{"id":13744685,"url":"https://github.com/plotly/dash-bio","last_synced_at":"2025-10-20T16:10:31.012Z","repository":{"id":37664641,"uuid":"141365566","full_name":"plotly/dash-bio","owner":"plotly","description":"Open-source bioinformatics components for 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Dash Bio\n[![CircleCI](https://circleci.com/gh/plotly/dash-bio/tree/master.svg?style=svg)](https://circleci.com/gh/plotly/dash-bio)\n[![PyPI version](https://badge.fury.io/py/dash-bio.svg)](https://badge.fury.io/py/dash-bio)\n\n\u003cdiv align=\"center\"\u003e\n  \u003ca href=\"https://dash.plotly.com/project-maintenance\"\u003e\n    \u003cimg src=\"https://dash.plotly.com/assets/images/maintained-by-community.png\" width=\"600px\" alt=\"Maintained by the Plotly Community\"\u003e\n  \u003c/a\u003e\n\u003c/div\u003e\n\nDash Bio is a suite of bioinformatics components built to work with\n[Dash](https://github.com/plotly/dash/).\n\nAnnouncement: https://medium.com/@plotlygraphs/announcing-dash-bio-ed8835d5da0c\n\nDemo:\n[https://dash-gallery.plotly.host/Portal/?search=Bioinformatics](https://dash-gallery.plotly.host/Portal/?search=Bioinformatics)\n\nDocumentation:\n[https://dash.plotly.com/dash-bio](https://dash.plotly.com/dash-bio)\n\n## Components\n\nThe Dash Bio components each fall into one of three categories:\n\n- Custom chart types\n- Sequence analysis tools\n- 3D rendering tools\n\n\n### Custom chart types\n\n- Dash Circos\n- Dash Clustergram\n- Dash Manhattan Plot\n- Dash Needle Plot\n- Dash Volcano Plot\n\n### Sequence analysis tools\n\n- Dash Alignment Chart\n- Dash Onco Print\n- Dash Forna Container\n- Dash Sequence Viewer\n\n### Visualization tools\n\n- Dash Mol2D\n- Dash Mol3D\n- Dash Speck\n- Dash Ngl\n\n\n## Using Dash Bio\n\nIt's easy to add a fully interactive chromosomal, molecular or genomic visualization to your Dash app by simply\nincluding the Dash Bio component into your app layout as follows:\n\n```python\nimport urllib.request as urlreq\nfrom dash import Dash, html\nimport dash_bio as dashbio\n\napp = Dash(__name__)\n\ndata = urlreq.urlopen(\n    'https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/alignment_viewer_p53.fasta'\n).read().decode('utf-8')\n\napp.layout = html.Div([\n    dashbio.AlignmentChart(\n        id='my-default-alignment-viewer',\n        data=data\n    )\n])\n\nif __name__ == '__main__':\n    app.run(debug=True)\n```\n\nSee the [Dash Bio documentation](https://dash.plotly.com/dash-bio) for more components and examples.\n\n\n## Run Dash Bio in a JupyterLab environment\n\n1. Create a virtual environment:\n\n    The following steps require a virtual environment tool to be installed on your computer: `pip install virtualenv`\n\n    a. On macOS and Linux: `python3 -m venv env`\n\n    b. On Windows, enter: `py -m venv env`\n\n2. Activate your new environment:\n\n    a. On macOS and Linux, enter: `source env/bin/activate`\n\n    b. On Windows, enter: `.\\env\\Scripts\\activate`\n\n3. Install required libraries (make sure you have pip installed with `pip help`):\n```\npip install dash dash-bio pandas numpy Jupyterlab\n```\n\n4. To run Dash inside Jupyter lab:\n\n    a. Install jupyter-dash:  `pip install jupyter-dash`\n\n    b. Enter `jupyter lab build`\n\n    (Note: This step requires Node.js and NPM installed on yourcomputer. To check if Node and NPM are installed, enter `node -v` and `npm -v` in your terminal. For install instructions see [nodejs.org](https://nodejs.org/en/).\n\n5. To display Plotly figures in JupyterLab:\n```\npip install jupyterlab \"ipywidgets\u003e=7.5”\njupyter labextension install jupyterlab-plotly@4.14.3\n```\n\n6. Start JupyterLab by typing: `jupyter lab`\n\n    Important: JupyterLab must be run within the virtual environment that was previously activated.\n\n\nFor more on running a Dash app in Jupyter Lab visit [Getting Started with Jupyter Dash](https://github.com/plotly/jupyter-dash/blob/master/notebooks/getting_started.ipynb).\n\n## Dash\n\nLearn more about Dash at\n[https://plotly.com/products/dash/](https://plotly.com/products/dash/).\n\n## Consulting and OEM\n\nFor inquiries about Dash app development, advanced OEM integration,\nand more, please [reach\nout](https://plotly.typeform.com/to/mH1Cpb).\n\n## Contributing and Local Development\n\nIf you would like to contribute to this repository, or run demo apps and tests, please refer to\nthe [contributing\nguidelines](https://github.com/plotly/dash-bio/blob/master/CONTRIBUTING.md).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fplotly%2Fdash-bio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fplotly%2Fdash-bio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fplotly%2Fdash-bio/lists"}