Joint Genome Institute

JGI Annual User Meeting

2016 Workshops

Workshops held during the week of the JGI User Meeting require pre-registration.

Fungal Genomics Workshop

Monday, March 21st 9:00 a.m.- 4:00 p.m.

This full-day workshop will be devoted to discussions of the ground-breaking science coming from approved Community Science Proposals (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 writing successful proposals. A spectrum of genomics and other omics technologies, including epigenomics, DNA synthesis, metabolomics, and analytical tools available from JGI and partners, will be discussed.

Location: Contra Costa Room II

Host: Igor Grigoriev

Admin Contact: Casey Rundles

NERSC Workshop: Reproducible Bioinformatics Pipelines

Monday, March 21st 9:00 a.m.-4:00 p.m.

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!

Location: California Ballroom

Hosts: Kjiersten Fagnan & Michael Barton              

Admin Contact:  Terri Bartolome       

Synthetic Biology Meeting

Monday, March 21st  Noon – 4:00 p.m.

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.  This workshop will also provide an overview of the current metabolomics capabilities at JGI that can be included in CSPs. We will introduce the vision for metabolomics at JGI and describe 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.

Location: Contra Costa Room I

Host: Yasuo Yoshikuni

Admin Contact: David Haak

Confirmed Speakers:

  • Yasuo Yoshikuni, JGI – “Introduction to the DOE JGI’s Synthetic Biology – DNA Synthesis Science Program”
  • Sam Deutsch, JGI – “Synthetic Biology Tools for Pathway Refactoring to Advance Biomanufacturing”
  • Trent Northen, JGI – “Metabolomic Technologies at JGI for High Throughput Sequence to Function”
  • Lisa Simirenko, JGI – “BLiSS Black List Sequence Screening”
  • Ernst Oberortner, JGI – “Automation of the Design for Synthesis and Assembly Process using the Sequence Polishing Library (SPL)”
  • Howard Salis, Penn State University – “An Automated Pipeline for Engineering and Optimizing Metabolic Pathways and Gene Clusters”
  • Maureen Hillenmeyer, Stanford University – “Genomes to Natural Products: Computational Discovery of Natural Product Gene Clusters and Heterologous Expression in Yeast”
  • Jeffrey Kim, Radiant Genomics
  • Patrick Shih, JBEI – “Development of Plant Synthetic Biology Tools and Resources”
  • Pamela Peralta-Yahya, Georgia Institute of Technology – “GPCR-Based Sensors to Accelerate the Engineering of Chemical-Producing Microbes”

Genomic Technologies Workshop

Tuesday, March 22nd 8:30 a.m.- 2:30 p.m.

Download the agenda.

This all-day workshop will give an overview of the genomic capabilities available to JGI users through the genomic technologies group. In the morning session, we will focus on capabilities in genome sequencing, genome variation analysis, RNA sequencing and epigenomics. A lunchtime break-out session will focus on sample management and logistics of approved JGI projects. In the first afternoon session, we will cover metabolomics and gene functional genomics. The concluding session will cover DNA synthesis and genome engineering 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.  This workshop will also provide an overview of the current metabolomics capabilities at JGI that can be included in CSPs. We will introduce the vision for metabolomics at JGI and describe 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.

Topics to be covered:

  • Genomic Technnologies
  • Sequence Analysis
  • DNA Synthesis
  • DNA/RNA Sample Quality Assessment

Location: Salon D-F

Host: Matt Blow

Admin Contact: Margie Lozano

Sample QC Workshop

Tuesday, March 22nd 2:30 p.m.- 4:00 p.m.

This workshop aims at providing general training to the participants on DNA and RNA sample quantification and quality assessment.  We will share tips, provide technical support and help to address issues most often faced by JGI users during sample QC. We aim for this to be highly interactive and participants are welcome to contribute sample quality images as part of the discussion.

Host: Matt Blow

Admin Contact: Margie Lozano

Location: Salon D-F

The KBase User Meeting

Tuesday, March 22nd 9:00 a.m. – 3:00 p.m.

KBase, the DOE Systems Biology Knowledgebase (kbase.us), is a platform for users to interact with experimental data and analysis tools for comparative functional genomics and systems biology research of microbes, plants and their communities. The Second Annual KBase User Meeting will include a quick introduction to the KBase Narrative Interface, and “walk through” example analyses showing science that can be accomplished using KBase such as assembly, annotation, metabolic modeling and RNA-Seq analysis with time allowed for hands on experience, an overview of the new App Catalog and Narrative Library, how to push your JGI data to KBase for analysis, and a demonstration of the new SDK that enables users to integrate their analysis tools into KBase.

Location: Contra Costa Room II

Host: Bob Cottingham

Admin Contact: Meghan Drake