DOE JGI Genomics of Energy and Environment Meeting
Tuesday, March 13, 2018
KBase Workshop: Genome Analysis
8:30 AM – 12:30 PM
This workshop will cover analysis tools for quality control and assessment of NGS reads, de novo assembly, genome annotation, comparative genomics and modeling with both microbial and plant examples with reference to published examples using KBase. There will also be a short session on KBase extensibility and discussion of relevant aspect of the KBase data model to solicit feedback on suggested future development.
Host: Bob Cottingham
Fungal Genomics Workshop
9:00 AM – 5:00 PM
This full-day workshop will be devoted to discussions of the ground-breaking science coming from the JGI Community Science Projects (CSP), recent developments of the JGI Fungal 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
Prokaryotic Program Workshop – Exploring Strategies for Microbial/Metagenome Discovery
9:00 AM – 5:00 PM
This workshop will better prepare researchers to tap into the JGI’s capabilities residing in the Prokaryotic Super Program. The session will include presentations about the Microbial and Metagenome Programs as well as the Informatics and Data Science resources available. Discussions will include current research, scientific vision and future technological advances. We aim for this to be a highly interactive session, including a brief tutorial of Integrated Microbial Genomes & Microbiomes (IMG/M). We welcome comments and questions about existing technologies, as well as suggestions for new user capabilities that JGI should explore in the future.
Agenda for the Prokaryotic Program Workshop.
Host: Nikos Kyrpides
KBase Workshop: Community Analysis
1:00 PM – 5:00 PM
This section will cover the analysis of microbial communities such as microbiomes. Microbial community analysis identifies diverse metabolic potential of a community and the trophic interactions that are essential to sustainability of the community. Topics covered include: contig binning and genome annotation; metabolic model reconstruction and analysis; and community model reconstruction and analysis. There will also be a short session on KBase extensibility and discussion of relevant aspect of the KBase data model to solicit feedback on suggested future development.
Host: Bob Cottingham
KBase Workshop: Functional Analysis
1:00 PM – 5:00 PM
The aim of this session is to familiarize users with the resources available for comparative genomics and gene expression analysis. Comparative genomics resources include apps that range from basic functional analysis for gene function prediction using homology based approaches to multiple genome comparisons. Gene expression analysis resources include apps for quality control, alignment, assembly and downstream gene enrichment analysis to link dynamics of gene activity to phenotypes. There will also be a short session on KBase extensibility and discussion of relevant aspect of the KBase data model to solicit feedback on suggested future development.
Host: Bob Cottingham
Wednesday, March 14, 2018
KBase Workshop – How to integrate your tools into KBase using the SDK
8:30 AM– 12:00 PM
This session will demonstrate how bioinformatics tool developers can integrate their command-line tools into the KBase platform. KBase staff will walk through a detailed example of adding an application using the KBase SDK, discussing topics such as how to handle dependencies, retrieve and store data in KBase, and debug new applications.
Host: Bob Cottingham
Technology Overview
8:30 AM – 12:00 PM
This half-day workshop will give a comprehensive overview of the capabilities available to JGI users through the genomic technologies group. We will give updates on the latest sequencing platforms (Illumina, PacBio, Oxford Nanopore) and functional genomics technologies (transcriptomics, epigenomics), introductions to metabolomics and synthetic biology capabilities, and an overview of production informatics analysis capabilities. Each talk will provide an overview of the experimental and computational approaches employed, followed by an illustrative case study from a recent sequencing project. We intend for this to be a highly interactive session, and welcome comments and questions about existing technologies, as well as suggestions of new technologies that JGI should explore in the future.
Technology Overview UM 2018 Agenda
Host: Matt Blow
Synthetic Biology Metabolomics Workshop
1:00 PM – 4:00 PM
This workshop will provide an overview of the DNA Synthesis Program and its platform capabilities and Metabolomics Program capabilities at the JGI with a view toward enabling new users to tap into the JGI via the Community Science Program mechanism. The DNA synthesis portion of the session will include presentations explaining the program, capabilities, current research, scientific vision, and future technological advances. The metabolomics portion will provide an overview of JGI capabilities, an introduction to metabolomic technologies, relevant data analysis, and key experimental considerations. We aim for this to be an informative and highly interactive session allowing users to share their experience working with the JGI and audience to learn how DNA synthesis and metabolomics capabilities complement their genomics research.
Agenda for the Synthetic Biology Metabolomics Joint Workshop.
Hosts: Yasuo Yoshikuni and Trent Northen
Sequencing tools, technologies, and advanced methods at the JGI
1:00 PM – 4:00 PM
This is a two part workshop focused on Sample Management and new Library developmental activities at the JGI. In the first half we will begin with an introduction by the Project Management team on the logistics for submitting samples for approved JGI projects. This is followed by an overview of the JGI Sample Management processes for assessing user samples. We will discuss how we determine quantity and quality for genomic DNA samples for the Pacific Biosciences and the Illumina platforms, and RNA samples for various transcriptomic applications including RNA-seq, small RNA-seq and full-length cDNA sequencing (Iso-seq). We will share best-practices and tips to address common issues faced by JGI users. In the second half of the workshop we will discuss new epigenomic and single-cell products under-development at the JGI including ChIP-seq, ATAC-seq, DAP-seq and Drop-seq. Presentations will include a general overview of protocols, troubleshooting, and how data is analyzed and applied to address important biological questions. Our aim is for the workshop to be interactive and we encourage an open discussion between participants and our Sample Management and Libraries teams at the JGI.
Agenda for the Sequencing tools, technologies, and advanced methods at the JGI Workshop.
Host: Yuko Yoshinaga
Sequence to Science: An Overview of Analysis at JGI
1:00 PM – 4:00 PM
JGI will host a four hour tutorial covering data analysis tools and procedures used by QAQC, genome assembly, and user support teams. We will cover data flow through the analysis pipelines and describe details of various tools and processes we use for converting sequence data into high quality completed user projects.
This workshop is broken into two parts. The first half will cover general sequence analysis workflows following data generation at the JGI. The majority of product types will be discussed. The second half will focus on more detailed use cases and live tutorials as examples of real user projects. The hosts of this workshop will be members from the Quality Control, Genome Assembly, and User Support Groups.
Host: Alex Copeland