Mercurial > repos > laurenmarazzi > netisce_test
view tools/myTools/bin/sfa/data/steinway_2015/__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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# -*- coding: utf-8 -*- """ [Reference] [1] Steinway et al. Combinatorial interventions inhibit TGFβ-driven epithelial-to-mesenchymal transition and support hybrid cellular phenotypes. Npj Systems Biology and Applications (2015) 1(1), 15014. [2] Steinway, S. N. et al. Network modeling of TGFβ signaling in hepatocellular carcinoma epithelial-to-mesenchymal transition reveals joint sonic hedgehog and Wnt pathway activation. Cancer Research (2014) 74(21), 5963–77. [Information] The topology of network is curated from reference [1]. """ import os import pandas as pd import sfa import sfa.base def create_data(): return SteinwayData() class SteinwayData(sfa.base.Data): def __init__(self): self._abbr = "steinway_2015" self._name = "Steinway et al. Npj Syst Biol Appl (2015) 1(1), 15014" inputs = {} inputs['TGFβ'] = 1.0 dpath = os.path.dirname(__file__) fpath_network = os.path.join(dpath, 'network.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 # The following members are not defined due to the lack of data. self._df_conds = None self._df_exp = None self._df_ptb = None self._has_link_perturb = False self._names_ptb = None self._iadj_to_idf = None # end of def __init__ # end of def class