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SBOLExplorer is a service that simplifies the process of analyzing and searching for parts within genetic design repositories. For questions, contact Michael Zhang at


  1. These installation steps assume you have the latest version of SynBioHub up and running on http://localhost:7777. For instructions, see
  2. Clone this repository with git clone
  3. Install and run ElasticSearch 6.3 (
    • The exact steps will depend on your environment, so read the manual (aka RTFM).
    • Set up the package repo to install ElasticSearch from.
    • Install ElasticSearch.
    • Start ElasticSearch (will be different depending on init vs systemd).
    • Optionally, configure ElasticSearch to start on boot.
  4. Install the latest version of Python 3 (
  5. Go to the SBOLExplorer/flask directory and run pip install -r requirements.txt to install all the dependencies. Try pip3 instead of pip if that doesn't work.
  6. Run SBOLExplorer using ./ in the SBOLExplorer/flask directory.
  7. To update the index for the first time, run curl -X GET "localhost:13162/update". Depending on repository size, this can take a couple of minutes.
  8. Optionally, run crontab update.cron to automatically update SBOLExplorer periodically.
    • To change the update period, edit update.cron
  9. In SynBioHub, go to the Admin->General page and specify http://localhost:13162/ as the SBOLExplorer endpoint, check the Searching Using SBOLExplorer checkbox, and click Save. Searches will now go through SBOLExplorer.

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To run a neat visualization, go to the force_directed_graph folder and run "http-server" in the command line. Then, open the browser to the hosted page. Shown is a network visualization of part usage in SynBioHub.

Automatic build and deploy

On each commit to master, a new Docker image is built and pushed to Docker Hub. This is done by TravisCI. The credentials used to push the image are stored in Travis.

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