{"id":29224673,"url":"https://github.com/sing-group/dreimt-backend","last_synced_at":"2025-07-03T06:07:34.451Z","repository":{"id":37269458,"uuid":"268739404","full_name":"sing-group/dreimt-backend","owner":"sing-group","description":"A Java backend for the DREIMT application","archived":false,"fork":false,"pushed_at":"2022-06-23T18:09:23.000Z","size":98791,"stargazers_count":0,"open_issues_count":4,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2023-02-27T07:56:25.259Z","etag":null,"topics":["drug-repositioning","immune-system","transcriptomics"],"latest_commit_sha":null,"homepage":"http://www.dreimt.org","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sing-group.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}},"created_at":"2020-06-02T08:06:18.000Z","updated_at":"2021-01-12T07:22:13.000Z","dependencies_parsed_at":"2022-08-29T18:30:41.581Z","dependency_job_id":null,"html_url":"https://github.com/sing-group/dreimt-backend","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"purl":"pkg:github/sing-group/dreimt-backend","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fdreimt-backend","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fdreimt-backend/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fdreimt-backend/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fdreimt-backend/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sing-group","download_url":"https://codeload.github.com/sing-group/dreimt-backend/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fdreimt-backend/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263271499,"owners_count":23440396,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["drug-repositioning","immune-system","transcriptomics"],"created_at":"2025-07-03T06:07:33.451Z","updated_at":"2025-07-03T06:07:34.428Z","avatar_url":"https://github.com/sing-group.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DREIMT [![license](https://img.shields.io/github/license/sing-group/dreimt-backend)](https://github.com/sing-group/dreimt-backend) [![release](https://img.shields.io/github/release/sing-group/dreimt-backend.svg)](https://github.com/sing-group/dreimt-backend/releases)\n\n\u003e DREIMT - A tool for immune modulation drug prioritization (http://www.dreimt.org)\n\n\u003cp align=\"center\"\u003e\n\t\u003cimg src=\"additional-material/dreimt-logo.png\" alt=\"DREIMT logo\"\u003e\u003c/img\u003e\n\u003c/p\u003e\n\n**DREIMT** is a bioinformatics tool for hypothesis generation and prioritization of drugs capable of modulating immune cell activity from transcriptomics data.\n\nDREIMT integrates 4,694 drug profiles from The Library of Network-Based Cellular Signatures (LINCS) L1000 data set and 2,687 manually curated immune gene expression signatures from multiple resources to generate a drug-immune signature association database.\n\nDREIMT can also prioritize drug associations from user-provided immune signatures. \n\n## Development \n\n### Running the application\nThe application has been configured to be easily run locally, by just invoking a Maven command.\n\nTo do so, Maven will download (if it is not already) a clean WildFly distribution to the `target` folder, configure it, start it and deploy the application on it.\n\nThis makes very easy and straightforward to manually test the application.\n\n#### Configure a local MySQL\nTo execute the application you need a MySQL server running in `localhost` and using the default port (3306).\n\nIn this server you have to create a database named `dreimt` accessible for the `dreimt` user using the `dreimtpass` password.\n\nThis can be configured executing the follow SQL sentences in your MySQL:\n\n```SQL\nCREATE DATABASE dreimt;\nGRANT ALL ON dreimt.* TO dreimt@localhost IDENTIFIED BY 'dreimtpass';\nFLUSH PRIVILEGES;\n```\n\nOf course, this configuration can be changed in the POM file.\n\n#### Development database initialization\n\nThe `additional-material/db` contains several files related with the DREIMT db initialization. After creating a new database as described in the previous step, you can populate it with the following commands:\n\n```\nsudo mysql dreimt \u003c additional-material/db/dreimt-db-initialization.sql\nsudo mysql dreimt \u003c additional-material/db/dreimt-schema.sql\nzcat additional-material/db/dreimt-data.sql.gz | sudo mysql dreimt\nsudo mysql dreimt \u003c additional-material/db/fill_full_drug_signature_interaction_table.sql\n```\n\n#### Building the application\nThe application can be built with the following Maven command:\n\n```\nmvn clean install\n```\n\nThis will build the application launching the tests on a **Wildfly 10.1.0** server.\n\n#### Starting the application\nThe application can be started with the following Maven command:\n\n```\nmvn package wildfly:start wildfly:deploy-only -P wildfly-mysql-run\n```\n\nThis will start a **WildFly 10.1.0** serving the DREIMT application.\n\n#### Redeploying the application\nOnce it is running, the application can be re-deployed with the following Maven command:\n\n```\nmvn package wildfly:deploy-only -P wildfly-mysql-run\n```\n\n#### Stopping the application\nThe application can be stopped with the following Maven command:\n\n```\nmvn wildfly:shutdown\n```\n\n#### REST API documentation\nThe REST API is documented using the [Swagger](https://swagger.io/) framework. It can be browsed using the [Swagger UI](http://petstore.swagger.io/) application to access the following URL:\n\n```\nhttp://localhost:8080/dreimt-backend/rest/api/swagger.json\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Fdreimt-backend","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsing-group%2Fdreimt-backend","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Fdreimt-backend/lists"}