DOE JGI User Meeting (March 23, 2010)

Workshop Report now available - click here to download final report

The DOE Joint Genome Institute's (JGI) Genomics of Energy & Environment 5th Annual User Meeting was held March 24-26, 2010 in Walnut Creek, California (website). The JGI invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual JGI Genomics of Energy & Environment meeting. This international gathering of researchers with an interest in sequence-based science offered three days of presentations, tours, workshops, and poster sessions. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting featured presentations by leading scientists advancing these topics.

The Knowledgebase Workshop was held on Tuesday, March 23rd and is part of a series of meetings aimed at engaging the scientific community in discussing the scientific goals and development strategy for the Kbase. The workshop was scheduled in conjunction with JGI’s Annual User Meeting, and thus will allow setting the Kbase discussions in the context of JGI’s genome and metagenome sequence data generation and analysis services. The main theme of this workshop was to discuss the Kbase as a system that would build on existing “omics” data management and analysis systems while achieving a higher level of support for the scientific community.

Research projects supported by the DOE Genomic Science program are working towards achieving a predictive, systems-level understanding of plants, microbes, and biological communities, via integration of fundamental science and technology development, to enable biological solutions to DOE mission challenges, including energy, environment, and climate. The Genomic Science program objectives are:

Determine the genomic properties, molecular and regulatory mechanisms, and resulting functional potential of microbes, plants, and biological communities central to DOE missions.
Develop the experimental capabilities and enabling technologies needed to achieve a genome-based, dynamic systems-level understanding of organism and community functions.
Develop the knowledgebase, computational infrastructure, and modeling capabilities to advance the understanding, prediction, and manipulation of complex biological systems.

Important Topics Relevant to this Workshop

Future directions for Metagenomics and implications for the DOE Systems Biology Knowledgebase
Building toward an open community Knowledgebase to meet scientific objectives

Registration for Workshop

To register for this Workshop, please click this link and provide your name, organization, telephone number and e-mail address.

Workshop Organizers

Susan Gregurick, Department of Energy

Bob Cottingham, Oak Ridge National Laboratory

Co-Chairs

Victor Markowitz, JGI and Lawrence Berkeley National Lab
Jill Banfield, University of California, Berkeley

Charge Questions

We are soliciting responses to the charge questions listed below (not more than 2 pages). Please email your response (please click this link) by March 22, 2010. Please use PDF, ASCII or DOC formats. Responses will be posted.

What are key experimental and computational next steps that build on the sequencing data and information provided by JGI and are feasible for an initial Knowledgebase implementation associated with research in microbial communities?
What types of data and information are currently available or required to accomplish these objectives?
How these research goals are hindered by an inability to access and integrate data from various sources or of other types?
What are the bottlenecks in bioinformatics and computational algorithms that need to be addressed to accomplish these goals? Specifically, is there a benefit to closer collaboration between sequencing analysis and the downstream analysis?

Response to Charge Questions

Response to Charge Questions, Louis Sherman
Response to Charge Questions, Ernest Szeto
Response to Charge Questions, Mavrommatis Konstantinos
Response to Charge Questions, Robert Landick
Response to Charge Questions, Matthias Hess
Response to Charge Questions, Igor Brown
Response to Charge Questions, Janet Jansson
Response to Charge Questions, Patrik D’haeseleer
Response to Charge Questions, Steven Hallam
Response to Charge Questions, Kerstin Kleese van Dam

Agenda

Walnut Creek Marriott, California Ball Room A, B, and C

8:30 a.m. – 8:40 a.m.               Welcome, Susan Gregurick

8:40 a.m. – 9:00 a.m.                Introduction to Knowledgebase Initiative /Workshop Objectives
                                             Bob Cottingham

9:00 a.m. – 9:30 a.m.                Science Presentation on Metagenomics: Current Experience and
                                            Future Expectations for the Kbase
                                             Phil Hugenholtz

9:30 a.m. – 10:00 a.m.              Science Presentation on Metagenomics: Current Experience and Future
                                             Expectations for the Kbase
                                             Jill Banfield

10:00 a.m. - 10:30 a.m.            Panel Summary/Audience Questions

10:30 a.m. – 11:00 a.m.            Break

11:00 a.m. – 12:30 p.m.            Informatics Perspectives and Roundtable: How to Transition from the
                                             Present Towards an Open, Shared, Integrated Kbase

Discussion Leads: Adam Arkin, Folker Meyer, Ed Uberbacher, Nikos Kyrpides, Peter Karp, Tatiana Tatusova, Victor Markowitz, Bob Cottingham

12:30 p.m. – 1:00 p.m. Working Lunch

1:00 p.m. – 1:30 p.m. Presentation of Metagenomic Workflow Example, Jill Banfield

1:30 p.m. – 3:00 p.m.                Panel Discussion, Jill Banfield

3:00 p.m. – 3:30 p.m.                Break

3:30 p.m. – 4:30 p.m.                Panel Discussion, Jill Banfield

4:30 p.m. – 5:00 p.m.                Conclusions and Adjourn, Bob Cottingham

List of Presentations

Metagenomics: Current Experience and Future Expectations for the Kbase, Jill Banfield
Introduction to the Knowledgebase Initiative, Bob Cottingham
Introduction to the Joint Genome Institute DOE Systems Biology Knowledgebase Workshop, Susan Gregurick