Joint Genome Institute

JGI Annual User Meeting

2017 Workshops

Monday, March 20, 2017

Fungal Genomics Workshop

9:00am – 5:00pm

Host: Igor Grigoriev

Administrative Support: Casey Rundles

This full-day workshop will be devoted to discussions of the ground-breaking science coming from the 1000 Fungal Genomes Project and other fungal 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.

NERSC Computing Workshop

9:00am – 4:00pm

Host: Kjiersten Fagnan

Administrative Support: Terri Bartolome

Have you ever wanted to run someone else’s software to reproduce some analysis in a publication? Have you ever wanted to easily compare two different tools on the same data set? Are you interested in running bioinformatics tools in the cloud? In this workshop we will cover the basic tools you need to make your software portable. The Docker (https://www.docker.com/) container system makes portability straightforward and maintains good performance. We will cover how to use Docker containers on your own laptop, NERSC (LBNL/DOE Supercomputing) systems, and the cloud (AWS); build your own Docker containers; and share your work with the broader bioinformatics community. We will also cover tools for building workflows with Docker containers and a special bioinformatics flavor of containers called Bioboxes (http://bioboxes.org/). The first half of the workshop will be hands-on lectures and the second half will be a hackathon where you can build a pipeline and run it on JGI/NERSC compute resources!

Metabolomics Workshop

8:30am – 12:30pm

Host: Trent Northen

Administrative Support: Margie Lozano

This half-day workshop will provide a brief introduction to metabolomics and an overview of the JGI’s metabolomics capabilities. Topics to be covered will include important experimental design considerations, metabolomics data, and data analysis. Selected talks will provide diverse examples of current research projects integrating metabolomics with DNA sequencing and with DNA synthesis technologies. We aim for this to be an informative and highly interactive session such that attendees will leave with an understanding of how metabolomics can complement their genomics research.

Synthetic Biology Workshop

1:30pm – 5:30pm

Host: Yasuo Yoshikuni

Administrative Support: Stephanie Canon

This workshop will provide an overview of the Synthetic Biology Program at the JGI. The session will include presentations explaining the program and discussions to include current research, scientific vision and future technological advances. We aim for this to be a highly interactive session allowing users to share their experience working with DNA Synthesis Science Program with other users.

Tuesday, March 21, 2017

Genomic Technologies Workshop

9:30am – 3:30pm

Host: Len Pennacchio

Administrative Support: Melissa Trevizo

This all-day workshop will give an overview of the genomic capabilities available to JGI users through the genomic technologies group.  In the morning sessions, we will focus on genome sequencing and analysis capabilities including genome assembly, variation analysis, RNA sequencing and epigenomics.  In the afternoon session, we will discuss functional genomics capabilities, including an introduction to the JGI DNA synthesis and metabolomics programs. Finally we will give an overview of JGI sample management and logistics of approved JGI projects. We intend for these to be highly interactive sessions, and welcome comments and questions about existing technologies, as well as suggestions of new technologies that JGI should explore in the future.

KBase Workshop

9:00am – 3:00pm

Host: Bob Cottingham

Administrative Support: Meghan Drake

KBase, the DOE Systems Biology Knowledgebase, is a collaborative, open environment for computational systems biology of plants, microbes and their communities. The third annual KBase User Meeting will begin with a brief introduction to KBase for those who are not yet familiar with it. Presentations and hands-on sessions at the meeting will cover KBase’s current and planned capabilities, science workflows that can be accomplished using KBase, and examples of published results obtained using KBase tools and resources. Analysis workflows to be covered will include assembling and annotating bacterial genomes; constructing metabolic models of microbes, plants and their communities; and RNA-seq analysis. There will be a session on the KBase Software Development Kit (SDK) for developers who are interested in integrating their tools as KBase apps. The meeting will take place from 9am-3pm on March 21st in conjunction with the DOE JGI User Meeting. We encourage you to take a look at KBase (http://kbase.us/) before attending, so that you can bring any questions you may have about how to leverage KBase tools and data to address your scientific research.