IMG – IMG/metagenomes – RNA Technologies & Analyis – Resequencing Analysis –
Mycocosm – Phytozome – MENGO – KBase Outreach
IMG Workshop
Date: Monday, March 19
Time: 9:00 AM – 5:00 PM
Location: Walnut Creek Marriott
Audience: Users and potential users of the Integrated Microbial Genomes (IMG) data analysis systems.
Description: 1-day workshop with hands-on tutorials on IMG. Note: To participate in this hands-on-tutorial workshop, you will need to bring your own laptop computer.
Website: http://img.jgi.doe.gov/
IMG/Metagenomes Workshop
Date: Tuesday, March 20
Time: 9:00 AM – 12:00 PM
Location: Walnut Creek Marriott
Audience: Users and potential users of the Integrated Microbial Genomes (IMG) with Microbiome Samples (IMG/M) data analysis system.
Description: Half-day workshop with hands-on tutorials on IMG/M. Note: To participate in this hands-on-tutorial workshop, you will need to bring your own laptop computer.
Website: http://img.jgi.doe.gov/cgi-bin/m/main.cgi
RNA Technologies and Analysis Workshop
Date: Tuesday, March 20
Time: 8:00 – 11:00 AM
Location: Walnut Creek Marriott
Audience: All current and potential JGI users with an interest in RNA projects.
Description:This workshop provides an overview of the RNA/transcriptome technology and analysis pipelines at the JGI. We will present a comprehensive overview of the current technology suite for transcriptome interrogation, including RNA-seq for expression profiling, 5’&3′ paired-end sequencing on transcript boundaries and smRNA discovery. The last half of the workshop will consist of breakout sessions to demonstrate in-depth hands-on exercise. We will guide you through the complex analysis of RNA-Seq data by using representative, real-world examples. To participate in the optional hands-on portion of the workshop you will need to provide your own laptop.
Website: http://galaxy.jgi-psf.org
Resequencing Analysis Workshop
Date: Tuesday, March 20
Time: 8:00 AM – 11:00 AM
Location: Walnut Creek Marriott
Audience: All current and potential JGI users with an interest in resequencing projects.
Description:This workshop provides an overview of the resequencing analysis performed at the JGI. The workshop consists of a PowerPoint presentation walking through every step of resequencing from receiving your sample to delivery of the analysis followed by hands-on exercises with analysis output. Additionally, we show examples of how to visualize the data, discuss common pitfalls which lead to false positive and false negative calls, and demonstrate some techniques for troubleshooting the data. To participate in the optional hands-on portion of the workshop you will need to provide your own laptop. For instructions on how to set up your laptop with the appropriate software and data sets for the demonstrations go to http://sites.google.com/a/lbl.gov/reseq/.
Mycocosm Workshop
Date: Tuesday, March 20
Time: 1:00 PM – 4:00 PM
Location: Walnut Creek Marriott
Audience: Users and potential users of the Mycocosm fungal genomics portal.
Description: The JGI Mycocosm web-portal provides data access, visualization, and analysis tools for comparative genomics of fungi. The goal of this workshop is to train both new and experienced users on how to use the key elements of Mycocosm including navigation across sequenced fungal genomes, comparative and genome-centric analyses of fungi and community annotation. Participants will learn how to analyze genome structure, gene families and pathways, search for genes of interest, add and curate your own data. This is a hands-on tutorial using laptop computers; please bring your own laptop. Note: To participate in this hands-on-tutorial workshop, you will need to bring your own laptop computer.
Website: http://genome.jgi-psf.org/programs/fungi/
Phytozome Workshop
Date: Tuesday, March 20
Time: 1:00 PM – 4:00 PM
Location: Walnut Creek Marriott
Audience: Users and potential users of the Phytozome plant genomics portal.
Description: The Joint Genome Institute’s Phytozome web portal provides data access and visualization tools for comparative plant genomics. Phytozome integrates a number of widely used Open Source genomics platforms (GBrowse, BioMart, Jalview) with data systems, search, and visualization tools developed at JGI. This workshop will provide participants with an overview of the plant genomic data available at Phytozome, the various “entry points” to the Phytozome portal (e.g. sequence similarity search, functional and keyword search, genome browsing), data retrieval tools, and the types of analyses that are facilitated by Phytozome’s integrated environment. Note: To participate in this hands-on-tutorial workshop, you will need to bring your own laptop computer.
Website: www.phytozome.net/
MENGO Workshop
MENGO Workshop (Gene Ontology Terms for Energy-Related Microbial Genomes)
Date: Friday, March 23
Time: 8:30 AM – 5:00 PM
Location: Walnut Creek Marriott
Description: The MENGO project’s goal is to create new Gene Ontology (GO) terms that can be used in the annotation of microbial genomes of bioenergy interest. The aims of the workshop are to present current status of term development – over 300 terms have been developed to date, and over 200 annotations made. The discussion session will focus on feedback from the community on the current terms and other bioenergy areas to be targeted for further term development. The workshop flier and agenda is attached to this message.
Workshop Hosts:
Brett Tyler, Oregon State University
Biswarup Mukhopadhyay, Virginia Bioinformatics Institute, Virginia Tech
Endang Purwantini, Virginia Bioinformatics Institute, Virginia Tech
Trudy Torto-Alalibo, Virginia Bioinformatics Institute, Virginia Tech
Joao Setubal, University São Paulo, Brazil
Nikos Kyrpides, DOE Joint Genome Institute (Local Host)
Registration is required; no registration fee.
Breakfast, lunch and dinner will be provided.
Lodging reimbursement: see below
Register:
*Requests for lodging funds are included here. Should funding be granted, the participant will only be guaranteed reimbursement for the double room rate.
*Please note that registration for this workshop is separate from other JGI User Meeting events.
Dinner sign up:
*For further details and information, please contact:*
Maureen Lawrence-Kuether
Erin Sexton
Trudy Torto-Alalibo
Biswarup Mukhopadhyay
KBase Workshop
Date: Monday, March 19, 2012
Description: The DOE Office of Biological and Environmental Research Genomic Science program funds a portfolio of systems biology research that produces petabytes of data annually. To provide the research community with improved access to this resource and enhance scientific productivity, the Genomic Science program is developing the DOE Systems Biology Knowledgebase (KBase). The KBase: An Integrated Knowledgebase for Predictive Biology and Environmental Research Project will develop a community-driven software framework enabling data-driven prediction of microbial, plant, and biological community function in an environmental context. Extensible and scalable, KBase also will feature 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 will 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 introduction and timeline for the KBase Project. The Plants, Microbes, Communities, and Infrastructure teams will present short introductions to the objectives for prototype demonstrations for March 2013. Subsequently there will be separate breakout sessions for the Plants, Microbes and Microbial Communities science domains to provide detailed descriptions of the planned demonstrations, how they are being developed, and current status. The breakout sessions will focus on the following issues in order to cultivate deeper discussions, and to obtain the science community’s feedback and suggestions for improvements. The Workshop Agenda is shown below.
- Plants – improvements in data exploration, integration and genotype workflows.
- Microbes – improvements in data integration and visualization, metabolic modeling and regulatory networks.
- Microbial Communities – improvements in data analysis, visualization, and bioprospecting.
The purpose of this Workshop is to foster deeper engagement from the science community’s key partners and stakeholders, provide information and plans on how the KBase system is being developed, the progress to date, and the targets.
The expected outcomes are to (1) strengthen, engage, and obtain commitments from the science community’s working groups of key power users and partners, (2) confirm that the planned developments will be used, (3) ensure that the required data is available, and (4) coordinate to minimize duplication of effort.
The Workshop will be limited to 100 participants.
KBase Outreach Workshop Agenda:
12:00 p.m. – 12:10 p.m. Introduction to KBase Overview and Timeline
12:10 p.m. – 12:30 p.m. Plants Science Team Presentation
12:30 p.m. – 12:50 p.m. Microbes Science Team Presentation
12:50 p.m. – 01:10 p.m. Communities Science Team Presentation
01:10p.m. – 01:30 p.m. Infrastructure Team Presentation
01:30 p.m. – 01:45 p.m. Break
01:45 p.m. – 03:45 p.m. Breakout Sessions for Plants, Microbes, and Communities
03:45 p.m. – 04:05 p.m. Plants Session Summary Presentation
04:05 p.m. – 04:25 p.m. Microbes Session Summary Presentation
04:25 p.m. – 04:45 p.m. Communities Session Summary Presentation
4:45 p.m. – 05:00 p.m. Further Actions
05:00 p.m. Adjourn
For more information, please contact Cheri Bandy Foust ( [email protected])