bioactivity-prediction-app's Introduction

bioactivity-prediction-app

Watch the tutorial video

Bioinformatics Project from Scratch - Drug Discovery #6 (Deploy Model as Web App) | Streamlit #22

Reproducing this web app

To recreate this web app on your own computer, do the following.

Create conda environment

Firstly, we will create a conda environment called bioactivity

conda create -n bioactivity python=3.7.9

Secondly, we will login to the bioactivity environement

conda activate bioactivity

Install prerequisite libraries

Download requirements.txt file

wget https://raw.githubusercontent.com/dataprofessor/bioactivity-prediction-app/main/requirements.txt

Pip install libraries

pip install -r requirements.txt

Download and unzip contents from GitHub repo

Download and unzip contents from https://github.com/dataprofessor/bioactivity-prediction-app/archive/main.zip

Generating the PKL file

The machine learning model used in this web app will firstly have to be generated by successfully running the included Jupyter notebook bioactivity_prediction_app.ipynb. Upon successfully running all code cells, a pickled model called acetylcholinesterase_model.pkl will be generated.

Launch the app

streamlit run app.py

bioactivity-prediction-app's Issues

Doubts

Hello prof Chanin Nantasenamat,
first, let me say thanks for your videos. It's opening a part of my lab for Chemoinformatics in Rio (Brazil).

So, let me go for a question: I'm having a though time to run padelpy to get descriptors from a list of SMILES and structure Objects in a dataframe I have in Jupyter Notebook. Maybe I installed padelpy wrongly or my limitation in understanding this can also be the error I'm getting from using wget. I'm following this: https://github.com/ecrl/padelpy and https://analyticsindiamag.com/hands-on-guide-to-padelpy-for-ml-model-building/, but I think I need extensions that I don't know of..
Any tips?

Thank you
Ricardo Borges

error in ubuntu 20

git clone https://github.com/dataprofessor/bioactivity-prediction-app.git
cd bioactivity-prediction-app
wget https://raw.githubusercontent.com/dataprofessor/moldesc-app/main/requirements.txt
pip install -r requirements.txt

show this

root@two-ubuntu-s-8vcpu-16gb-nyc1-01:~/bioactivity-prediction-app# pip install -r requirements.txt
Collecting streamlit==0.71.0
  Downloading streamlit-0.71.0-py2.py3-none-any.whl (7.4 MB)
     |████████████████████████████████| 7.4 MB 27.4 MB/s
Collecting pandas==1.1.3
  Downloading pandas-1.1.3-cp38-cp38-manylinux1_x86_64.whl (9.3 MB)
     |████████████████████████████████| 9.3 MB 38.3 MB/s
Collecting base58==2.0.1
  Downloading base58-2.0.1-py3-none-any.whl (4.3 kB)
ERROR: Could not find a version that satisfies the requirement subprocess (from -r requirements.txt (line 4)) (from versions: none)
ERROR: No matching distribution found for subprocess (from -r requirements.txt (line 4))

Wrong Links

Hi there! I absolutely love your content. I just wanted to share that the first link actually takes you to the #21 linked below:
https://www.youtube.com/watch?v=htBIP17S-20&t=277s

Obviously that is the wrong tutorial video. But the picture takes you to the correct video.

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