JBioFramework Web Application

The JBioFramework Web Application is a more efficient method of performing 1-Dimensional through the use of a browser and file selection in the format of FASTA files. This document will contain information regarding Download and Installation, Usage for Development, and Testing Usage for the application.

Project Sponsor

Dr. Paul Craig received his B.S. in Chemistry from Oral Roberts University in 1979, and his Ph.D. in Biological Chemistry from The University of Michigan in 1985. Following a post-doc at Henry Ford Hospital (biophysical chemistry of blood clotting; 1985-1988), he spent five years as an analytical biochemist at BioQuant, Inc., in Ann Arbor, Michigan before joining RIT in 1993.

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Download and Installation

git clone https://github.com/paulcraig/ProSep
cd ProSep

VSCode Dev Container

This repository includes a Python 3.12 slim dev container. Install the Dev Containers extension in VSCode, open the command palette, and choose:

• Dev Containers: Rebuild and Reopen in Container or
• Dev Containers: Reopen in Container

Manual Installation

python -m pip install -r requirements.txt

• On Windows, use py instead of python if python doesn't work.

Pre-Commit Hooks

This repository has several checks which run before approval is allowed. These are included by python's Pre-Commit. To install the hooks, run the following in your shell:

pre-commit install

This will install all the hooks. Any freshly committed files should have the hooks fix and apply.

Software Requirements

• Python 3.7 or higher
• Node.js 20.11.0 or higher
• React 18.2.0 or higher

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Usage for Development

Navigate to the top level directory by typing in the command line

cd ProSep

Launch the API server by typing in the command line:

uvicorn server:app --reload

Navigate to the jbio-app subdirectory by typing in the command line

cd frontend/jbio-app

Then install the npm files

npm install

Launch the application by typing in the command line:

npm start

A browser will open with the URL: http://localhost:3000/

Press the 1D Electrophoresis button on the left.

Follow the instructions listed beneath the simulation to load the desired FASTA files and begin the simulation:

Tagging Policy

The server picks up changes via semantic versioning. As such, all tags must come from the main branch and be tagged semantically.

For example: v1.1.1 -> v1.1.2

Testing Usage

• TODO

Backend Guide

Author: Mack Leonard

Navigate to the top level directory by typing in the command line

cd ProSep

Then execute a test with

python -m unittest backend.Electro1DTests.ProteinTest

OR

Some IDEs have a built-in run function for files that can be executed. If you wish to do this, navigate to the ProteinTest.py or any other test file and click the run button.

Analyze results from the tests being run and modify the test or method being tested if failed.

API Guide:

• TODO

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Project Teams

• Fall 2025 to Spring 2026:

  • Coach:
    • Mark Wilson
  • Developers:
    • Luke Knofczynski
    • Zachary Van Horn
    • Shreyas Gadwalker
    • Jacob Fey
    • Aditya Vikram

• Fall 2023 to Spring 2024:

  • Coach:
    • Mark Wilson
  • Developers:
    • Chase Amador
    • Beck Anderson
    • Landon Heatly
    • Mack Leonard
    • Amr Mualla