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1 # -*- coding: utf-8 -*-
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2
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3 """
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4 [Reference]
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5 Cho et al.
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6 Attractor landscape analysis of
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7 colorectal tumorigenesis and its reversion.
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8 BMC Systems Biology (2016) 10:96.
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9 """
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10
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11 import os
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12
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13 import pandas as pd
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14
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15 import sfa
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16 import sfa.base
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17
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18
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19 def create_data():
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20 return ChoData()
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21
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22
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23 class ChoData(sfa.base.Data):
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24
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25 def __init__(self):
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26
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27 self._abbr = "CHO_2015"
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28 self._name = "Cho et al. BMC Systems Biology (2016) 10:96"
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29
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30 inputs = {}
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31 inputs['ECM'] = 1.0
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32 inputs['Tgf-b'] = 1.0
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33 inputs['IL1-TNF'] = 1.0
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34 inputs['EGF'] = 1.0
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35 inputs['alpha_i_lig'] = 1.0
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36 inputs['alpha_12_13_lig'] = 1.0
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37 inputs['alpha_s_lig'] = 1.0
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38 inputs['alpha_q_lig'] = 1.0
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39 inputs['Stress'] = 1.0
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40 inputs['WNT'] = 1.0
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41 inputs['Fas'] = 1.0
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42 inputs['ExtPump'] = 1.0
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43 inputs['DNA_damage'] = 1.0
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44
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45 dpath = os.path.dirname(__file__)
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46 fpath_network = os.path.join(dpath, 'network_all_pos.sif')
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47 A, n2i, dg = sfa.read_sif(fpath_network, as_nx=True)
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48 self._A = A
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49 self._n2i = n2i
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50 self._i2n = {idx: name for name, idx in n2i.items()}
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51 self._dg = dg
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52 self._inputs = inputs
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53
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54
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55 # end of def __init__
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56 # end of def class
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57
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