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Garny"},"license":"Apache-2.0","homepage":"https://github.com/ABI-Software/simulationvuer#readme","repository":{"type":"git","url":"git+https://github.com/ABI-Software/simulationvuer.git"},"description":"SimulationVuer is a [Vue](https://vuejs.org/) component to configure and run a [CellML](https://cellml.org/)-based model of some biological process, and to visualise the results of that simulation.","maintainers":[{"name":"hsorby","email":"h.sorby@auckland.ac.nz"},{"name":"alan-wu","email":"alan.wu@auckland.ac.nz"},{"name":"agarny","email":"agarny@hellix.com"},{"name":"dbrnz","email":"d.brooks@auckland.ac.nz"},{"name":"akhuoa","email":"aung.kyaw.hein@auckland.ac.nz"}],"readme":"# SimulationVuer\n\nSimulationVuer is a [Vue](https://vuejs.org/) 3 component used in the [SPARC portal](https://sparc.science/) to run some simulation-based [datasets](https://sparc.science/data?type=dataset) that include a [JSON](https://json.org/) file. That JSON file is used by SimulationVuer to create a user interface (Fig. 1) which can then be used by someone to configure a simulation before running it.\n\nThe simulation is run either on [oSPARC](https://osparc.io/) or in a user's browser, depending on how the simulation-based dataset is referenced (see the `id` property below). In the oSPARC case, SimulationVuer relies on the [SPARC API](https://github.com/nih-sparc/sparc-api) to ask oSPARC to run the model and to retrieve the simulation results, which can then be visualised and interacted with using the interface.\n\n![SimulationVuer](res/135.png)\n_Figure 1: user interface for dataset [135](https://sparc.science/datasets/simulationviewer?id=135)._\n\n## How to use\n\nTo install the package in your Vue application:\n\n```bash\nnpm install @abi-software/simulationvuer\n```\n\nTo include the package in your script:\n\n```javascript\nimport { SimulationVuer } from \"@abi-software/simulationvuer\";\n```\n\nTo register the package as a Vue component:\n\n```javascript\nexport default {\n  ...\n  components: {\n    ...,\n    SimulationVuer,\n    ...\n  }\n  ...\n}\n```\n\nThe above registers the SimulationVuer component into the global scope. You can now use SimulationVuer in your Vue template as follows:\n\n```html\n<SimulationVuer :apiLocation=\"apiLocation\" :id=\"123\" />\n```\n\nwhere:\n\n- `apiLocation` is the URL of a running copy of the [SPARC API](https://github.com/nih-sparc/sparc-api); and\n- `id` is:\n  - the id of a SPARC simulation-based dataset (as a `Number`, e.g., `135`);\n  - the [PMR](https://models.physiomeproject.org/) path to an [OMEX](https://combinearchive.org/) file (as a `String`, e.g., `workspace/b7c/rawfile/e0ae8d2d56aaaa091e23e1ee7e84cacbda1dfb6b/135.omex`);\n  - the direct URL to an OMEX file (as a `String`, e.g., `https://raw.githubusercontent.com/opencor/webapp/refs/heads/main/tests/models/ui/135.omex`); or\n  - a raw OMEX file (as a `Uint8Array`).\n\nNote that a simulation will be run on oSPARC if the `id` references a SPARC simulation-based dataset, in a user's browser otherwise.\n\n## Deployment\n\nSimulationVuer uses [@opencor/opencor](https://www.npmjs.com/package/@opencor/opencor), which relies on [libOpenCOR](https://github.com/opencor/libopencor)'s threaded WebAssembly (WASM) to run simulations in the browser. Threaded WASM requires [`SharedArrayBuffer`](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/SharedArrayBuffer), which in turn requires the page to be served with **cross-origin isolation** headers.\n\nWhen deploying an application that uses SimulationVuer, your Web server **must** must send the following headers with the HTML document:\n\n```http\nCross-Origin-Opener-Policy: same-origin\nCross-Origin-Embedder-Policy: require-corp\n```\n\nWithout these headers, @opencor/opencor will fail to initialise libOpenCOR and will not function.\n\nThe exact steps to set these headers depend on your Web server. Here are the steps for Apache:\n\n1. **Enable `mod_headers`**. Ensure the `headers` module is enabled (e.g., `a2enmod headers` or add it to your modules list).\n2. **Set headers on the HTML path**. In your virtual host config, add:\n\n   ```apache\n   <Location \"/app\">\n       Header set Cross-Origin-Opener-Policy \"same-origin\"\n       Header set Cross-Origin-Embedder-Policy \"require-corp\"\n   </Location>\n   ```\n\n   Adjust the `Location` path to match the URL prefix where the Web app is served (here, we use `/app` assuming the Web app is served from `https://your-domain.com/app`).\n\n3. **Reload Apache**. Apply the changes with `sudo apachectl reload` or the equivalent for your distribution.\n4. **Verify**. Check the response headers on your deployed HTML page using:\n\n   ```bash\n   curl -I https://your-domain.com/app/\n   ```\n\n   You should see:\n\n   ```http\n   cross-origin-opener-policy: same-origin\n   cross-origin-embedder-policy: require-corp\n   ```\n\n## Project setup\n\n### Clone the respository\n\n```bash\ngit clone https://github.com/ABI-Software/simulationvuer.git\n```\n\n### Vue component\n\n#### Setup\n\n```bash\nnpm install\n```\n\n#### Run the sample application\n\n```bash\nnpm run serve\n```\n\n#### Compile and minify for production\n\n```bash\nnpm run build-bundle\n```\n\n## Vue 2 vs. Vue 3\n\nSimulationVuer is now being developed as a Vue 3 component only. The [Vue 2 version of SimulationVuer](https://github.com/ABI-Software/simulationvuer/tree/vue2) is not maintained anymore.\n\n## Documentation\n\nThe documentation is written using [VitePress](https://vitepress.dev/) and [vuese](https://github.com/vuese/vuese#readme), and it can be found in the `docs` folder.\n\n#### To run in local development mode\n\n```bash\nnpm run docs:watch\n```\n\nThis will start the documentation server with [VitePress](https://vitepress.dev/) on port `5173`: http://localhost:5173/simulationvuer/.\n","readmeFilename":"README.md"}