{"id":22377330,"url":"https://github.com/csbiology/deepstabp","last_synced_at":"2025-07-30T23:32:09.293Z","repository":{"id":83225775,"uuid":"586898000","full_name":"CSBiology/deepStabP","owner":"CSBiology","description":"A small web ui and python api service to predict protein melting point temperatures.","archived":false,"fork":false,"pushed_at":"2025-01-21T10:04:19.000Z","size":146824,"stargazers_count":14,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-06T16:12:14.449Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://csb-deepstabp.bio.rptu.de","language":"F#","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/CSBiology.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}},"created_at":"2023-01-09T13:46:55.000Z","updated_at":"2025-01-23T04:57:05.000Z","dependencies_parsed_at":null,"dependency_job_id":"4f518674-204e-4e0f-ab21-d4c2baf8406a","html_url":"https://github.com/CSBiology/deepStabP","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/CSBiology/deepStabP","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CSBiology%2FdeepStabP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CSBiology%2FdeepStabP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CSBiology%2FdeepStabP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CSBiology%2FdeepStabP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CSBiology","download_url":"https://codeload.github.com/CSBiology/deepStabP/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CSBiology%2FdeepStabP/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267960696,"owners_count":24172506,"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","status":"online","status_checked_at":"2025-07-30T02:00:09.044Z","response_time":70,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2024-12-04T22:13:37.532Z","updated_at":"2025-07-30T23:32:04.280Z","avatar_url":"https://github.com/CSBiology.png","language":"F#","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DeepStabP - WebUI\n\n## Install pre-requisites\n\nYou'll need to install the following pre-requisites in order to build SAFE applications\n\nYou can check if you have these installed with the cmd command written below each 👀\n\n- The [.NET 6 SDK](https://dotnet.microsoft.com/en-us/download/dotnet/6.0)\n  - test with `dotnet --list-sdks`\n- [node.js (v16.x || v18.x)](https://nodejs.org/en)\n  - Will most of the time also install npm\n  - test with `node --version`\n- [npm (\u003ev8.x)](https://docs.npmjs.com/downloading-and-installing-node-js-and-npm)\n  - test with `npm --version`\n- [Python 3.9](https://www.python.org/downloads/release/python-3916/) (used for ml api)\n  - test with `py --version`\n\n## Starting the application\n\n1. Before you run the project **for the first time only** you must install dotnet \"local tools\" with this command:\n\n```bash\ndotnet tool restore\n```\n\n2. To concurrently run the server, client and the python fastapi components in watch mode use the following command:\n\n```bash\n./build.cmd\n```\n\nThen open `http://localhost:8080` in your browser for the web ui and `http://localhost:8000/docs` for the python api OpenApi docs.\n\n\n## Docker\n\n### Environment\n\n- **DEEPSTABP_URL**: Sets the url for the api predictor backend.\n\n  Default: *\"http://localhost:8000\"*\n\n### Publish\n\n1. Before publishing make sure to commit all changes and update the version with\n\n   `./build.cmd releasenotes semver:xxx`, where xxx is the required version [major|minor|patch].\n2. If the backend api was changed update the static version string in `src/api/app/main.py` **predictor_version**.\n3. Use `./build.cmd dockerbundle [--uionly]` to create new docker images\n4. Use `./build.cmd dockertest [--uionly]` to run both images for testing.\n\n   This might take some time as the api image will downloag ~7GB model.\n   Use the `--uionly` option to only bundle/test the ui and not the api.\n5. Use `./build.cmd dockerpublish`, after logging into the csbdocker account (docker login) to push both images to dockerhub\n6. Use `./build.cmd dockertestproduction` to pull and test both images from remote as docker compose stack.\n\n   Ui will be accessible on `localhost:5000` and api on `localhost:8000`\n\n## Supported formats\n\ndeepSTAPp expects input in either the FASTA format or as pure amino acid sequence. \nThe FASTA format consists of two building blocks. The first is a description which explains the following sequence. This description starts with \"\u003e\" and is written in a single line. The amino acid sequence follows in the next line and can span multiple lines. An example for this format is:\n```\n\u003esp|A0A178WF56|CSTM3_ARATH Protein CYSTEINE-RICH TRANSMEMBRANE MODULE 3 OS=Arabidopsis thaliana OX=3702 GN=CYSTM3 PE=1 SV=1\nMAQYHQQHEMKQTMAETQYVTAPPPMGYPVMMKDSPQTVQPPHEGQSKGSGGFLRGCLAA\nMCCCCVLDCVF\n\u003esp|A1YKT1|TCP18_ARATH Transcription factor TCP18 OS=Arabidopsis thaliana OX=3702 GN=TCP18 PE=1 SV=1\nMNNNIFSTTTTINDDYMLFPYNDHYSSQPLLPFSPSSSINDILIHSTSNTSNNHLDHHHQ\nFQQPSPFSHFEFAPDCALLTSFHPENNGHDDNQTIPNDNHHPSLHFPLNNTIVEQPTEPS\nETINLIEDSQRISTSQDPKMKKAKKPSRTDRHSKIKTAKGTRDRRMRLSLDVAKELFGLQ\nDMLGFDKASKTVEWLLTQAKPEIIKIATTLSHHGCFSSGDESHIRPVLGSMDTSSDLCEL\nASMWTVDDRGSNTNTTETRGNKVDGRSMRGKRKRPEPRTPILKKLSKEERAKARERAKGR\nTMEKMMMKMKGRSQLVKVVEEDAHDHGEIIKNNNRSQVNRSSFEMTHCEDKIEELCKNDR\nFAVCNEFIMNKKDHISNESYDLVNYKPNSSFPVINHHRSQGAANSIEQHQFTDLHYSFGA\nKPRDLMHNYQNMY\n```\ndeepSTABp was developed with the assumption that the description follows the standard used by the Universal Protein Resource ([Uniprot](https://www.uniprot.org/)) and only returns the Uniprot ID as description in the output table. This can be circumvented by removing the \"|\" in the description. In this case the complete description gets returned.\n\nThe only other supported format are pure amino acid sequences. An example for this format is:\n```\nMAQYHQQHEMKQTMAETQYVTAPPPMGYPVMMKDSPQTVQPPHEGQSKGSGGFLRGCLAA\nMCCCCVLDCVF\n```\nThis format can only be used for a single amino acid sequence. Multiple amino acid sequences must be in the following format:\n```\n\u003e!MAQYHQQHEMKQTMAETQYVTAPPPMGYPVMMKDSPQTVQPPHEGQSKGSGGFLRGCLAA\nMCCCCVLDCVF\n\u003e!MNNNIFSTTTTINDDYMLFPYNDHYSSQPLLPFSPSSSINDILIHSTSNTSNNHLDHHHQ\nFQQPSPFSHFEFAPDCALLTSFHPENNGHDDNQTIPNDNHHPSLHFPLNNTIVEQPTEPS\nETINLIEDSQRISTSQDPKMKKAKKPSRTDRHSKIKTAKGTRDRRMRLSLDVAKELFGLQ\nDMLGFDKASKTVEWLLTQAKPEIIKIATTLSHHGCFSSGDESHIRPVLGSMDTSSDLCEL\nASMWTVDDRGSNTNTTETRGNKVDGRSMRGKRKRPEPRTPILKKLSKEERAKARERAKGR\nTMEKMMMKMKGRSQLVKVVEEDAHDHGEIIKNNNRSQVNRSSFEMTHCEDKIEELCKNDR\nFAVCNEFIMNKKDHISNESYDLVNYKPNSSFPVINHHRSQGAANSIEQHQFTDLHYSFGA\nKPRDLMHNYQNMY\n```\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcsbiology%2Fdeepstabp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcsbiology%2Fdeepstabp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcsbiology%2Fdeepstabp/lists"}