The National Microbiome Data Collaborative: Enabling search and discovery of microbiome data with metadata standards
The NMDC team will host an interactive, two-hour workshop to showcase the features of the NMDC Data Portal and NMDC Submission Portal. During the first hour of the workshop, attendees will explore the datasets on the NMDC Data Portal, and generate hypotheses in small breakout groups to drive search and discovery of microbiome data. During the second hour, attendees will receive hands-on experience in preparing study and biosample metadata to adhere to metadata standards used by the JGI, EMSL, and the NMDC using the NMDC Submission Portal. Researchers who are preparing to submit samples to JGI and/or EMSL are highly encouraged to attend this workshop.
Hosts: Pajau Vangay, NMDC; Montana Smith, NMDC
Wednesday, August 31st 3:30PM – 5:30PM (max 40 attendees / virtual only)
Hands-On Petabyte Scale Sequence Search of SRA
The goal of this workshop is to train participants in the use of the cloud-based tools to search SRA. Participants will have access to ElasticBLAST and Sourmash, and will be able to put these tools into some basic workflows.
The large growth in sequence data deposited in SRA coupled with a lack of accurate metadata is driving the need for new approaches to search based on the content of files. NCBI has recently shifted SRA to the cloud and has built ElasticBLAST to enable more performant search across the repository. Sourmash is a tool developed by the Luiz Irber and Titus Brown that is a MinHash based approach that they have used to create sketches of SRA data. The combination of these tools is potentially quite powerful as a way to quickly refine a subset of data with a k-mer based approach like Sourmash, and validate those results with ElasticBLAST.
Participants will need to have access to a laptop and the internet to participate.
Hosts: Kjiersten Fagnan, JGI; Tom Madden, NCBI; Titus Brown, UC Davis
Thursday, September 1st 8:00AM – 12:00PM (max 40 attendees – in person / virtual combined)
Hands-On Metabolomics Data Analysis
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.
Hosts: Trent Northen, EGSB; Ben Bowen, JGI; Mingxun Wang, JGI
Thursday, September 1st 12:30PM – 3:00PM (max 30 in person)
Explore KBase and Learn About our Newest Features
KBase is a knowledge creation and discovery environment designed for both biologists and bioinformaticians. KBase integrates a variety of data and analysis tools, from DOE and other public resources, into an easy-to-use platform that leverages scalable computing infrastructure to perform sophisticated systems biology analyses. KBase is a freely available and developer extensible platform where scientists can analyze their own data within the context of public data, using a variety of open-source bioinformatics apps to power their workflows. This workshop will provide an introduction to KBase and show new users how to navigate the platform and run several of our core workflows. We will also demonstrate our newest features that support representation of environmental samples and bulk upload of data.
Hosts: Ellen Dow, KBase; Elisha Wood-Charlson, KBase
Thursday, September 1st 3:00PM – 5:00PM (max 60 in person / 200 virtual)
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.
Host: David Goodstein, JGI
Friday, September 2nd 8:30AM – 10:00AM (max 30 in person / 30 virtual)
Multi-Omics of Microbial Eukaryotes – Workshop Agenda Here
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: Igor Grigoriev, JGI
Friday, September 2nd 10:00AM – 12:00PM (max 50 in person / 100 virtual)