Experiments

PathwayExperiment

Model

• SBML: models/liver_glucose.xml
• HTML: models/liver_glucose.html

Datasets

• Nuttal2008_TabA.tsv

Figures

• PathwayExperiment_fig1.svg

fig1

Code

https://github.com/matthiaskoenig/exsimo/tree/master/pyexsimo/experiments/hgp_gng.py

from typing import Dict
from matplotlib.pyplot import Figure
import numpy as np

from sbmlsim.experiment import SimulationExperiment
from sbmlsim.data import DataSet
from sbmlsim.timecourse import Timecourse, TimecourseSim, TimecourseScan
from sbmlsim.plotting_matplotlib import add_data, add_line, plt


class PathwayExperiment(SimulationExperiment):
    """Timecourse simulations of HGP, GNG, GLY and HGP/GNG.

    Time varying contribution of pathways to hepatic gluconeogenesis.
    """
    @property
    def datasets(self) -> Dict[str, DataSet]:
        dsets = {}
        dset_id = "Nuttal2008_TabA"
        df = self.load_data(dset_id)
        df = df[df.condition == "normal"]  # only healthy controls
        udict = {key: df[f"{key}_unit"].unique()[0] for key in
                 ["time", "hgp", "gng", "gly", "gng_hgp"]}

        dsets[dset_id] = DataSet.from_df(df, udict=udict, ureg=self.ureg)
        return dsets

    @property
    def scans(self) -> Dict[str, TimecourseScan]:
        Q_ = self.ureg.Quantity
        glc_scan = TimecourseScan(
            tcsim=TimecourseSim([
                Timecourse(start=0, end=70 * 60, steps=500, changes={
                    '[glyglc]': Q_(350, 'mM')
                })
            ], time_offset=600),
            scan={'[glc_ext]': Q_(np.linspace(3.6, 4.6, num=6), 'mM')},
        )
        return {
            "glc_scan": glc_scan
        }

    @property
    def figures(self) -> Dict[str, Figure]:
        xunit = "hr"
        yunit_flux = "µmol/kg/min"
        yunit_ratio = "percent"

        fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2, figsize=(10, 10))
        fig.subplots_adjust(wspace=.3, hspace=.3)
        axes = (ax1, ax2, ax3, ax4)

        result = self.scan_results['glc_scan']
        kwargs = {
            'color': "black",
            'linestyle': "-",
            'linewidth': "2",
        }
        add_line(ax1, result, xid="time", yid="HGP", xunit=xunit,
                 yunit=yunit_flux,
                 all_lines=True, **kwargs)
        add_line(ax2, result, xid="time", yid="GNG", xunit=xunit,
                 yunit=yunit_flux,
                 all_lines=True, **kwargs)
        add_line(ax3, result, xid="time", yid="GLY", xunit=xunit,
                 yunit=yunit_flux,
                 all_lines=True, **kwargs)

        # manual plot of s.GNG/s.HGP * 100
        for df in result.frames:
            xk = df['time'].values * result.ureg(result.udict['time'])
            xk = xk.to(xunit)
            yk = df['GNG'].values / df['HGP'].values * 100
            ax4.plot(xk, yk, '-', **kwargs)

        # experimental data
        dset = self.datasets["Nuttal2008_TabA"]
        kwargs = {
            'color': "black",
            'linestyle': "None",
            'alpha': 0.6,
        }
        add_data(ax1, dset, xid="time", yid="hgp", xunit=xunit,
                 yunit=yunit_flux, label="HGP", **kwargs)
        add_data(ax2, dset, xid="time", yid="gng", xunit=xunit,
                 yunit=yunit_flux, label="GNG", **kwargs)
        add_data(ax3, dset, xid="time", yid="gly", xunit=xunit,
                 yunit=yunit_flux, label="GLY", **kwargs)
        add_data(ax4, dset, xid="time", yid="gng_hgp", xunit=xunit,
                 yunit=yunit_ratio, label="GNG/HGP", **kwargs)

        ax1.set_ylabel(f'HGP [{yunit_flux}]')
        ax1.set_ylim(top=30)
        ax2.set_ylabel(f'GNG [{yunit_flux}]')
        ax2.set_ylim(top=14)
        ax3.set_ylabel(f'GLY [{yunit_flux}]')
        ax3.set_ylim(top=20)
        ax4.set_ylabel(f'GNG/HGP [{yunit_ratio}]')
        ax4.set_ylim(top=100)
        for ax in axes:
            ax.set_xlabel(f'time [{xunit}]')
            ax.set_ylim(bottom=0)
            ax.set_xlim(left=10)
            ax.legend()

        return {
            "fig1": fig
        }