Updated Readme

README.md

@@ -1 +1,66 @@
 # SS-Analyzer
+
+SS-Analyzer (State Space Analyzer) is a tool that allows the user to process a microfluidic design described that conforms to the ParchMint ([http://parchmint.org](http://parchmint.org)) standard to be be analyzed for Pressure and Flow Rate data. In this demonstration version of SS-Analyzer, the tool can only work with 1-1 `CONNECTION` and `MIXER` object used by 3DµF ([http://3duf.org](http://3duf.org)). Future versions of SS-Analyzer will be extended to support more component definitions and be able to complex connectivity.
+
+## Installation
+
+### Dependencies
+
+In order to use SS-Analyzer, Python 3.6.3 or greater is required to be installed on the computer. The analyzer also uses the following packages as dependencies. `flask`, `numpy`, `networkx`, `argparse`. The project uses `pipenv` to simplify the dependency management. 
+
+### pipenv based installation
+
+```
+# This assumes you clone the repo and have python installed on your machine
+
+pip install pipenv          #Install pipenv 
+cd <project directory>
+pipenv install              #Creates sandbox runtime env and downloads all dependencies
+pipenv shell                #Changes the terminal environment into the sandbox env, <ctrl + D> to exit
+pip freeze                  #Ensures the runtime python interpreter finds all modules
+python tool.py  <design file> -i <config>   #Runs the primary application
+``` 
+
+## Usage
+
+### Config File Format
+In order to run the tool, the user needs to pair the design created using 3DµF with a corresponding config file that is encoded in plain text. An example of the config file is as follows:
+
+```
+port_in1, IN, 1
+port_in2, IN, 1
+port_out, OUT, 101325
+```
+
+Where each line corresponds follows the below format :
+
+```
+<component name> <state> <flowrate (IN) / pressure(OUT)>
+```
+
+**Note**  - The current version of SS-Analyzer only annotates flow-rate for inputs and pressure for outputs. Future versions of SS-Analyzer will support additional features.
+
+### Command Line Interface
+```
+usage: tool.py [-h] [-i INPUT] design
+```
+
+```
+positional arguments:
+  design                JSON file to Analyze
+```
+```
+optional arguments:
+  -h, --help    show this help message and exit
+  -i INPUT, --input INPUT Config file
+```
+### Demonstration Files
+
+The demonstration design file and config file are available with the v0.1 release ([https://github.com/CIDARLAB/SS-Analyzer/releases/](https://github.com/CIDARLAB/SS-Analyzer/releases/))
+
+## License 
+
+BSD 2-Clause License
+
+Copyright (c) 2019, CIDAR LAB
+All rights reserved.