links to examples folder

UserManual.md

@@ -1,12 +1,14 @@
-# User manual for *sbmodelr* - a tool to replicate one SBML/COPASI model into a set of replicas
+# User Manual for *sbmodelr* - a tool to replicate one SBML/COPASI model into a set of replicas
 
 ## Summary
-*sbmodelr* takes as input an SBML or COPASI file describing a model. It then creates a new model that replicates the original in several copies ('units') where each one may interact with other ones. The topology of the connections can be arbitrary (described in a DOT network file), a 2D rectangular matrix, or a 3D cuboid array.
+*sbmodelr* takes as input an SBML or COPASI file describing a model. It then creates a new model that replicates the original in several copies ('units') where each one may interact with other ones. The topology of the connections can be arbitrary (described in a DOT network file), a 2D rectangular matrix, or a 3D cuboid array. Several options are available to randomize parameter values, supress creation of compartments, etc.
+
+For a full set of options run `sbmodelr --help` on the command line.
 
 ## Examples
 The rest of this document describes the many options that are available in *sbmodelr*, but specific examples of usage are provided in the `examples` folder, which illustrate real-world usage of this tool, mostly replicating existing modeling papers. The examples are:
 
- - Cells in a medium
+ - [Cells in a medium](examples/Cells_in_medium)
  - Row of cells with gap junctions
  - Array of oscillating cells
  - Neuron networks I: small(ish) networks using a Hodgkin-Huxley-type model