Add README

.gitignore

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 *.py[cod]
 *$py.class
 
+# Test data
+data
+
 # C extensions
 *.so
 

README.md

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+# SIMBA🦁 Downstream toolkit
+This repository contains the source code of the python shiny app which is recommended to be used for the downstream analysis of the output of the SIMBA🦁 pipeline. Available instances can be found at at [https://exbio.wzw.tum.de/cost/overview/](https://exbio.wzw.tum.de/cost/overview/).
+
+## Offline Usage
+### Docker
+The app can be run using the docker image `bigdatainbiomedicine/simba-downstream`. The image can be pulled from the docker hub using the following command:
+```bash
+docker run -p <port>:8080 bigdatainbiomedicine/simba-downstream
+```
+Assuming that the port 1234 is used, the app can be accessed at [http://localhost:1234](http://localhost:1234).
+
+### Local
+The app can also be run locally. The following steps are required to run the app locally:
+1. Clone the repository:
+```bash
+git clone https://github.com/Mye-InfoBank/SIMBA-Downstream.git
+```
+2. Install the required packages:
+```bash
+pip install -r requirements.txt
+```
+3. Run the app:
+```bash
+cd src
+uvicorn app:app --host 0.0.0.0 --port <port>
+```
+Assuming that the port 1234 is used, the app can be accessed at [http://localhost:1234](http://localhost:1234).