Updated readme

README.md

@@ -1,22 +1,29 @@
 # BatMass
-### Mass spectrometry data visualization tools
 
-It was originally created to provide an extensible platform with basic functionality, like project management, raw mass-spectrometry data access, various GUI widgets and extension points. E.g. project system, option panels, a system for easy addition of support for new file types, actions for those files, memory management for viewers, etc.
+Please visit http://batmass.org for more information.
 
-More specifically, the original goal was to be able to visualize results of LC/MS feature-finding algorithms (a feature in this context is an isotopic cluster as it elutes from the chromatographic column over time).
+## Mass spectrometry data visualization tools
+BatMass is a mass-spectrometry data visualization tool, with the main focus on being fast and interactive while providing comprehensive visualizations without any parameter tweaking. It is written in pure Java and built on top of the [NetBeans Platform](https://netbeans.org/features/platform/all-docs.html).
 
-### What can we offer so far
 
-As there is no paper yet, we can not release the full source code, however, the code will be out as soon as the paper lands. The software is in alpha stage.
+## Features
+- Support for the open standard _mzML_ and _mzXML_ mass spectrometry data types. We are hoping to bring native vendor format support as well.
 
-The binaries are released in the hopes that it might help you take a fresh look at the raw data from your experiments.
+- Viewer synchronization. Link any number of viewers and zooming/panning will be synchronized across them. If you're viewing MS<sup>1</sup> data in one view and MS<sup>2</sup> data in the other the retention time is synchronized, while m/z is not. Open a detected LC/MS feature table or a peptide identification table, a double click on the row will open the corresponding spectrum, or bring you to the corresponding location in a 2D Map viewer.
 
-### How to start
+- Data access layer. For the Java developers out there, the highly optimized mzML/mzXML parsers can be used in any standalone Java program as a simple _jar_ dependency. Parsing has been manually tuned to produce few garbage objects, thus minimizing time spent in GC (Garbage Collection), the speed is comparable to or better than in C/C++ implementations. The API for LC/MS data files gives access to most of the features supported by mzML/mzXML standards.
 
-Check out the releases section, choose the latest release, download the isntaller for your system.
-You can also download the zip file, which does not require any installation.
-If you had BatMass installed previously, you'll have to manually uninstall it.
 
+
+## Installation
+Download an installer for your system [here](https://github.com/chhh/batmass/releases/latest).  
+If you choose to use the platform independent _zip_ file (batmass.zip), you'll need to run the launcher for your system in `<install_path>/bin`, e.g. `<install_path>/bin/batmass64.exe` if you're running a 64 bit version of Windows. For linux-based systems there is `<install_path>/bin/batmass` shell script to start BatMass.  
+
+If you have an earlier version of BatMass installed, you have to manually uninstall it.  
+
+For more detailed instructions see the [getting started guide](http://www.batmass.org/getting-started/).
+
+## Important before you begin
 The only 2 parameters that you mgiht want to change after installing/unzipping is the amount of memory allowed to be used by BatMass and the path to JRE (Java Runtime Environment) to be used. The minimum supported version is Java 7, which is also the recommended one.<br/>
 These parameters are stored in `<install_path>/etc/batmass.conf`<br/>
 - To change the memory limit, change `default_options` parameter, look for `-J-Xmx` in its value string. The default is `-J-Xmx4G`, which means 4Gb max will be allowed and if your machine does not have enough free memory, the JVM (Java Virtual Machine) might fail to start.<br/>