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Spec

  • A web form accepts one or more genome IDs.
  • The VectorSearch python script is called with the given IDs.
    • The form POSTs a userInput field
      • The VectorSearch script loads the genome .csv files for the given species.
        • The VectorSearch script returns a csv string
        • The form reloads with the output and the input variables
        • The form re-renders with the output CSV string displayed
        • The from re-renders with a link to the /get?id=<input>, to link to the file download
  • /get?id=<input> Calls the VectorSearch function with the id query parameter
    • the route handler returns the csv string as a csv file, starting a download.
  • The csv results are visualized via chart.

Budget

Project budget is approximately 50,000 SEK, which maps to ~62 billable hours, or 14 billable work chunks. If this were a freelance project I would be aiming to get it done in 6 billable work chunks.

Schedule

6-Blob Schedule

  1. Initial application setup, CI/CD pipelines, and stubbed UX flow.
  2. Integrate the VectorSearch python script with i/o.
  3. Tighten up visual design of the user experience.
  4. Overflow Buffer Blob
  5. Integrate the genome CSV visualizer.
  6. Adjust UX to enable batch search and download.

14-Blob Schedule

  1. Initial applications setup, CI/CD pipeline
  2. Stubbed UX and appliation flow
  3. Integrate the VectorSearch python script
  4. Ensure correct function signtite i/o
  5. Visual design of user experience.
  6. Wrap up the design of the user experience.
  7. Overflow buffer blob
  8. Overflow buffer blob
  9. Overflow buffer blob
  10. Start integrating genome visualizer.
  11. Finish the genome visualizer.
  12. Adjust the user experience to allow multiple in/out.
  13. Finalize the user experience for batch downloading.
  14. Final wiggle all the knobs and dials.

Questions

When writing the Reverse Complement HR1 and HR2 from the source fasta files, does that process need to run on each request, or can we run that once and commit the reverse compliment files into the codebase?

Can you help me understand the function signature of the program? Right now it looks like it doesn't accept any parameters, and returns a CSV for each of the predefined Carina_Genes. What should our user input be? Is there a list of acceptable inputs?

What is the visualization tool called? Where does that code live?