fba.ipynb

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   "source": [
    "# Introduction to Flux Balance Analysis\n",
    "\n",
    "Author: Daniel Machado [(CC BY-SA 4.0)](http://creativecommons.org/licenses/by-sa/4.0/)\n",
    "\n",
    "In this tutorial you will learn how to perform flux balance analysis \n",
    "using a model of the central carbon metabolism of *E. coli*."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 1: Loading a model stored in SBML format"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from reframed import load_cbmodel\n",
    "model = load_cbmodel('models/e_coli_core.xml.gz')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's learn some details about the model."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.summary()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 2: Running an FBA simulation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from reframed import FBA\n",
    "solution = FBA(model)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The solution object contains the objective value (the growth rate in this case), and the respective flux distribution. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print(solution)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's look at the uptake and secretion rates."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "solution.show_values(pattern=\"R_EX\", sort=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can see that *E. coli* is consuming glucose and oxygen and producing CO2."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 3: Visualizing fluxes with Escher\n",
    "\n",
    "Escher is a tool for displaying fluxes in a metabolic map.\n",
    "\n",
    "It makes your life easier, especially when comparing flux distributions after genetic or environmental perturbations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from reframed import fluxes2escher"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fluxes2escher(solution.values)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 4: Changing the environmental conditions\n",
    "\n",
    "Let's observe what happens if we cut down the oxygen supply. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "solution2 = FBA(model, constraints={'R_EX_o2_e':0})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print(solution2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "solution2.show_values(pattern=\"R_EX\", sort=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As expected, *E. coli* switched to a fermentation mode, which resulted in the secretion of fermentation products and a decrease in growth rate.\n",
    "\n",
    "Again, we can see it better by displaying the flux distribution in a metabolic map."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fluxes2escher(solution2.values)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 4: Rational strain design\n",
    "\n",
    "Imagine you want to produce succinate using *E. coli* under anaerobic conditions. Let's look at the so-called *production envelope*, which shows the relationship between growth and production."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "from reframed import plot_flux_envelope\n",
    "\n",
    "model.reactions.R_EX_o2_e.lb = 0\n",
    "\n",
    "plot_flux_envelope(model, model.biomass_reaction, 'R_EX_succ_e')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can see there is a trade-off between growing and secreting succinate, evolution is not on our side.\n",
    "\n",
    "So let's re-engineer metabolism by gene knockout, which results in the deletion of the respective reactions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "knockouts = {'R_PFL':0, 'R_LDH_D':0, 'R_ACALD':0, 'R_ACKr':0}\n",
    "\n",
    "plot_flux_envelope(model, model.biomass_reaction, 'R_EX_succ_e', constraints=knockouts)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This is what we call a growth-coupled design. This *E. coli* mutant **must** secrete succinate in order to grow.\n",
    "\n",
    "Let's see how this looks in terms of flux distribution."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "solution3 = FBA(model, constraints=knockouts)\n",
    "\n",
    "fluxes2escher(solution3.values)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Feel free to explore other features. Check the online documentation of the [**ReFramed**](https://reframed.readthedocs.io) library for details."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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