The Collaborative Microbial Metabolite Center (CMMC) will be offering a hands-on workshop Global Natural Products Social Molecular Networking (GNPS version 2.0). GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS aids in the identification and discovery of natural products throughout the entire life cycle of data. In this workshop, we will introduce the participants to how to use molecular networking and repository scale metabolomics analysis of microbial data in the GNPS analysis ecosystem. Specifically, participants will be introduced to: (i) untargeted metabolomics, (ii) molecular networking, (iii) GNPS dashboard, a Google doctype infrastructure for collaborative inspection of raw data, (iv) MicrobeMASST searches for molecules, (v) CMMCkb enrichment (microbial metabolite knowledgebase) and (v) MassQL, a repository query of MS data for identification.

Instructor

Prof. Pieter Dorrestein, PhD, University of California – San Diego

Certificate of Attendance

A certificate of attendance is available after the completion of the workshop and by email request only. Please contact registrar@simbhq.org.

After 12/9/2024 on-site registration rates apply.
SIMB Member Rate: $75

After 12/9/2024 on-site registration rates apply.
Non-Member Rate: $85

Workshops are for registered attendees of the Natural Product Discovery and Development meeting only.

Although there are still a large number of secondary metabolites yet to be discovered and their biosynthetic logics to be understood, accessing these untapped metabolic capabilities is often tedious and resource intensive. This is often due to, for example, tight regulation of biosynthetic gene clusters (BGCs) in native hosts, the complexity of cloning and expressing a given BGC in various hosts, availability of sequenced genomes, and computing resources needed to predict BGCs from available genome sequences. The DOE Joint Genome Institute (JGI), a DOE Office of Science User Facility, has been developing and applying new genomics capabilities that address these issues. During the first half of the workshop, we will introduce these capabilities such as large-scale (meta)genome and (meta)transcriptome sequencing, DNA synthesis and host engineering, FACS, metabolomics and DAP-seq, which the attendees may access through the Community Science Program. During the second half, we will introduce JGI’s web portal for the BGC data, the Secondary Metabolism Collaboratory (SMC), the largest public database of BGCs, their sources, and their genes. We will provide attendees hands-on experience navigating data in SMC via the web interface, demonstrate programmatic data access via the SMC API, and provide a roadmap for the future of this exciting new data platform.

Instructors

Drs. Hiroshi Otani, Dan Udwary, Drew Doering and Nigel Mouncey at DOE Joint Genome Institute

Certificate of Attendance

A certificate of attendance is available after the completion of the workshop and by email request only. Please contact registrar@simbhq.org.

After 12/9/2024 on-site registration rates apply.
SIMB Member Rate: $75 SOLD OUT

After 12/9/2024 on-site registration rates apply.
Non-Member Rate: $85 SOLD OUT

Workshops are for registered attendees of the Natural Product Discovery and Development meeting only.