NMDC Hands-On Workshop
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).
Thursday, August 24th
8:00AM – 10:00AM
30 In Person / 30 Virtual
Host: Emiley Eloe-Fadrosh: NMDC Project Lead
Host: Julia Kelliher: NMDC Engagement Team Lead
Co-hosts: Thomas Pitot and Josué Rodríguez-Ramos
Multi-Omics of Microbial Eukaryotes
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.
Thursday, August 24th
10:15AM – 12:15PM
30 In Person / 50 Virtual
Host: Igor Grigoriev – Fungal & Algal Program Head
Metabolomics Data Analysis Hands-On Workshop
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.
Thursday, August 24th
1:00PM – 5:00PM
50 In Person Only
Host: Trent Northen – Metabolomics Program Head
Host: Ben Bowen – Metabolomics Group
Secondary Metabolites Collaboratory
This workshop will introduce attendees to JGI’s new portal for natural product biosynthetic gene cluster (BGC) data, the Secondary Metabolism Collaboratory, or “SMC”. We’ll explore SMC’s options to navigate its data, participate in annotation of BGCs, write a script to interact with SMC via its API, and utilize SMC’s capabilities for collaborative investigation of cryptic pathways. The workshop will give users hands-on experience and provide a greater understanding of how SMC can integrate into natural product biosynthesis investigations.
Thursday, August 24th
8:00AM – 10:00AM
Host: Dan Udwary – Secondary Metabolites
Host: Drew Doering – Secondary Metabolites
20 In Person Only
KBase: Analyzing Microbial Genomes and Community Metagenomes with KBase
This workshop will introduce the Department of Energy Systems Biology Knowledgebase (kbase.us) and showcase popular protocols for multi-omics analysis on the platform. Attendees will learn how to import data and use KBase apps for processing next-generation sequencing reads and performing assembly, annotation, feature analysis, and taxonomic assessment of genomes. 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 or get support from KBase staff.
Thursday, August 24th
1:00PM – 4:00PM
Host: Ben Allen – Oak Ridge National Laboratory
12 In Person / 50 Virtual
IMG Present Capabilities and Future Plans
We will give an overview of the current IMG system, including data processing and analysis workflows, and discuss future development plans. We will open the discussion with the participants both on the current functionality and invite feedback and ideas for the future developments and new capabilities IMG should have.
Friday, August 25th
8:00AM – 12:00PM
Host: Nikos Krypides – Microbiome Data Science Lead
Host: Natalia Ivanova – Functional Annotation Lead
Host: Rekha Seshadri – Functional Annotation Group
40 In Person Only
Navigating the Phytozome Plant Genomics Portal
Phytozome, the Plant Comparative Genomics portal of the Department of Energy Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies
This hands-on workshop will guide users through the data, analyses and tools available in Phytozome 13, and will cover the following:
– Overview of the Data Available in Phytozome 13
– Finding Your Way around: Browsing Genomes and Searching for Genes
– Gene and Gene Family Reports
– Collecting, Downloading and Sharing Data
– Special Tools: CladeCuts, Synteny Browsing, Single-Cell Transcriptome Viewer
-“So, you want to submit your genome to Phytozome”
By the end of the workshop, participants should be comfortable browsing genomes, finding genes of interest by keyword, sequence similarity, protein classification, and genomic location; identifying gene homologs and co-expressed genes; fine tuning the content of data sets for download, and creating custom genome-restricted portals.
Friday, August 25th
1:00PM – 3:00PM
Host: David Goodstein – Plant Comparative Analysis Lead
10 In Person
40 Virtual