Initial commit for instructions on how to use analysis and learn.

analysis/README.md

@@ -0,0 +1,21 @@
+
+<p align="center">
+  <img  src="docs/media/iBioSim_horizontal.png">
+</p>
+
+# iBioSim Analysis
+
+The analysis project encapsulates the different java-based simulation and 
+verification methods that is used in the iBioSim tool. 
+
+## How to use it:
+
+After building the executable jar, you need to invoke the following command:
+
+```
+  java -jar target/iBioSim-analysis-3.0.0-SNAPSHOT-jar-with-dependencies.jar <input file>
+```
+
+where <input file> is an arbitrary SED-ML file.
+
+

learn/README.md

@@ -0,0 +1,25 @@
+
+<p align="center">
+  <img  src="docs/media/iBioSim_horizontal.png">
+</p>
+
+# iBioSim Learn
+
+The learn project includes parameter estimation and a regulatory network learning method from time-series data based on the GeneNet procedure.
+
+## How to use it:
+
+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 file> <directory>
+```
+
+where 
+
+* <input file> is an arbitrary SBML file
+* <directory> is the location of the time-series data
+* -e is a flag to perform parameter estimation. Default is GeneNet. 
+* -l is a flag to specify which parameters need to be estimated.
+
+

learn/src/main/java/edu/utah/ece/async/ibiosim/learn/Learn.java

@@ -43,7 +43,7 @@ import edu.utah.ece.async.ibiosim.learn.parameterestimator.ParameterEstimator;
  * Options:
  * <p>
  * -e: when specified, the program will run parameter estimation.
- * -l: when specified, parameter estimation will use the estimate the value of the paramaters in the list.
+ * -l: when specified, parameter estimation will use the estimate the value of the parameters in the list.
  * 
  * @author Leandro Watanabe
  * @author Tramy Nguyen