Update coupling constraint derivations in docs

SBRG · Mar 24, 2018 · 99c2fff · 99c2fff
1 parent 2890fe9
commit 99c2fff
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diff --git a/docs/MEModelFundamentals.ipynb b/docs/MEModelFundamentals.ipynb
@@ -35,13 +35,12 @@
    ]
   },
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "metadata": {
-    "raw_mimetype": "text/restructuredtext"
+    "raw_mimetype": "text/markdown"
    },
    "source": [
-    ".. math::\n",
-    "    \\frac{\\mu}{k_{eff}}"
+    "$$\\frac{\\mu}{k_{eff}}$$"
    ]
   },
   {
@@ -95,15 +94,16 @@
    ]
   },
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "metadata": {
     "raw_mimetype": "text/restructuredtext"
    },
    "source": [
-    ".. math::\n",
-    "    \\textbf{Enzyme Priming:  }   \\mathrm{enzyme} \\xrightarrow{v0} \\mathrm{enzyme\\_primed + } \\alpha \\cdot \\mathrm{coupling} \\\\\n",
-    "    \\textbf{Enzymatic Reaction:  }  \\mathrm{a + enzyme\\_primed} \\xrightarrow{v1} \\textrm{enzyme + b}\\\\\n",
-    "    \\textbf{Dilution Coupling Reaction:  }  \\textrm{enzyme + coupling} \\xrightarrow{v2} \\emptyset \\\\"
+    "$$\n",
+    "\\textbf{Enzyme Priming:  }   \\mathrm{enzyme} \\xrightarrow{v0} \\mathrm{enzyme\\_primed + } \\alpha \\cdot \\mathrm{coupling} \\\\\n",
+    "\\textbf{Enzymatic Reaction:  }  \\mathrm{a + enzyme\\_primed} \\xrightarrow{v1} \\textrm{enzyme + b}\\\\\n",
+    "\\textbf{Dilution Coupling Reaction:  }  \\textrm{enzyme + coupling} \\xrightarrow{v2} \\emptyset \n",
+    "$$"
    ]
   },
   {
@@ -117,13 +117,12 @@
    ]
   },
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "metadata": {
     "raw_mimetype": "text/restructuredtext"
    },
    "source": [
-    ".. math::\n",
-    "    \\textrm{a} + \\alpha \\cdot \\textrm{enzyme} \\xrightarrow{v1} \\textrm{ b}"
+    "$$ \\textrm{a} + \\alpha \\cdot \\textrm{enzyme} \\xrightarrow{v1} \\textrm{ b}$$ "
    ]
   },
   {
@@ -174,13 +173,12 @@
    ]
   },
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "metadata": {
     "raw_mimetype": "text/restructuredtext"
    },
    "source": [
-    ".. math::\n",
-    "    v_i \\Rightarrow \\frac{mmol}{gDW \\cdot hr}"
+    "$$v_i \\Rightarrow \\frac{mmol}{gDW \\cdot hr}$$"
    ]
   },
   {
@@ -191,13 +189,12 @@
    ]
   },
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "metadata": {
     "raw_mimetype": "text/restructuredtext"
    },
    "source": [
-    ".. math::\n",
-    "    molecular\\_weight \\Rightarrow kDA[\\frac{g}{mmol}]"
+    "$$molecular\\_weight \\Rightarrow kDA[\\frac{g}{mmol}]$$"
    ]
   },
   {
@@ -208,13 +205,12 @@
    ]
   },
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "metadata": {
     "raw_mimetype": "text/restructuredtext"
    },
    "source": [
-    ".. math::\n",
-    "    molecular\\_weight \\cdot v_i \\Rightarrow hr^{-1}[\\mu]"
+    "$$molecular\\_weight \\cdot v_i \\Rightarrow hr^{-1}[\\mu]$$"
    ]
   }
  ],