase team.
Host: Ben Allen – Oak Ridge National Laboratory
Host: Ellen Dow – Lawrence Berkeley National Lab
Multi-Omics of Microbial Eukaryotes
Thursday, October 3
01:30-03:30PM
This workshop will be devoted to discussions of the ground-breaking science on fungi and algae coming from the JGI Community Science Projects (CSP), recent developments of the JGI Fungal & Algal Program and ways to start new projects with JGI. PIs of successful CSP projects will present their research and share their tips on developing successful proposals. A spectrum of genomics, omics, and analytical tools from JGI and partners will be discussed.
Host: Alan Kuo – Fungal & Algal Program
Host: Stephen Mondo – Fungal & Algal Program
Metabolomics Data Analysis Hands-On Workshop
Thursday, October 3
01:30-5:30PM
Here we will introduce the JGI metabolomics experimental design, JGI metabolomics data analysis pipelines, interactive data analysis and exploration of JGI results via the web, and help users do hands-on data analysis using GNPS to mine metabolomics dark matter.
Host: Trent Northen – Metabolomics Program Head
Host: Ben Bowen – Metabolomics Program Group
Satellite Conference: Advancing terrestrial microbiome science through fabricated ecosystems
Thursday, October 3
01:30-06:00PM
This satellite conference will bring together scientists using synthetic microbial communities (SynComs) to study microbial interactions within controlled laboratory ecosystems. Leaders in the field will present the latest progres in using these laboratory methods to study plant-microbe interactions, bacterial interactions, and fungal interactions including development of advanced imaging and Omics analyses to study spatiotermporal dymamics. We will also describe resources that are available at both JGI and PNNL to support these studies. Please note that space is limited for this first annual conference.
Host: Trent Northen – Metabolomics Program Head
IMG Workshop
Thursday, October 3 | 01:30-05:30PM AND Friday, October 4 | 09:00AM-05:00PM
This 1.5 day workshop is designed to familiarize JGI users with the Integrated Microbial Genomes & Microbiomes (IMG/M) data and workflows for computational analysis and interpretation of sequence data. IMG/M is a web-based platform that provides access to the wealth of public microbiome sequence data and enables the user to analyze and compare these data in order to bridge the gap from sequence to biology. Learn more about IMG/M’s capabilities by watching our introductory video.
Users will learn how JGI-generated sequence data is processed by assembly and annotation pipelines. A brief overview of JGI portals (IMG, GOLD, and Data Portal) will be presented to highlight tools for small-scale sequence retrieval and large-scale data downloads. Users will also complete hands-on exercises employing advanced search (using metadata), comparative analysis, and visualization tools within IMG.
Attendees are expected to have basic understanding of microbiology, biochemistry or molecular biology, and computational biology concepts (e.g., multiple sequence alignment, phylogenetic tree construction, metagenomics, binning). Although this workshop centers on computational topics, no programming knowledge is required; all exercises will be performed using the IMG web user interface.
Host: Natalia Ivanova – Functional Annotation Lead
Host: Rekha Seshadri – Functional Annotation Group
JGI’s Scalable Metagenomics Toolbox Workshop
Friday, October 4 | 09:00AM-12:00NN
This workshop serves as an introduction to JGI’s scalable metagenomics toolbox. Presentations will cover large-scale metagenome assembly using MetaHipMer, metagenome binning with MetaBAT and GenomeFace, and large-scale metagenome protein family detection with HipMCL. We will also introduce a new Apache Spark based scalable genomics library, Axolotl, and demo its usage in large-scale biosynthetic gene cluster discovery. The workshop will also have a hands-on component focused on customized analysis with Axolotl using cloud computing. This workshop is designed for users who are interested in using the JGI scalable tools for customized large-scale data analysis.
Host: Zhong Wang – Genome R&D Lead
Host: Satria Kautsar – Genome R&D Group