Update README.md

README.md

@@ -9,16 +9,16 @@ At least one of Java 1.8, Java 9, or Java 10 must be installed in order to run P
 ## Video Tutorials
 We've recorded two video tutorials that show how to download and run Proteinarium using the command line and graphical user interfaces. Click the video thumbnails below to watch them.
 
-#### Command Line Interface Video Tutorial
+## Command Line Interface Video Tutorial
 [![Alt text](https://img.youtube.com/vi/bC6nTe2I2P4/0.jpg)](https://www.youtube.com/watch?v=bC6nTe2I2P4)
 
 
-#### Graphical User Interface Video Tutorial
+## Graphical User Interface Video Tutorial
 [![Alt text](https://img.youtube.com/vi/50AyOLp-Zi4/0.jpg)](https://www.youtube.com/watch?v=50AyOLp-Zi4)
 
 ----------------------------------------------
 
-### Running Proteinarium on Command Line
+## Running Proteinarium on Command Line
 
 ## 1. Getting Started
 If you are a new user looking to analyze or visualize a dataset for the first time, we recommend the following steps:
@@ -43,17 +43,17 @@ java -jar <path to Proteinarium.jar> <arguments>
 ```
 This will work regardless of what operating system you are using, so long as you jave Java 1.8 or above installed. The helper files simply invoke `java -jar Proteinarium.jar` along with any additional arguments you passed in from the command line.
 
-##### Mac OS X and Unix Environments
+## Mac OS X and Unix Environments
 Open up a terminal, navigate to the folder containing Proteinarium.jar, and execute:
 ```bash
 ./proteinarium.sh <arguments>
 ```
-##### Windows Environments
+## Windows Environments
 Open a command prompt, navigate to the folder containing Proteinarium.jar, and execute:
 ```bash
 proteinarium.bat <arguments>
 ```
-### Arguments
+## Arguments
 The `<arguments>` are allowed to take one of the following forms:
 1. Show help: `-h` or `--help`
 2. Show available configuration options: `-o` or `--options`
@@ -67,7 +67,7 @@ This option is provided primarily for scripting purposes; it is instead recommen
 
 For a complete list of configuration options and explanations of how they affect Proteinarium, refer to [Configuration](Configuration.pdf).
 
-### Output
+## Output
 All output files go to the folder specified by the `outputDirectory` configuration option. By default, this goes to a folder called `output` in the same directory that you run Proteinarium from.
 * **\<projectName\>_ClusterAnalyses.csv**: cluster analysis files
 * **\<projectName\>_Dendrogram.png**: dendrogram image
@@ -99,7 +99,7 @@ To view the summary information for a particular cluster or sample, enter "info
 **Note**: the above information is available for all patients at any time in the **\<projectName\>_ClusterAnalyses.csv** output file.
 
 ----------------------------------------------
-### Running Proteinarium with Graphical User Interface (GUI)
+## Running Proteinarium with Graphical User Interface (GUI)
 
 ## 1.	Getting Started
 
@@ -109,7 +109,7 @@ To view the summary information for a particular cluster or sample, enter "info
 
 ## 2.	Running Proteinarium
 
-### Selecting Files
+## Selecting Files
 
 *	In the GUI, select **File > Home**
 
@@ -124,7 +124,7 @@ To view the summary information for a particular cluster or sample, enter "info
 
 *	For Advance Settings Select **File > Settings** and click on the “Advance Settings” button. Once changed click on “Set Settings” and the “Apply Changes” buttons.
 
-### Running Proteinarium
+## Running Proteinarium
 *	Once files are uploaded and parameters are set, click “Run Proteinarium”
 
 *	If more than one sample is contained within the input file (s), the dendrogam will be displayed.  All output files generated by Proteinarium will be saved to the folder specified by the outputDirectory configuration option. By default, this goes to a folder called “Output” in the same directory as the Proteinarium.jar file.