Fix readme

Updated the old README.md file with the content found in README_v0.1.1.txt, so that the landing page of the repository will look nicely and explain a bit already.

README.md

-SIAMCAT - Statistical Inference of Associations between 
-Microbial Communities And host phenoTypes
+# SIAMCAT - Statistical Inference of Associations between Microbial Communities And host phenoType
 
-More information can be found in
-README_v0.1.1.txt
\ No newline at end of file
+## Overview
+
+SIAMCAT is a pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes.  
+A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with 
+environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has 
+become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially 
+needed.  
+SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical 
+modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross 
+validation, parameter selection, ROC analysis and diagnostic model plots).  
+SIAMCAT is available in three different flavors: 
+ + Galaxy web server
+ + command line tool
+ + R package
+
+Please see the Support Section if you run into problems when using SIAMCAT.
+
+## Input data format
+
+The input data should be organized in the same way for every version of SIAMCAT. All files are in tab-separated column format
+
+ + **Label data**: First row is expected to be `#BINARY:1=[label for cases];-1=[label for controls]`  
+    Second row should contain the sample identifiers as tab-separated list (consistent with feature and metadata). 
+    Third row is expected to contain the actual class labels (tab-separated), e.g. `1` for each case and `-1` for each 
+    control.  
+    Note: Labels can take other numeric values (but not characters or strings); importantly, the label for cases has to 
+    be greater than the one for controls.
+
+ + **Feature matrix**: _features_ (in rows) _x samples_ (in columns)  
+    First row should contain sample labels (consistent with label data), while the first column should contain feature 
+    labels (e.g. taxonomic identifiers). The remaining entries are expected to be real values >= 0 that quantify the 
+    abundance of each feature in each sample.
+
+ + **Metadata** (optional): _samples_ (in rows) _x metadata_ (in columns)  
+    Metadata needs to be converted to numerical values by the user (This is necessary for heatmap displays)!
+
+
+## Galaxy interface:
+
+The Galaxy interface can be found here: http://siamcat.embl.de/
+
+### Galaxy in brief
+
+
+ + **Left panel**: `TOOLS` lists available analysis modules.  
+    Click to choose which ones you'd like to run.
+ + **Right panel**: `HISTORY` keeps track of every analysis step you have perfomed.  
+  + Click on the "eye" icon to view data, or click on the "floppy disk" icon to download results  
+  + If something goes wrong the "i" icon can provide useful details
+  + the "circular arrows" icon allows to rerun a job
+  + you can delete analysis steps from your history using the "x" icon
+
+ + **Central panel**: `ANALYZE DATA` allows to specify input data sets and parameters for each analysis module
+
+
+Additional info: https://usegalaxy.org/ (in particular the Help menu) and
+                 https://wiki.galaxyproject.org/Learn
+
+
+### Getting started with Galaxy
+
+Start by uploading your data (see above for input data formats) using the `DATA IMPORT / Import Data module / Upload File`
+
+Then procede by executing all SIAMCAT modules in order (from A to I). 
+See example history / Workflow as well as each module's description for specific information on input and output data
+
+
+## Commandline version 
+
+The commandline version are a collection of modules implemented in R which are called via a bash script.
+
++ Stable version: https://github.com/gezel/siamcat/
+
++ Developmental version (only available inside the EMBL intranet): `beta:/g/bork4/zeller/dev/siamcat`
+
+```
+# type
+git clone beta:/g/bork4/zeller/dev/siamcat
+# in the folder in which you'd like to clone the siamcat repository
+```
+
+R packages required to run SIAMCAT:
+```R
+install.packages('optparse')
+install.packages('LiblineaR')
+install.packages('pROC')
+install.packages('colorRamps')
+install.packages('RColorBrewer')
+install.packages('beanplot')
+```
+
+### Using the Commandline version
+
+...COMING SOON...
+
+## R package
+
+The SIAMCAT R package ...COMING SOON...
+
+### Using the R package
+
+...COMING SOON...
+
+## Support
+
+Google user group for support:
+
+https://groups.google.com/d/forum/siamcat-users
+
+
+### Known issues
+
+Examples are weighted differently between classes (a remnant of our colorectal cancer 
+microbiome study). Fixed in Galaxy, will be pushed to GitHub soon.
+
+Class labels are somehow swapped in the LASSO module, so that prediction scores are 1 - p
+instead of p (posterior probability), consequently precision-recall curves are incorrect,
+but ROC-curves are unaffected. Appears to only occur in a recent version of R and/or the
+LiblineaR package; will be fixed with high priority.
+
+### Contact 
+
+Please let me know if you run into any issues (mailto: zeller@embl.de)