Made mindcontrol link, linkable. Updated reference

README.markdown

@@ -6,7 +6,7 @@ Introduction
 
 [MindControl][1] is a software tool that allows a researcher to utilize [optogenetics][2] to manipulate neural activity in a freely moving worm for behavioral neuroscience experiments. MindControl analyzes a video stream of a swimming nematode and in real time it generates an illumination pattern that targets specific neurons or cells within the worm. The software can output these patterns to a digital micrommirror device in a closed loop. In this way, a researcher can train arbitrary pulses of laser light only on specific cells or neurons of a worm as it moves. The software records detailed information about the worm's position, orientation and the state of the system for every frame of the video stream. This data is recorded in a human- and computer- readable YAML file. The software optionally also outputs raw and annotated video streams for later analysis. The [MindControl-analysis][3] software suite generates quantitative graphs and figures of nematode behavior based on the output from MindControl.
 
-MindControl is the software component of [CoLBeRT] [4] (**Co**ntrolling **L**ocomotion and **Be**havior in **R**eal-**T**ime) as described in Leifer, A.M., Fang-Yen, C., Gershow, M., Alkema, M., Samuel, A.D.T., "Optogenetic manipulation of neural activity with high spatial resolution in freely moving Caenorhabditis elegans," Nature Methods, in press (2010).
+MindControl is the software component of [CoLBeRT] [4] (**Co**ntrolling **L**ocomotion and **Be**havior in **R**eal-**T**ime) as described in Leifer, A.M., Fang-Yen, C., Gershow, M., Alkema, M., Samuel, A.D.T., "Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans," Nature Methods, in press (2010).
 
   [1]: http://github.com/samuellab/mindcontrol
   [2]: 	http://en.wikipedia.org/wiki/Optogenetics
@@ -26,7 +26,9 @@ MindControl is written by Andrew Leifer with help from Marc Gershow. It is a pro
 
 Most Up To Date Version
 -----------------------
-The most up to date version of the MindControl software will always be available at http://github.com/samuellab/mindcontrol 
+The most up to date version of the MindControl software will always be available at [http://github.com/samuellab/mindcontrol] [9]
+
+  [9]: http://github.com/samuellab/mindcontrol  
 
 License
 -------
@@ -38,15 +40,16 @@ How to Cite
 
 If you use any portion of this code or software in your research, please cite:
 
-> Leifer, A.M., Fang-Yen, C., Gershow, M., Alkema, M., Samuel, A.D.T., "Optogenetic manipulation of neural activity with high spatial resolution in freely moving Caenorhabditis elegans," Nature Methods, in press (2010).
+> Leifer, A.M., Fang-Yen, C., Gershow, M., Alkema, M., Samuel, A.D.T., "Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans," Nature Methods, in press (2010).
 
 Requirements
 ============
-The software has different requirements depending on whether you plan to compile the code, or run an existing pre-compiled binary. Moreover, there are different compile targets and executables for different hardware environments. 
+The software was developed on Intel hardware running Windows XP. It was compiled with the MinGW gcc compiler.  The software has different requirements depending on whether you plan to compile the code, or run an existing pre-compiled binary. Moreover, there are different compile targets and executables for different hardware environments. For example, to control a micromirror device requires compiling an executable that links to commercial software libraries included with the micromirror device.
+
 
 Quick Start
 ------------------
-The quickest way to get a feel for the software is to run the VritualMC.exe pre-built executable which is packaged in a zip file and availabe for download at [http://github.com/downloads/samuellab/mindcontrol/MindControlDEMO.zip][mc] VirtualMC.exe will run on any Windows XP system and requires only the OpenCV 1.1 run-time libraries  which are bundled in the zip file. Follow the README included in the zip.
+The quickest way to get a feel for the software is to run the VritualMC.exe pre-built executable which is packaged in a zip file and availabe for download at [http://github.com/downloads/samuellab/mindcontrol/MindControlDEMO.zip][mc] VirtualMC.exe will run on any Windows XP system and requires only the included OpenCV 1.1 run-time libraries. No special hardware is required. Follow the README in the zip.
 
 [mc]: http://github.com/downloads/samuellab/mindcontrol/MindControlDEMO.zip