From 6d2fdce4959e871015c5e40567d1f7458491802a Mon Sep 17 00:00:00 2001
From: Jonas Verhellen <32571076+Jonas-Verhellen@users.noreply.github.com>
Date: Thu, 2 Jul 2020 19:09:52 +0200
Subject: [PATCH 1/3] Update README.md

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 59e6438..762a2c7 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,11 @@
 # Argenomic
 Argenomic is  an open-source implementation of an illumination algorithm for optimization of small organic molecules.
 
-
 ## Getting Started
 
-To run the the argenomic software:
+To run the the argenomic software (rediscovery of Thiotixene):
 ```
-python3 main.py configuration_file= ./configuration/config.json generations= 100
+python3 illuminate.py configuration_file=./configuration/config.yaml generations=50
 ```
 
 ### Installing
@@ -23,6 +22,7 @@ Verify that the new environment was installed correctly:
 ```
 conda env list
 ```
+
 ## Authors
 
 * **Jonas Verhellen** - *Concept, implementation, and development*

From 1eb4740b04d4a31d9ec5906d505208d7d33a8949 Mon Sep 17 00:00:00 2001
From: Jonas Verhellen <32571076+Jonas-Verhellen@users.noreply.github.com>
Date: Thu, 2 Jul 2020 19:10:27 +0200
Subject: [PATCH 2/3] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 762a2c7..e15b08b 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ conda env list
 
 ## Copyright License
 
-This project is licensed under the GNU General Public License v3 (GPLv3)".
+This project is licensed under the GNU General Public License v3 (GPLv3).
 
 ## Acknowledgments
 

From 3bfa9feba01b515f780b8574b8e0d84e722cd3e4 Mon Sep 17 00:00:00 2001
From: Jonas Verhellen <32571076+Jonas-Verhellen@users.noreply.github.com>
Date: Thu, 2 Jul 2020 19:17:50 +0200
Subject: [PATCH 3/3] Update README.md

---
 README.md | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/README.md b/README.md
index e15b08b..f9f21b5 100644
--- a/README.md
+++ b/README.md
@@ -32,6 +32,15 @@ conda env list
 
 This project is licensed under the GNU General Public License v3 (GPLv3).
 
+## Dependencies
+
+Important dependencies of the Argenomic software environment and where to find the source.
+
+* [Python](https://www.python.org/) - Python is a widely used scientific and numeric programming language.
+* [RDKit](https://github.com/rdkit/rdkit) - Cheminformatics and machine-learning software toolkit.
+* [Scikit-learn](https://github.com/scikit-learn/scikit-learn) - Data science and deep learning toolset in Python.
+* [Omegaconf](https://github.com/omry/omegaconf) - Configuration system for multiple sources, providing a consistent API.
+
 ## Acknowledgments
 
 * Jan Jensen for his work in developing and open-sourcing a graph-based genetic algorithm for molecular optimisation, which served as impetus for this project.