Initial / Detailed Specifications: Pipette Training Automation_ Design Specifications.pdf
The goal of this project is to use create accompanying software to the Tecan fluorescence plate reader instrument in order to more efficiently determine the accuracy of a student's pipetting skills. The general idea is to have the students follow a simple liquid-transfer protocol (included in the Protocols directory). The liquid the students transfer has already been dyed using Fluorescein (and/or Rhodamine). After using the Tecan to read the fluorescence within various dilutions the students have made in a 96-well plate, this software, using mostly regression analysis and some experimental machine-learning approaches, will be able to determine whether the student has administered correct amounts of liquid, and thus whether the student has demonstrated competency in basic pipetting techniques.
Data – contains all the information procured from our experimentation, as well student data from the wet-lab teams, in the form of excel (.xls, .xlsx) sheets. Protocols – contains all the written protocols (and their past versions) for the students to follow. Src – contains scripts, models, and visualizations (not all are finished / some were dropped) for ways to parse, analyze, and visualize the experimental data. Webapp – contains the Python-Flask web application that is to be launched by the student when submitting their wet-lab pipetting data to be analyzed.
- Clone the repository from Github (https://github.com/nathan2wong/PipetteTraining)
- Change directory into "webapp"
git clone https://github.com/nathan2wong/PipetteTraining
cd ~/PipetteTraining/webapp
- Recommended: Use a Python virtual environment (Guide here: https://docs.python-guide.org/dev/virtualenvs/) at this step. Enter the virtualenv, or ensure that your system has Python3 (3.5 or later) installed.
- View the requirements in requirements.txt. Download all python packages to make sure those requirements are met. How to download: Using pip, install the requirements using the command pip install -r requirements.txt. (Note: This step may require some light dependency sorting / debugging depending on your system setup).
cat requirements.txt
pip install -r requirements.txt
- Launch the web application by running manage.py. You can now visit the application at http://localhost:4000
python3 manage.py
