Author Archives: Elisha Wood-Charlson

Planet Microbe Townhall at 2018 Ocean Sciences

February 14, 2018, 6:30-7:30 pm, room D137-138 at the Convention Center in Portland, Oregon.

Planet Microbe, a 2017 NSF EarthCube Building Block award, aims to reunite diverse oceanographic and geobiology data types through a federated search platform that adaptively connects data repositories in ways that will enable data discovery and open data sharing for historical and on-going research efforts.

A short presentation (~30min) will start the town hall:
  1. Introduction to the project’s three-phased data integration plan,
  2. Some specifics on how Planet Microbe is linking up with BCO-DMO (Phase I)
  3. Demonstration of the current data discovery capabilities, and
  4. Ideas for community engagement – how you can get involved.

The reminder of the time will be open for questions and sharing of ideas with OSM’s microbial ecology community. We value your contributions! How we can help make ‘omics data do more for our field?

Planet Microbe arose from a community identified need for data discovery during discussions around science/cyberinfrastructure challenges. More information can be found at and our recent article at Ocean and Carbon Biogeochemistry.

Planet Microbe is about data integration

Two major issues in our field are data discovery and data integration, so Bonnie and I (Elisha) wanted to explore how Planet Microbe might help. We had a recent brainstorming event in Bonnie’s office at the University of Arizona about how Planet Microbe fits into the bigger picture of her research world (see chalkboard brainstorm below). We decided that….

Planet Microbe is about data integration.

It is NOT about building another sequencing platform or data repository. Those already exist (e.g., iMicrobe, IMG, MG-RAST, BCO-DMO, R2R, etc), but the data they contain aren’t easily discoverable across platforms.

Planet Microbe is about working to improve data integration for existing resources, and doing it in a way that enables data discovery, data exploration, and best practices for reproducible and open data sharing. By using her existing iMicrobe platform to connect sequence data sets with associated contextual data at BCO-DMO (for example), we can expand iMicrobe’s search parameters to discover data based on parameters specified in either repository.

In addition, iMicrobe will soon allow you to create a novel, user-generated data sets from disparate data repositories through the Ocean Cloud Commons (OCC). The OCC allows for remote data sets to be accessed and analysed through iMicrobe’s connection with CyVerse and the Texas Advanced Computing Center (TACC), without the time and expense of massive data transfers, local storage, and personal compute resources!

Planet Microbe is NOT about re-inventing, but it is about reconnecting you with data sets and resources.

Brainstorming data integration to kick off Planet Microbe

Planet Microbe is here!

Aloha from Planet Microbe!


Planet Microbe, a NSF EarthCube Building Block, arose from workshop conversations, mostly focused on cyberinfrastructure challenges, organized by the EarthCube Oceanography and Geobiology Environmental ‘Omics (ECOGEO) Research Coordination Network.

Planet Microbe is designed with an iterative development plan (full project summary in Planet Microbe Trellis Library), and the funding allows Dr. Bonnie Hurwitz’s development team at iMicrobe to work on some of the key cyberinfrastructure challenges from those community conversations including:

  • Data discovery
  • Data sharing
  • Access to tools for analysis and visualization
  • HPC resources
Therefore, over the next 3 years, we will still need your ideas, feedback, feature requests, etc. We encourage everyone to continue these important cyberinfrastructure conversations at Planet Microbe on Trellis.

Finally, if you like to think across microbiomes, we also recommend joining the National Microbiome Data Collaborative Trellis Group. The NMDC group is exploring ways to further integrate databases, analytics, and data sharing across diverse science domains, and is working in parallel on similar problems in metagenomics and microbiome science. Updates will be shared via their Trellis site, a place where community feedback and ideas are encouraged.

Please share this news with your collaborators and reach out if you have any Qs. Otherwise, see you on Twitter and Trellis!