Recent changes to Tutorials

Tutorials modified by Maxwell Neal

Maxwell Neal — Thu, 07 Nov 2013 21:16:41 -0000

--- v11
+++ v12
@@ -28,14 +28,14 @@
     // called "common" that includes files such as "nsrunit.mod", etc.

     File afile = new File("path/to/MML/file.mod");
-    String jsimHomeDir = ""path/to/jsimhome";  
+    String jsimHomeDir = "path/to/jsimhome";  
     SemSimModel model = new MMLreader(jsimhomeDir).readFromFile(afile);
 ---

 ####Read an SBML model file into the API

     File afile = new File("path/to/SBML/file.xml");
-    String jsimHomeDir = ""path/to/jsimhome"; 
+    String jsimHomeDir = "path/to/jsimhome"; 
     SemSimModel model = new MMLreader(jsimHomeDir).readFromFile(afile);

     // Currently, the SemSimAPI uses MML as an intermediary language to convert from

Tutorials modified by Maxwell Neal

Maxwell Neal — Thu, 07 Nov 2013 21:07:21 -0000

--- v10
+++ v11
@@ -21,15 +21,22 @@

 ####Read an MML model file into the API
-    
+        
+    // MMLreader calls the JSim API, which requires some JSim-specific files to read MML models.
+    // You can point the way to these files using a path to the "jsimhome" directory that is provided in the SemSimAPI source code
+    // Specifically, the JSim API is looking for a directory with a sub-directory
+    // called "common" that includes files such as "nsrunit.mod", etc.
+
     File afile = new File("path/to/MML/file.mod");
-    SemSimModel model = new MMLreader().readFromFile(afile);
+    String jsimHomeDir = ""path/to/jsimhome";  
+    SemSimModel model = new MMLreader(jsimhomeDir).readFromFile(afile);
 ---

 ####Read an SBML model file into the API

     File afile = new File("path/to/SBML/file.xml");
-    SemSimModel model = new MMLreader().readFromFile(afile);
+    String jsimHomeDir = ""path/to/jsimhome"; 
+    SemSimModel model = new MMLreader(jsimHomeDir).readFromFile(afile);

     // Currently, the SemSimAPI uses MML as an intermediary language to convert from
     // SBML to the SemSim object model.

Tutorials modified by Maxwell Neal

Maxwell Neal — Mon, 28 Oct 2013 19:46:11 -0000

--- v9
+++ v10
@@ -41,12 +41,10 @@

     // A table that relates ontology URIs to their free-text descriptions
     Hashtable ontologyTermsAndNamesCache = new Hashtable();
-
     SBMLAnnotator.annotate(afile, model, online, ontologyTermsAndNamesCache);

     // optional step to cache free-text names
     ontologyTermsAndNamesCache.putAll(ReferenceTermNamer.getNamesForOntologyTermsInModel(model,online));    
-
     SBMLAnnotator.setFreeTextDefinitionsForDataStructuresAndSubmodels(model);

 ---

Tutorials modified by Maxwell Neal

Maxwell Neal — Mon, 28 Oct 2013 19:36:49 -0000

--- v8
+++ v9
@@ -51,6 +51,7 @@

 ---

+

Tutorials modified by Maxwell Neal

Maxwell Neal — Thu, 24 Oct 2013 22:57:45 -0000

--- v7
+++ v8
@@ -42,6 +42,13 @@
     // A table that relates ontology URIs to their free-text descriptions
     Hashtable ontologyTermsAndNamesCache = new Hashtable();

+    SBMLAnnotator.annotate(afile, model, online, ontologyTermsAndNamesCache);
+
+    // optional step to cache free-text names
+    ontologyTermsAndNamesCache.putAll(ReferenceTermNamer.getNamesForOntologyTermsInModel(model,online));    
+
+    SBMLAnnotator.setFreeTextDefinitionsForDataStructuresAndSubmodels(model);
+
 ---

 ### Working with the physical model components of a SemSim model
@@ -52,14 +59,4 @@
     // represents calcium concentration in the cytosol of a cardiac myocyte 

     DataStructure ds = semsimmodel.getDataStructure("x1");
-    ds
-    
-
-
-
-    SBMLAnnotator.annotate(afile, model, online, ontologyTermsAndNamesCache);
-
-    // optional step to cache free-text names
-    ontologyTermsAndNamesCache.putAll(ReferenceTermNamer.getNamesForOntologyTermsInModel(model,online));    
-
-    SBMLAnnotator.setFreeTextDefinitionsForDataStructuresAndSubmodels(model);
+    ds...

Tutorials modified by Maxwell Neal

Maxwell Neal — Thu, 24 Oct 2013 22:56:57 -0000

--- v6
+++ v7
@@ -1,14 +1,18 @@
+[TOC]
+
+---
+
 ###Reading models into the API

-**Read an OWL-formatted SemSim model file into the API:**
+####Read an OWL-formatted SemSim model file into the API

     File afile = new File("path/to/OWL/file.owl");
     SemSimModel model = new SemSimOWLreader().readFromFile(afile);
 ---

-**Read a CellML model file into the API:**
+####Read a CellML model file into the API

     File afile = new File("path/to/CellML/file.cellml");
     SemSimModel model = new CellMLreader().readFromFile(afile);
@@ -16,13 +20,13 @@

-**Read an MML model file into the API:**
+####Read an MML model file into the API

     File afile = new File("path/to/MML/file.mod");
     SemSimModel model = new MMLreader().readFromFile(afile);
 ---

-**Read an SBML model file into the API:**
+####Read an SBML model file into the API

     File afile = new File("path/to/SBML/file.xml");
     SemSimModel model = new MMLreader().readFromFile(afile);
@@ -38,6 +42,21 @@
     // A table that relates ontology URIs to their free-text descriptions
     Hashtable ontologyTermsAndNamesCache = new Hashtable();

+---
+
+### Working with the physical model components of a SemSim model
+
+#### Creating a composite annotation for a data structure
+
+    // This code creates a composite annotation for a DataStructure named "x1" that
+    // represents calcium concentration in the cytosol of a cardiac myocyte 
+
+    DataStructure ds = semsimmodel.getDataStructure("x1");
+    ds
+    
+
+
+
     SBMLAnnotator.annotate(afile, model, online, ontologyTermsAndNamesCache);

     // optional step to cache free-text names

Tutorials modified by Maxwell Neal

Maxwell Neal — Thu, 24 Oct 2013 22:00:29 -0000

--- v5
+++ v6
@@ -1,14 +1,14 @@
-###Loading models into the API
+###Reading models into the API

-**Load an OWL-formatted SemSim model file into the API:**
+**Read an OWL-formatted SemSim model file into the API:**

     File afile = new File("path/to/OWL/file.owl");
     SemSimModel model = new SemSimOWLreader().readFromFile(afile);
 ---

-**Load a CellML model file into the API:**
+**Read a CellML model file into the API:**

     File afile = new File("path/to/CellML/file.cellml");
     SemSimModel model = new CellMLreader().readFromFile(afile);
@@ -16,13 +16,13 @@

-**Load an MML model file into the API:**
+**Read an MML model file into the API:**

     File afile = new File("path/to/MML/file.mod");
     SemSimModel model = new MMLreader().readFromFile(afile);
 ---

-**Load an SBML model file into the API:**
+**Read an SBML model file into the API:**

     File afile = new File("path/to/SBML/file.xml");
     SemSimModel model = new MMLreader().readFromFile(afile);

Tutorials modified by Maxwell Neal

Maxwell Neal — Thu, 24 Oct 2013 21:40:31 -0000

tutorials modified by Maxwell Neal

Maxwell Neal — Thu, 24 Oct 2013 21:39:19 -0000

--- v3
+++ v4
@@ -27,7 +27,8 @@
     File afile = new File("path/to/SBML/file.xml");
     SemSimModel model = new MMLreader().readFromFile(afile);

-    //Currently, the SemSimAPI uses MML as an intermediary language to convert from SBML to the SemSim object model.
+    // Currently, the SemSimAPI uses MML as an intermediary language to convert from
+    // SBML to the SemSim object model.
     // This process leaves out most of the semantic content of the SBML model. 
     // To include the semantic content, a bit more effort is required:

tutorials modified by Maxwell Neal

Maxwell Neal — Thu, 24 Oct 2013 21:38:45 -0000

--- v2
+++ v3
@@ -1,8 +1,7 @@
-
 ###Loading models into the API

-**Load an OWL-foramtted SemSim model file into the API:**
+**Load an OWL-formatted SemSim model file into the API:**

     File afile = new File("path/to/OWL/file.owl");
     SemSimModel model = new SemSimOWLreader().readFromFile(afile);
@@ -22,3 +21,25 @@
     File afile = new File("path/to/MML/file.mod");
     SemSimModel model = new MMLreader().readFromFile(afile);
 ---
+
+**Load an SBML model file into the API:**
+
+    File afile = new File("path/to/SBML/file.xml");
+    SemSimModel model = new MMLreader().readFromFile(afile);
+
+    //Currently, the SemSimAPI uses MML as an intermediary language to convert from SBML to the SemSim object model.
+    // This process leaves out most of the semantic content of the SBML model. 
+    // To include the semantic content, a bit more effort is required:
+
+    // Determine whether the user has a live connection to the web
+    boolean online = false;
+
+    // A table that relates ontology URIs to their free-text descriptions
+    Hashtable ontologyTermsAndNamesCache = new Hashtable();
+
+    SBMLAnnotator.annotate(afile, model, online, ontologyTermsAndNamesCache);
+
+    // optional step to cache free-text names
+    ontologyTermsAndNamesCache.putAll(ReferenceTermNamer.getNamesForOntologyTermsInModel(model,online));    
+
+    SBMLAnnotator.setFreeTextDefinitionsForDataStructuresAndSubmodels(model);