ckrusemd / meta-analysis-tool

Systematic Reviews and Meta-analyses using Biopython and Dash.

Meta-Analysis Tool

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Why are systematic reviews still tediously done by hand from A-Z, saved in spreadsheets and intransparently across several software suites?

This project aims to accelerate the process using readily available tools:

• Biopython: We can query the Entrez API to collect abstract information and text from Pubmed.
• MongoDB: We can store the results as JSON to include, label and reproduce abstracts.
• Dash: We can make it all interactive with the Python Dash framework. And follow PRISMA guidelines.
• PythonMeta: We can arrive at the beautiful forest and funnel plots and customize the look.
• Docker: Keep it reproducible, save the images.

Please chip in with issues, suggestions and pull requests if you want to contribute.

Docker services:

• FastAPI (:80)
• Plotly Dash Development, enabling hot-reload, (:8051)
• Plotly Dash Production, Gunicorn (:8050)
• MongoDB (:27017)
• Pytest-html w/ nginx (:8080)

How to run:

docker-compose up -d