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README.md

Microbial Strain Navigator


Navigate and edit microbial strains, plasmids, and genes with a Flask web UI and MySQL database.


Usage:

  1. Viewing strains, plasmids, and genes

    Image description

  2. Adding elements

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  3. Deleting elements

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  4. Viewing details of a given element

    Image description

  5. Uploading and associating files with an element (multiple file upload is supported, but not shown here)

    Image description

Local Installation:

  1. Install docker and docker-compose (cannot use Windows 7)

    • I used Docker version 19.03.4, build 9013bf5 and docker-compose version 1.24.1, build 4667896b, but should work across other versions too
  2. Clone this repo (git clone https://github.com/robinovitch61/impossible_app.git)

  3. Navigate to the local version in a terminal and run the start_app.sh script.

    • NOTE: this script includes docker system prune -f, which removes unused data. Comment this out if you'd like to keep your currently unused containers, images, and volumes.
  4. Wait ~1min for startup. Then navigate to http://localhost:5000/ and have a blast.

  • If there are any startup issues, use docker logs -f app to view possible errors. Contact leorobinovitch@gmail.com with any questions.

Improvements/Next Steps:

  • Remove .secret.env file from version control - there for demo purposes only right now

  • Remove the debug mode/debugging from the app for production

  • Improve code comments and add docstrings

  • "Delete file" feature

  • Fill Date Created field with current date by default and add time info if required

  • Create cool top level graph visualization of all links/associations using graphviz or networkx and display as landing page

  • Check file types to ensure safety (snapgene format only or something like that)

  • Easier updating of elements (currently relies on overwriting with new element with same ID) - maybe edit tables directly and send UPDATE mysql queries on backend

  • Possibly have X's next to table rows for easier deletion (although might make it too easy and mistakes could occur - include a confirmation box)

  • Make the effects on the links/associations more explicit when an update/delete is made (currently clears all files and direct associations on an update)

  • "Download All Files" button

  • Fix bug with hover style on row turning off when hovers over text (detected as mouseout )

  • Fix the small bugs that may exist from doing this relatively quickly

  • If needed, scale up:

    • Put behind gunicorn for multiple workers on single machine

    • Use Kubernetes to distribute over multiple servers

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