From environment, to base pairs, to ocean science and geobiology: Defining the tools and technologies for an interoperable environmental ‘omics cyberinfrastructure.
July 2016: Workshop 2 - ECOGEO "Introduction to Environmental 'Omics" Training Materials
Training materials developed for the July 2016 ECOGEO workshop include a virtual machine containing tools and data sets, videos of presentations, and online protocols for:
- Unix for bioinformatics - Dr. Benjamin Tully (@phantomBugs, github; C-DEBI, USC; and Master of the ECOGEO 'Omics Virtual Machine!)
- Quality Control for Illumina Sequencing - Dr. Tully
- Design and Analysis of 16S rRNA Amplicon Surveys (Dr. Tully) including:
- Design and Analysis of Metagenomic Survey (Dr. Tully) with 1-1.5hr sessions on:
- Video of some participants on "Why I Love 'Omics"
August 2015: Workshop 1 - ECOGEO: A community focused on solutions
The aim of ECOGEO’s first workshop was to enable domain scientists and cyberinfrastructure experts to collaboratively discuss grand challenges in ‘omics science and explore use cases that translate those challenges into cyberinfrastructure needs. The group also worked to outline existing resources, brainstormed how to best leverage and expand those resources, and discussed ways to better establish best practices in the community. Information and outcomes from the workshop:
- Final Report (includes agenda, participant list, use case template and example, and results from community survey)
- Community webinar (Vimeo, slides)
We are still an active community!
- Become a member of EarthCube and join our group!
Fill out the "Join EarthCube" form and list "Oceanography and Geobiology Environmental 'Omics" as a group you would like to join.
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- Check out topics on our Forum.
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Mission Statement - Identify community needs and develop necessary plans to create a federated cyberinfrastructure to enable ocean and geobiology environmental ‘omics.
- Create a strategic network and community of field and cyber scientists to explore new facets of ‘omics data.
- Articulate the needs, challenges, and practical solutions that address: 1) development of infrastructure, 2) integration and implementation of workflows, and 3) database and resource sustainability to support ocean and geobiology environmental ‘omics research.
- Develop a community-based framework that integrates best practices for curation and analysis of ‘omics data and metadata, and facilitates collaboration and training among environmental microbiology, geobiology, and computer science disciplines.
The EarthCube Oceaography and Geobiology Environmental 'Omics (ECOGEO) Reseach Coordination Network is an NSF funded RCN that arose out of a very successful Earth Cube workshop in August 2013 called "Ocean 'omics and technology cyberinfrastructure: current challenges and future requirements". Reports from that workshop are available as a publication in Standards in Genomic Science (2014) and as an Executive Summary.
ECOGEO Steering Committee
- Edward F. DeLong (Massachusetts Institute of Technology, Univ. Hawai‛i, Mānoa) - Lead PI
- Eric Allen (Scripps Institute of Oceanography, UC San Diego) - Lead of Technology and Cyberinfrastructure (TCI) Team
- Bethany Jenkins (Univ. Rhode Island) - Co-Lead of Ocean and Geobiology Science (OGS) Team
- Jack A. Gilbert (Argonne National Laboratory) - Co-Lead of OGS Team
- Virginia Armbrust (Univ. Washinton) - OGS Team
- Dylan Chivian (Lawrence Berkeley National Laboratory) - TCI Team
- Greg J. Dick (Univ. of Michigan) - OGS Team
- John Heidelberg (Univ. Southern California) - OGS Team
- Bonnie L. Hurwitz (Univ. Arizona) - TCI Team
- Nikos Kyrpides (Joint Genome Institute) - TCI Team
- Folker Meyer (Argonne National Laboratory) - TCI Team
- Mak Saito (Woods Hole Oceanographic Institution) - OGS Team
- Erik Zinser (Univ. Tennessee) - OGS Team
- Elisha M. Wood-Charlson (Univ. of Hawai‛i, Mānoa) - Communications Manager