From 431bcfed721d9ec81400f48dc6b8009be27474e1 Mon Sep 17 00:00:00 2001
From: Henning Redestig <henning.red@gmail.com>
Date: Thu, 4 May 2017 12:49:50 +0200
Subject: [PATCH] doc: fix formatting in notebook

---
 documentation_builder/gapfilling.ipynb | 42 ++++++++++++++++++++------
 1 file changed, 33 insertions(+), 9 deletions(-)

diff --git a/documentation_builder/gapfilling.ipynb b/documentation_builder/gapfilling.ipynb
index 2af8bfedf..a149f00df 100644
--- a/documentation_builder/gapfilling.ipynb
+++ b/documentation_builder/gapfilling.ipynb
@@ -2,21 +2,45 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "metadata": {
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "source": [
     "# Gapfillling\n",
     "\n",
-    "Model gap filling is the task of figuring out which reactions have to be added to a model to make it feasible. Several such algorithms have been reported e.g. [Kumar et al. 2009](http://dx.doi.org/10.1371/journal.pcbi.1000308) and [Reed et al. 2006](http://www.pnas.org/content/103/46/17480.short). Cobrapy has a gap filling implementation that is very similar to that of Reed et al. where we use a mixed-integer linear program to figure out the smallest number of reactions that need to be added for a user-defined collection of reactions, i.e. a universal model. Briefly, the problem that we try to solve is\n",
-    "$$\\textrm{minimize}: \\sum_i c_i * z_i$$\n",
-    "subject to\n",
+    "Model gap filling is the task of figuring out which reactions have to be added to a model to make it feasible. Several such algorithms have been reported e.g. [Kumar et al. 2009](http://dx.doi.org/10.1371/journal.pcbi.1000308) and [Reed et al. 2006](http://www.pnas.org/content/103/46/17480.short). Cobrapy has a gap filling implementation that is very similar to that of Reed et al. where we use a mixed-integer linear program to figure out the smallest number of reactions that need to be added for a user-defined collection of reactions, i.e. a universal model. Briefly, the problem that we try to solve is"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Minimize: $$\\sum_i c_i * z_i$$"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "subject to"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "$$Sv = 0$$\n",
     "$$v^\\star \\geq t$$\n",
     "$$l_i\\leq v_i \\leq u_i$$\n",
-    "$$v_i = 0 \\textrm{ if } z_i = 0$$\n",
-    "Where $l_i$, $u_i$ are lower and upper bounds for reaction $i$ and $z_i$ is an indicator variable that is zero if the reaction is not used and otherwise 1, $c_i$ is a user-defined cost associated with using the $i$th reaction, $v^\\star$ is the flux of the objective and $t$ a lower bound for that objective. To demonstrate, let's take a model and remove some essential reactions from it."
+    "$$v_i = 0 \\textrm{ if } z_i = 0$$"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "Where *l*, *u* are lower and upper bounds for reaction *i* and *z* is an indicator variable that is zero if the reaction is not used and otherwise 1, *c* is a user-defined cost associated with using the *i*th reaction, $v^\\star$ is the flux of the objective and *t* a lower bound for that objective. To demonstrate, let's take a model and remove some essential reactions from it."
    ]
   },
   {