{"id":29433802,"url":"https://github.com/openms/quantms-web","last_synced_at":"2026-04-08T18:06:40.709Z","repository":{"id":295123201,"uuid":"988980934","full_name":"OpenMS/quantms-web","owner":"OpenMS","description":null,"archived":false,"fork":false,"pushed_at":"2026-03-14T14:16:49.000Z","size":24480,"stargazers_count":0,"open_issues_count":10,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-03-14T19:36:57.677Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OpenMS.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-05-23T11:22:08.000Z","updated_at":"2026-03-14T07:07:19.000Z","dependencies_parsed_at":"2025-05-23T19:15:23.095Z","dependency_job_id":"7c256464-3856-4221-802a-69e3a7cd1626","html_url":"https://github.com/OpenMS/quantms-web","commit_stats":null,"previous_names":["openms/quantms-web"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/OpenMS/quantms-web","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMS%2Fquantms-web","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMS%2Fquantms-web/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMS%2Fquantms-web/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMS%2Fquantms-web/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenMS","download_url":"https://codeload.github.com/OpenMS/quantms-web/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMS%2Fquantms-web/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31567342,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-08T14:31:17.711Z","status":"ssl_error","status_checked_at":"2026-04-08T14:31:17.202Z","response_time":54,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: 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":[],"created_at":"2025-07-13T01:39:00.427Z","updated_at":"2026-04-08T18:06:40.698Z","avatar_url":"https://github.com/OpenMS.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# OpenMS streamlit template \n\n[![Open Template!](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://abi-services.cs.uni-tuebingen.de/streamlit-template/)\n\nThis repository contains a template app for OpenMS workflows in a web application using the **streamlit** framework. It serves as a foundation for apps ranging from simple workflows with **pyOpenMS** to complex workflows utilizing **OpenMS TOPP tools** with parallel execution. It includes solutions for handling user data and parameters in workspaces as well as deployment with docker-compose.\n\n## Features\n\n- Workspaces for user data with unique shareable IDs\n- Persistent parameters and input files within a workspace\n- local and online mode\n- Captcha control\n- Packaged executables for Windows\n- framework for workflows with OpenMS TOPP tools\n- Deployment [with docker-compose](https://github.com/OpenMS/streamlit-deployment)\n\n## 🔗 Try the Online Demo\n\nExplore the hosted version here:  👉 [Live App](https://abi-services.cs.uni-tuebingen.de/streamlit-template/)\n\n## 💻 Run Locally\n\nTo run the app locally:\n\n1. **Clone the repository**\n   ```bash\n   git clone https://github.com/OpenMS/streamlit-template.git\n   cd streamlit-template\n   ```\n\n2. **Install dependencies**\n   \n   Make sure you can run ```pip``` commands.\n   \n   Install all dependencies with:\n   ```bash\n   pip install -r requirements.txt\n   ```\n\n4. **Launch the app**\n   ```bash\n   streamlit run app.py\n   ```\n\n\u003e ⚠️ Note: The local version offers limited functionality. Features that depend on OpenMS TOPP tools are only available out of the box in the Docker setup. For the local version [OpenMS Command Line Tools](https://openms.readthedocs.io/en/latest/about/installation.html) must be installed separately.\n\n\n## 🐳 Build with Docker\n\nThis repository contains two Dockerfiles.\n\n1. `Dockerfile`: This Dockerfile builds all dependencies for the app including Python packages and the OpenMS TOPP tools. Recommended for more complex workflows where you want to use the OpenMS TOPP tools for instance with the **TOPP Workflow Framework**.\n2. `Dockerfile_simple`: This Dockerfile builds only the Python packages. Recommended for simple apps using pyOpenMS only.\n\n1. **Install Docker**\n\n   Install Docker from the [official Docker installation guide](https://docs.docker.com/engine/install/)  \n   \n   \u003cdetails\u003e\n   \u003csummary\u003eClick to expand\u003c/summary\u003e\n   \n   ```bash\n   # Remove older Docker versions (if any)\n   for pkg in docker.io docker-doc docker-compose docker-compose-v2 podman-docker containerd runc; do sudo apt-get remove -y $pkg; done\n   ```\n   \n   \u003c/details\u003e\n\n2. **Test Docker**\n   \n   Verify that Docker is working.\n   ```bash\n   docker run hello-world\n   ```\n   When running this command, you should see a hello world message from Docker.\n   \n3. **Clone the repository**\n   ```bash\n   git clone https://github.com/OpenMS/streamlit-template.git\n   cd streamlit-template\n   ```\n   \n4. **Specify GitHub token (to download Windows executables).**\n   \n   Create a temporary `.env` file with your Github token.\n   \n   It should contain only one line:\n   `GITHUB_TOKEN=\u003cyour-github-token\u003e`\n\n   ℹ️ **Note:** This step is not strictly required, but skipping it will remove the option to download executables from the WebApp.\n   \n3. **Build \u0026 Launch the App**\n\n   To build and start the containers.\n   From the project root directory:\n   \n   ```bash\n   docker-compose up -d --build\n   ```\n     At the end, you should see this:\n      ```\n      [+] Running 2/2\n       ✔ openms-streamlit-template            Built      \n       ✔ Container openms-streamlit-template  Started  \n      ```\n      \n      To make sure server started successfully, run `docker compose ps`. You should see `Up` status:\n      ```\n      CONTAINER ID   IMAGE                       COMMAND                  CREATED         STATUS                 PORTS                                           NAMES\n      4abe0603e521   openms_streamlit_template   \"/app/entrypoint.sh …\"   7 minutes ago   Up 7 minutes           0.0.0.0:8501-\u003e8501/tcp, :::8501-\u003e8501/tcp       openms-streamlit-template\n      ```\n   \n      To map the port to default streamlit port `8501` and launch.\n      \n      ```\n      docker run -p 8505:8501 openms_streamlit_template\n      ```\n\n## Documentation\n\nDocumentation for **users** and **developers** is included as pages in [this template app](https://abi-services.cs.uni-tuebingen.de/streamlit-template/), indicated by the 📖 icon.\n\n## Citation\n\nPlease cite:\nMüller, T. D., Siraj, A., et al. OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. Journal of Proteome Research (2025). [https://doi.org/10.1021/acs.jproteome.4c00872](https://doi.org/10.1021/acs.jproteome.4c00872)\n\n## References\n\n- Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods 21, 365–367 (2024). [https://doi.org/10.1038/s41592-024-02197-7](https://doi.org/10.1038/s41592-024-02197-7)\n\n- Röst HL, Schmitt U, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 2014 Jan;14(1):74-7. [https://doi.org/10.1002/pmic.201300246](https://doi.org/10.1002/pmic.201300246). PMID: [24420968](https://pubmed.ncbi.nlm.nih.gov/24420968/).\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenms%2Fquantms-web","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenms%2Fquantms-web","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenms%2Fquantms-web/lists"}