formulations (and format)

README.md

@@ -7,17 +7,21 @@ Contact:  [Stefan Kleeberger](mailto:stefan.kleeberger@gmail.com) (Programmer),
 
 ## Still in development!
 
-This tool recently reached the status of BETA. The core functionality is hereby given. If there is any interest in using this tool, I will continue adding features to it. If you are interested in working with this tool and need assistance, please leave [me a note](mailto:stefan.kleeberger@gmail.com) (email above).
+This tool recently reached the status of BETA. The core functionality is hereby given. If there is any interest in using this tool, I will continue adding features to it. If you are interested in working with this tool and need assistance, please leave [me a note](mailto:stefan.kleeberger@gmail.com).
 
 ## Compilation & needed technologies
 
-- You will have to have at least a CUDA 2.0 capable device (if not 3.5 you need to change the Makefile from sm_35 to sm_20)
-- ... the complete CUDA toolkit installed
-- You need (at the moment) a greater amount of memory (for 5k SNPs & 1k Individuals, we needed ~ 20 GB)
+
+#### Prerequisites
+- You will have to have at least a CUDA 2.0 capable device (if not 3.5 you need to change the Makefile from `sm_35` to `sm_20`)
+- the complete CUDA toolkit installed
+- You need (at the moment) a greater amount of memory (for 5000 SNPs & 1000 Individuals, we needed ~20 GB)
 - At least 8 cores
+
+#### Preparations
 - Candidate SNPs or at least pre-selected SNPs. Genome-wide won't be feasible ... yet.
-- make changes in the _Makefile_
-- make changes in the _helperzz/build.sh_ file
+- make appropriate changes in the _Makefile_ (see below)
+- make appropriate changes in the _helperzz/build.sh_ file
 - located in the kleEpistasis directory, you can either run
 `make`
 or,
@@ -28,11 +32,11 @@ which is a small script to create the needed filesystem structure and compile us
 ## Changes you may need to make in the _Makefile_
 
 Please customize your Makefile as you need. You may want to change
-(friendly reminder: in sh shells there must not be any whitespace in `VARIABLE=VALUE`)
+(friendly reminder: in `sh` shells there must not be any whitespace in `VARIABLE=VALUE`)
 
 
 - the location of your CUDA compiler nvcc (line 5)
-- change the compute capability according to your device (e.g. m_35 to sm_20, line 5)
+- change the compute capability according to your device (e.g. `m_35` to `sm_20`, line 5)
 - the location of your CUDA library (line 6)
 - add debugging flags `-g -G` to OPT (line 7)
 - and anything else you want to change, as long as you know what you are doing.