SBOLExplorer

View the Project on GitHub SynBioDex/SBOLExplorer

SBOLExplorer

SBOLExplorer is a service that simplifies the process of analyzing and searching for parts within genetic design repositories.

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.
    • Important: If you are running ElasticSearch in Docker, make sure to run sysctl -w vm.max_map_count=262144 on Linux, or docker-machine ssh then sysctl -w vm.max_map_count=262144 if you are on Windows or MacOS.
  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.
    • Note: If you want to manually rename your index name in Elasticsearch after the initial creation, make sure to change the “elasticsearch_index_name” field in the config file.
  8. Optionally, edit the “autoUpdateIndex” and “updateTimeInDays” fields in the config file to update your index automatically.
  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.

Setting up a virtual environment

Create a virtual environment in the parent directory. You can use the example commands below to create a virtualenv called sbol-explorer-venv.

OS Command
Ubuntu virtualenv sbol-explorer-venv
Mac pyvenv sbol-explorer-venv

Activate this virtualenv using the command source sbol-explorer-venv/bin/activate (note: for the remainder of this guide, it will be assumed that your virtualenv is named sbol-explorer-venv) You should see (sbol-explorer-venv) before your command prompt if you’ve correctly activated the virtualenv.

Navigate into the flask directory. Run the command pip install -r requirements.txt to install all of the necessary Python packages for SBOLExplorer. You should now be able to start SBOLExplorer by running the start.sh script using the ./start.sh command.

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.