diff --git a/learn/README.md b/learn/README.md
index 78b1aa432..b36f3e644 100644
--- a/learn/README.md
+++ b/learn/README.md
@@ -12,7 +12,7 @@ The learn project includes parameter estimation and a regulatory network learnin
 After building the executable jar, you need to invoke the following command:
 
 ```
-  java -jar target/iBioSim-learn-3.0.0-SNAPSHOT-jar-with-dependencies.jar [-e] [-l ...] input directory
+ java -jar target/iBioSim-learn-3.0.0-SNAPSHOT-jar-with-dependencies.jar [options] input directory
 ```
 
 where 
@@ -20,12 +20,34 @@ where
 
 | Required        |  Description  |
 | -------------   | ------------- |
-| ```input```     | arbitrary SBML file 
-| ```directory``` | location of the time-series data  |
+| input     | arbitrary SBML file 
+| directory | location of the time-series data  |
 
-| Optional        |  Description  |
+| Options        |  Description  |
 | -------------   | ------------- |
-|  ```-e```  | perform parameter estimation. Default is GeneNet. |
-```-l ...``` |a flag to specify which parameters need to be estimated, where the value is a comma separated list of parameter ids (e.g., "p1,p2,p3") |
-
+|  -e  | perform parameter estimation. Default is GeneNet. |
+| -l [list] | a flag to specify which parameters need to be estimated, where the value is a comma separated list of parameter ids (e.g., "p1,p2,p3") |
+| -ta [num] |  Sets the activation threshold.  Default 1.15| 
+| -tr [num] |  Sets the repression threshold.  Default 0.75| 
+| -ti [num] |  Sets how high a score must be to be considered a parent.  Default 0.5| 
+| -tm [num] |  Sets how close IVs must be in score to be considered for combination.  Default 0.01| 
+| -tn [num] |  Sets minimum number of parents to allow through in SelectInitialParents. Default 2| 
+| -tj [num] |  Sets the max parents of merged influence vectors, Default 2| 
+| -tt [num] |  Sets how fast the bound is relaxed for ta and tr, Default 0.025| 
+| -d [num] |   Sets the debug or output level.  Default 0| 
+| -wr [num] |  Sets how much larger a number must be to be considered as a rise.  Default 1| 
+| -ws [num] |  Sets how far the TSD points are when compared.  Default 1| 
+| -nb [num] |  Sets how many bins are used in the evaluation.  Default 4| 
+| --lvl |    Writes out the suggested levels for every specie| 
+| --readLevels |  Reads the levels from level.lvl file for every specie| 
+| --cpp_harshenBoundsOnTie |   Determines if harsher bounds are used when parents tie in CPP.| 
+| --cpp_cmp_output_donotInvertSortOrder |  Sets the inverted sort order in the 3 places back to normal| 
+| --cpp_seedParents  |  Determines if parents should be ranked by score, not tsd order in CPP.| 
+| --cmp_score_mustNotWinMajority |   Determines if score should be used when following conditions are not met a > r+n || r > a + n| 
+| --score_donotTossSingleRatioParents |    Determines if single ratio parents should be kept| 
+| --output_donotTossChangedInfluenceSingleParents |  Determines if parents that change influence should not be tossed| 
+| -binNumbers |  Equal spacing per bin| 
+| -noSUCC |  to not use successors in calculating probabilities| 
+| -PRED |  use preicessors in calculating probabilities| 
+| -basicFBP |  to use the basic FindBaseProb function|