See the source paper (Open Access): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10742026/
Zamora PO, Altay G, Santamaria U, Dwarshuis N, Donthi H, Moon CI, Bakalar D, Zamora M. Drug Responses in Plexiform Neurofibroma Type I (PNF1) Cell Lines Using High-Throughput Data and Combined Effectiveness and Potency. Cancers (Basel). 2023 Dec 12;15(24):5811. doi: 10.3390/cancers15245811. PMID: 38136356; PMCID: PMC10742026.
See the deployed version of this code at: https://nf.mocomakers.com
https://www.mocomakers.com/wp-content/uploads/2023/06/qHTS-NF1-Drugs-List-PosterV8-Final.pdf
This code hosts a web tool (DREA web tool) for exploring NF1 quantitative High Throughput Screening (qHTS) data.
Please visit this tool live here: http://nf.mocomakers.com - Use the Sign Up form on the page, and if there is an issue please contact [email protected]
A sister repo to this project is: https://github.com/MoCoMakers/hack4nf-2022
You can setup the project on your browser using your GitHub account by clicking this Codespaces deeplink.
Alternatively, install and setup the software listed in the Tech Stack section on your computer. Then take the following steps:
Using a bash terminal, clone the repository:
git clone https://github.com/MoCoMakers/nf_streamlit.gitGo into the cloned folder:
cd nf_streamlitOpen the project with Visual Studio code:
code .While the project is loading in the editor, watch out for a prompt with a button asking you to "Reopen in Container":
Click the "Reopen in Container" button and the project would be opened in Devcontainers with the database running in the background.
After setting up the project following the instructions above, you can run the project following the following steps:
- (Optional) Change the values in the cookie dictionary of the
secrets.toml.examplefile.- Download the files the project needs (this command has to be run the the
app/folder):pip install gdown gdown https://drive.google.com/drive/folders/1C3z88jbjXhffHG1qc6W4ExujADiKUinN -O data --folder
- Make copies of the templates of configuration files ending with the extension
.exampleand rename them:find . -name '*.example' -type f -exec bash -c 'cp "$1" ${1%.example} ' -- {} \;
- To run the streamlit server, use the following command (preferably in a new terminal that you can open by using the key combination
CTRL + SHIFT + `in Windows orCMD (⌘) + SHIFT + `in MacOS):streamlit run Home.py --server.fileWatcherType auto --server.headless trueAlternatively, the project can be run with hot reload where the server refreshes when the
PythonorTOMLproject files are modified:find . -name "*.py" -or -name "*.toml" | entr -r streamlit run Home.py --server.fileWatcherType auto --server.headless trueA default credential is setup for developers to log in:
Username:
example
Password:Makers
Clone repo, then copy config.toml.example to config.toml, and secrets.toml.example to secrets.toml and update the values.
Note that you will need a remote database connection (MySQL is the default) configured with a users table, for example:
table drea_users;
+--------------+--------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+--------------+--------------+------+-----+---------+-------+
| username | varchar(255) | NO | PRI | NULL | |
| email | text | YES | | NULL | |
| name | text | YES | | NULL | |
| passwordhash | text | YES | | NULL | |
| approved | tinyint(1) | YES | | NULL | |
+--------------+--------------+------+-----+---------+-------+
Put all of the data inside the folder named app/data.
You will need a valid synapse.org account and approved
access (portal request) to syn5522627 - which you can search for on synapse.org
Run the following inside the app/data folder
pip install synapseclient[pandas,pysftp]
mkdir syn5522627
cd syn5522627
synapse get -r syn5522627
Download here (if the direct link doesn't work, navigate to Downloads > File Downloads and continue):
https://depmap.org/portal/download/all/ -> Drug Screens -> PRISM Repurposing 19Q4
Download the file:
| File | Date | Size |
|---|---|---|
| secondary-screen-dose-response-curve-parameters.csv | 07/19 | 39.3 MB |
Save your csv file in app/data/DepMap/Prism19Q4/
And also download the latest mutation data from Downloads -> -> Current Release (tab) -> Mutations (tab) -> OmicsSomaticMutationsMatrixDamaging.csv
Save your csv file in app/data/DepMap/Public24Q4/
Change to app/ directory
Install Python requirements pip install -r requirements.txt
Start the app on Windows streamlit run .\Home.py
Start the app Linux/MacOS streamlit run ./Home.py
Note that on first run, you may need to do a page reload two times before the site displays a consistant view, or stable error message.
Log into the server
Clone the docker repo, and change into it:
https://github.com/MocoMakers/docker_streamlit
Run the command in the docker repo:
docker build . -t streamlit_app
Clone this repo.
Copy app/.streamlit/config.toml.example to be just config.toml.
Copy app/.streamlit/secrets.toml.example to be just secrets.toml and fill in the desired password.
Then run:
docker run -p 8501:8501 -v ~/nf_streamlit/app:/app streamlit_app
The first command only needs to be run one time. To run the server using the second command, chaging `~/docker_streamlit/app` for the location of the `app` directory in this repo.
This project uses the following technologies:
- Visual Studio Code (download here) or similar editor like GitHub's Codespaces (check out here or try out this codebase here)
- Git (download here)
- Docker (install along with
docker-composeplugin)- Streamlit (Custom container built from Python base)
- MySQL (official image)
If you face errors upon running the pip install -r requirements.txt, the following link may be of help.