Monday – Tuesday – Wednesday – Thursday – Friday
March 26-28, 2013 (TUESDAY-THURSDAY)
2013 JGI User Meeting
2013 Workshops
Other annual workshops held during the week of the JGI User Meeting require separate pre-registration. See below.
March 25, 2013 (MONDAY)
March 26, 2013 (TUESDAY)
MONDAY – March 25
KBase Outreach Workshop
Date: Monday, March 25
Time: 1:00 PM – 5:00 PM
Location: Walnut Creek Marriott at Salons A, B, C
Breakout sessions are as follows:
Plants: stays in Salons A, B, C
Microbes: Sacramento Room
Communities: Santa Rosa Room
Audience: All current and potential KBase users.
Description: The KBase: An Integrated Knowledgebase for Predictive Biology and Environmental Research Project is developing a community-driven software framework enabling data-driven prediction of microbial, plant, and biological community function in an environmental context. Extensible and scalable, KBase features open architecture, source code, and development. This cyberinfrastructure will vastly improve algorithmic development and deployment efficiency, as well as access to, and integration of data from heterogeneous sources. As a result, KBase is striving to provide the means for solving a wide range of biological problems that span understanding the reciprocal effects of community-environment interactions to creating advanced biofuels by leveraging laboratory microbes.
The KBase Outreach Workshop will begin with an overview the KBase Project followed by concurrent demos for the Plants, Microbes and Microbial Communities science domains.
The Workshop will be limited to 100 participants.
KBase Outreach Workshop Agenda:
- 1:00 p.m. – 2:00 p.m. KBase Overview
- 2:00 p.m. – 2:20 p.m. Break
- 2:20 p.m. – 5:00 p.m. Concurrent Demos for Plants, Microbes, and Microbial Communities
- 5:00 p.m. Adjourn
For further details and information, please contact: Meghan M. Drake ([email protected])
Workshop Hosts: Elizabeth Glass, Argonne National Laboratory
Registration: Pre-registration required.
Fee: No registration fee.
Metaproteomics of the Soil
The Challenges and Possibilities
Date: Monday, March 25
Time: 9:00 AM – 5:00 PM TBC
Location: TBA
Description: The contribution of microbial processes to soil biogeochemistry, particularly the management of soil carbon and nitrogen, is arguably one of the most important knowledge gaps in terrestrial ecology. Discovery and characterization of these microbial processes using environmental samples is being pursued by means of multiple “omics” approaches including metagenomics, metatranscriptomics, and metaproteomics. Metagenomic sequencing, enhanced by the latest advances in DNA sequencing technologies, is enabling unprecedented illumination of microbial community composition in soils. The sequence data alone, though, provides only limited information on the metabolic potential of the microbes to mediate terrestrial biogeochemistry. Metatranscriptomes, when directly associated with metagenomic data, elucidate the genes that are actively transcribed by a community, and, therefore, allow prediction of active metabolism in response to spatial or temporal environmental gradients. It is metaproteomics, however, that identifies the actual microbial proteins that are post-transcriptionally regulated and translated under particular environment conditions; ultimately, it is the protein activity or lack of activity that results in a phenotype. With approximately 30-40% of putative proteins encoded in any genome having no known function, environmental microbes represent a vast wealth of novel protein function and potential new biochemistry, the understanding of which will be critical to informing our understanding of the microbial component of soil biogeochemistry.
Significant technical and informatics challenges exist for soil metaproteomics, some of which are being addressed with some success using current methods, while others will require novel approaches. The goal of this workshop is to engage metaproteomics experts in a discussion with the “omics” community regarding the current status of soil metaproteomics, focusing on both the technical and informatics challenges encountered in the identification of the proteins isolated from soil samples. Invited speakers will provide their views of the challenges, as well as potential solutions, associated with protein identification, as well as integration with metagenome and metatranscriptome data, and, ultimately ecological characterization in soil environments. Breakout sessions will engage the community in the discussion, with the aim of developing consensus on questions such as:
- What existing tools can be leveraged to integrate multi-omics data sources to better inform metaproteomics studies, and what tool-gaps exist for analyzing existing datasets?
- How can multi-omics analyses be used to define ecological properties of soil systems, e.g. by defining niche space, and niche diversification in spatial and temporal dynamics.
- What is the correlation between metatranscriptomics and metaproteomics data?
- What are the challenges in assembling the metaproteome from the observed peptidome and how does this compare to the challenges in contig assembly from NGS data?
- Due to technical challenges, the metaproteomic data is not as complete as the metagenomic or metatranscriptomic counterparts. What are the consequences when attempting the reconstruction of activities in the microbial community?
- Can metagenomics and metatranscriptomics be used to define a core set of ‘unknown’ proteins to focus protein characterization?
- Can metaproteomics data be used to refine metagenome annotations?
Workshop organizers: Carol S. Giometti (Argonne National Laboratory), Janet R. Jansson (Lawrence Berkley National Laboratory), Robert L. Hettich (Oak Ridge National Laboratory).
For further details and information, please contact: Carol S. Giometti ([email protected]).
Workshop Host: Carol S. Giometti, Argonne National Laboratory
Registration: Pre-registration required.
Fee: No registration fee.
TUESDAY – March 26
Genomic Technologies Workshop
Date: Tuesday, March 26
Time: 9:00 AM – 3:00 PM
Location: TBA
Audience: All current and potential JGI users with an interest in Genomic Technologies.
Description: An all-day workshop highlighting the genomic capabilities that are available to JGI users through the genomic technologies group. In the morning session, we will discuss technologies applied to eukaryotic organisms. This includes techniques for comprehensive transcriptome analysis, epigenomics, and analysis of genome variation. In the afternoon we will focus on capabilities for genomic analysis of Prokaryotic organisms. This includes single cell genomics, epigenomics and functional genomics. Each talk will provide an overview of the experimental and computational approaches employed, followed by illustrate case studies from recent sequencing projects. 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.
Workshop Hosts: Zhong Wang, Tanja Woyke, Chia-Lin Wei, Len Pennacchio, JGI Genomic Technologies
Registration: Pre-registration required.
Meals provided: Morning refreshments, and lunch.
Fee: $100