updated version and instances and enhanced readme

vivarium-collective · Jan 9, 2024 · 158d08a · 158d08a
1 parent 137169e
commit 158d08a
Show file tree

Hide file tree

Showing 3 changed files with 130 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -48,4 +48,131 @@ Mac, please adhere to the following instructions:
         scripts/install-with-smoldyn-for-mac-silicon.sh 
 
 ### Quick Start Example:
-#### TODO: Add quickstart example of instance declarations.
+
+Composing, running, and viewing the results of a composite simulation can be achieved in as little as 4 steps. 
+In this example, we use the `CopasiProcess` implementation to compose a sbml-based simulation.
+
+1. Define the composite instance according to the `process_bigraph.Composite` API and relative process
+   implementation (in this case the `CopasiProcess`). Each instance of the Copasi process requires the specification
+   of an SBML model file, which is specified in the inner key, `'config'` :
+
+         from process_bigraph import Composite, pf
+
+         instance = {
+              'copasi': {
+                  '_type': 'process',
+                  'address': 'local:copasi',
+                  'config': {
+                      'model_file': 'biosimulator_processes/tests/model_files/Caravagna2010.xml'
+                  },
+                  'inputs': {
+                      'floating_species': ['floating_species_store'],
+                      'model_parameters': ['model_parameters_store'],
+                      'time': ['time_store'],
+                  },
+                  'outputs': {
+                      'floating_species': ['floating_species_store'],
+                      'time': ['time_store'],
+                  }
+              },
+              'emitter': {
+                  '_type': 'step',
+                  'address': 'local:ram-emitter',
+                  'config': {
+                      'ports': {
+                          'inputs': {
+                              'floating_species': 'tree[float]',
+                              'time': 'float'
+                          },
+                          'output': {
+                              'floating_species': 'tree[float]',
+                              'time': 'float'
+                          }
+                      }
+                  },
+                  'inputs': {
+                      'floating_species': ['floating_species_store'],
+                      'time': ['time_store']
+                  }
+              }
+         }
+
+   As you can see, each instance definition is expected to have the following key heirarchy:
+
+         instance[
+            <INSTANCE-NAME>['_type', 'address', 'config', 'inputs', 'outputs'], 
+            ['emitter']['_type', 'address', 'config', 'inputs', 'outputs']
+         ]
+   Each instance requires at least one process and one emitter. Usually, there may be multiple processes and just 
+      one emitter, thereby sharing memory amongst the chained processes.
+
+   Both `<INSTANCE-NAME>` and `'emitter'` share the same inner keys. Here, pay close attention to how the `'address'`
+      is set for both the instance name and emitter.
+
+2. Create a `process_bigraph.Composite` instance:
+
+         workflow = Composite({
+            'state': instance
+         })
+
+3. Run the composite instance which is configured by the `instance` that we defined:
+
+         workflow.run(10)
+
+4. Gather and pretty print results:
+
+         results = workflow.gather_results()
+         print(f'RESULTS: {pf(results)}')
+
+
+A simplified view of the above script:
+
+
+         from process_bigraph import Composite, pf
+
+         >> instance = {
+                 'copasi': {
+                     '_type': 'process',
+                     'address': 'local:copasi',
+                     'config': {
+                         'model_file': 'biosimulator_processes/tests/model_files/Caravagna2010.xml'
+                     },
+                     'inputs': {
+                         'floating_species': ['floating_species_store'],
+                         'model_parameters': ['model_parameters_store'],
+                         'time': ['time_store'],
+                     },
+                     'outputs': {
+                         'floating_species': ['floating_species_store'],
+                         'time': ['time_store'],
+                     }
+                 },
+                 'emitter': {
+                     '_type': 'step',
+                     'address': 'local:ram-emitter',
+                     'config': {
+                         'ports': {
+                             'inputs': {
+                                 'floating_species': 'tree[float]',
+                                 'time': 'float'
+                             },
+                             'output': {
+                                 'floating_species': 'tree[float]',
+                                 'time': 'float'
+                             }
+                         }
+                     },
+                     'inputs': {
+                         'floating_species': ['floating_species_store'],
+                         'time': ['time_store']
+                     }
+                 }
+            }
+
+         >> workflow = Composite({
+               'state': instance
+            })
+
+         >> workflow.run(10)
+         >> results = workflow.gather_results()
+         >> print(f'RESULTS: {pf(results)}')
diff --git a/biosimulator_processes/_VERSION.py b/biosimulator_processes/_VERSION.py
@@ -1 +1 @@
-__version__ = '0.0.11'
+__version__ = '0.0.12'
diff --git a/biosimulator_processes/tests/model_files/minE_model.txt b/biosimulator_processes/tests/model_files/minE_model.txt
@@ -22,7 +22,7 @@ define L_PARAM2		1.5	# half of cell length minus radius
 define NUMBER_MIND	4000	# number of MinD in cell 4000
 define NUMBER_MINE	1400	# number of MinE in cell 1400
 
-define TIME_STOP	10     # stopping time
+define TIME_STOP	1     # stopping time
 
 #define KICK_START	1	# start with MinD_ATP at an end