{"id":24129443,"url":"https://github.com/synbiodex/sbolexplorer","last_synced_at":"2026-03-13T23:34:44.447Z","repository":{"id":40295218,"uuid":"109059930","full_name":"SynBioDex/SBOLExplorer","owner":"SynBioDex","description":null,"archived":false,"fork":false,"pushed_at":"2024-11-13T18:17:29.000Z","size":68204,"stargazers_count":4,"open_issues_count":32,"forks_count":2,"subscribers_count":18,"default_branch":"master","last_synced_at":"2025-10-14T15:23:45.911Z","etag":null,"topics":["synthetic-biology"],"latest_commit_sha":null,"homepage":"","language":"UnrealScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/SynBioDex.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-10-31T22:42:48.000Z","updated_at":"2024-11-13T18:17:33.000Z","dependencies_parsed_at":"2024-11-10T23:29:20.219Z","dependency_job_id":null,"html_url":"https://github.com/SynBioDex/SBOLExplorer","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/SynBioDex/SBOLExplorer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SynBioDex%2FSBOLExplorer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SynBioDex%2FSBOLExplorer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SynBioDex%2FSBOLExplorer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SynBioDex%2FSBOLExplorer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SynBioDex","download_url":"https://codeload.github.com/SynBioDex/SBOLExplorer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SynBioDex%2FSBOLExplorer/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30479434,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-13T20:45:58.186Z","status":"ssl_error","status_checked_at":"2026-03-13T20:45:20.133Z","response_time":60,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["synthetic-biology"],"created_at":"2025-01-11T19:32:24.296Z","updated_at":"2026-03-13T23:34:44.430Z","avatar_url":"https://github.com/SynBioDex.png","language":"UnrealScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SBOLExplorer\n\nSBOLExplorer is a service that simplifies the process of analyzing and searching for parts within genetic design repositories.\n\n# Installation\n1. 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.\n2. Clone this repository with `git clone https://github.com/michael13162/SBOLExplorer.git`.\n3. Install and run ElasticSearch 6.3 (https://www.elastic.co/guide/en/elasticsearch/reference/current/install-elasticsearch.html).\n    * The exact steps will depend on your environment, so read the manual (aka RTFM).\n    * Set up the package repo to install ElasticSearch from.\n    * Install ElasticSearch.\n    * Start ElasticSearch (will be different depending on init vs systemd).\n    * Optionally, configure ElasticSearch to start on boot.\n    * **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.\n4. Install the latest version of Python 3 (https://www.python.org/downloads/).\n5. 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.\n6. Run SBOLExplorer using `./start.sh` in the SBOLExplorer/flask directory.\n7. 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.\n   * 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.\n8. Optionally, edit the \"autoUpdateIndex\" and \"updateTimeInDays\" fields in the config file to update your index automatically.\n9. In SynBioHub, go to the Admin-\u003eGeneral 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.\n\n![alt text](https://raw.githubusercontent.com/michael13162/SBOLExplorer/master/visualization/network.png)\n\nTo 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.\n\n\n# Setting up a virtual environment\nCreate a virtual environment in the parent directory. You can use the example commands below to create a virtualenv called `sbol-explorer-venv`.\n\n| OS | Command |\n| --- | --- |\n| Ubuntu | `virtualenv sbol-explorer-venv` |\n| Mac | `pyvenv sbol-explorer-venv` |\n\nActivate 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. \n\nNavigate 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.\n\n# Automatic build and deploy\nOn each commit to master, a new Docker image is built and pushed to [Docker Hub](https://hub.docker.com/r/michael13162/sbolexplorer). \nThis is done by TravisCI.\nThe credentials used to push the image are stored in Travis. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsynbiodex%2Fsbolexplorer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsynbiodex%2Fsbolexplorer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsynbiodex%2Fsbolexplorer/lists"}