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README.md

SBOLExplorer

SBOLExplorer is a service that simplifies the process of analyzing and searching for parts within genetic design repositories. For questions, contact Michael Zhang at michael13162@gmail.com

Installation

  1. These installation steps assume you have the latest version of SynBioHub up and running on http://localhost:7777. For instructions, see https://github.com/SynBioHub/synbiohub.
  2. Clone this repository with git clone https://github.com/michael13162/SBOLExplorer.git.
  3. Install and run ElasticSearch 6.3 (https://www.elastic.co/guide/en/elasticsearch/reference/current/install-elasticsearch.html).
    • 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 (https://www.python.org/downloads/).
  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 ./start.sh 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.

alt text

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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