Merge pull request #61 from BrainAnnex/dev

Dev Beta 30.1

Author: BrainAnnex

README.md

@@ -1,4 +1,4 @@
-### BETA 30 (v0.30.0)
+### BETA 30.1 (v0.30.1)
 
 
 

experiments/reactions_single_compartment/enzyme_1.ipynb

@@ -5,7 +5,7 @@
    "id": "49bcb5b0-f19d-4b96-a5f1-e0ae30f66d8f",
    "metadata": {},
    "source": [
-    "## Comparing the reaction `A <-> B` , with and without an enzyme\n",
+    "## Comparing the dynamics of the reaction `A <-> B` , with and without an enzyme\n",
     "\n",
     "LAST REVISED: Dec. 3, 2023"
    ]

experiments/reactions_single_compartment/enzyme_1.py

@@ -14,7 +14,7 @@
 # ---
 
 # %% [markdown]
-# ## Comparing the reaction `A <-> B` , with and without an enzyme
+# ## Comparing the dynamics of the reaction `A <-> B` , with and without an enzyme
 #
 # LAST REVISED: Dec. 3, 2023
 

experiments/reactions_single_compartment/enzyme_2.ipynb

@@ -5,7 +5,7 @@
    "id": "49bcb5b0-f19d-4b96-a5f1-e0ae30f66d8f",
    "metadata": {},
    "source": [
-    "## Coupled pair of reactions: `A <-> B` , and  `A` + `E` <-> `B` + `E`\n",
+    "## Coupled pair of reactions: `A <-> B` , and  `A + E <-> B + E`\n",
     "A direct reaction and the same reaction, catalyzed\n",
     "### Enzyme `E` initially zero, and then suddenly added mid-reaction\n",
     "\n",

experiments/reactions_single_compartment/enzyme_2.py

@@ -14,7 +14,7 @@
 # ---
 
 # %% [markdown]
-# ## Coupled pair of reactions: `A <-> B` , and  `A` + `E` <-> `B` + `E`
+# ## Coupled pair of reactions: `A <-> B` , and  `A + E <-> B + E`
 # A direct reaction and the same reaction, catalyzed
 # ### Enzyme `E` initially zero, and then suddenly added mid-reaction
 #

experiments/reactions_single_compartment/enzyme_3.ipynb

@@ -5,9 +5,9 @@
    "id": "49bcb5b0-f19d-4b96-a5f1-e0ae30f66d8f",
    "metadata": {},
    "source": [
-    "## Coupled pair of reactions: `S <-> P` , and  `S` + `E` <-> `P` + `E`\n",
+    "## Coupled pair of reactions: `S <-> P` , and  `S + E <-> P + E`\n",
     "A direct reaction and the same reaction, catalyzed\n",
-    "### Re-run from same initial concentrations of S (\"Substrate\") and P (\"Product\") for various concentations of the enzyme `E`: from zero to hugely abundant\n",
+    "### Re-run from same initial concentrations of S (\"Substrate\") and P (\"Product\"), for various concentations of the enzyme `E`: from zero to hugely abundant\n",
     "\n",
     "LAST REVISED: Dec. 3, 2023"
    ]

experiments/reactions_single_compartment/enzyme_3.py

@@ -14,9 +14,9 @@
 # ---
 
 # %% [markdown]
-# ## Coupled pair of reactions: `S <-> P` , and  `S` + `E` <-> `P` + `E`
+# ## Coupled pair of reactions: `S <-> P` , and  `S + E <-> P + E`
 # A direct reaction and the same reaction, catalyzed
-# ### Re-run from same initial concentrations of S ("Substrate") and P ("Product") for various concentations of the enzyme `E`: from zero to hugely abundant
+# ### Re-run from same initial concentrations of S ("Substrate") and P ("Product"), for various concentations of the enzyme `E`: from zero to hugely abundant
 #
 # LAST REVISED: Dec. 3, 2023
 

experiments/reactions_single_compartment/macromolecules_2.ipynb

@@ -6,7 +6,8 @@
    "metadata": {},
    "source": [
     "## A simple `A <-> B` reaction whose rate constants are to be estimated \n",
-    "## from a given time evolution of [A] and [B] (values on a *variable-time* grid.)\n",
+    "## from a given time evolution of [A] and [B]  \n",
+    "### (values given on a *variable-time* grid.)\n",
     "\n",
     "Assume the reaction is known to be 1st order (won't verify that.)  \n",
     "\n",

experiments/reactions_single_compartment/mystery_reaction_1.ipynb

@@ -14,7 +14,8 @@
 
 # %% [markdown]
 # ## A simple `A <-> B` reaction whose rate constants are to be estimated 
-# ## from a given time evolution of [A] and [B] (values on a *variable-time* grid.)
+# ## from a given time evolution of [A] and [B]  
+# ### (values given on a *variable-time* grid.)
 #
 # Assume the reaction is known to be 1st order (won't verify that.)  
 #