Mercurial > repos > laurenmarazzi > netisce_test
diff tools/myTools/bin/sfa/data/cho_2016/__init__.py @ 1:7e5c71b2e71f draft default tip
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author | laurenmarazzi |
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date | Wed, 22 Dec 2021 16:00:34 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/myTools/bin/sfa/data/cho_2016/__init__.py Wed Dec 22 16:00:34 2021 +0000 @@ -0,0 +1,57 @@ +# -*- coding: utf-8 -*- + +""" +[Reference] +Cho et al. +Attractor landscape analysis of +colorectal tumorigenesis and its reversion. +BMC Systems Biology (2016) 10:96. +""" + +import os + +import pandas as pd + +import sfa +import sfa.base + + +def create_data(): + return ChoData() + + +class ChoData(sfa.base.Data): + + def __init__(self): + + self._abbr = "CHO_2015" + self._name = "Cho et al. BMC Systems Biology (2016) 10:96" + + inputs = {} + inputs['ECM'] = 1.0 + inputs['Tgf-b'] = 1.0 + inputs['IL1-TNF'] = 1.0 + inputs['EGF'] = 1.0 + inputs['alpha_i_lig'] = 1.0 + inputs['alpha_12_13_lig'] = 1.0 + inputs['alpha_s_lig'] = 1.0 + inputs['alpha_q_lig'] = 1.0 + inputs['Stress'] = 1.0 + inputs['WNT'] = 1.0 + inputs['Fas'] = 1.0 + inputs['ExtPump'] = 1.0 + inputs['DNA_damage'] = 1.0 + + dpath = os.path.dirname(__file__) + fpath_network = os.path.join(dpath, 'network_all_pos.sif') + A, n2i, dg = sfa.read_sif(fpath_network, as_nx=True) + self._A = A + self._n2i = n2i + self._i2n = {idx: name for name, idx in n2i.items()} + self._dg = dg + self._inputs = inputs + + + # end of def __init__ +# end of def class +