diff tools/myTools/bin/sfa/data/cho_2016/__init__.py @ 1:7e5c71b2e71f draft default tip

Uploaded

--- /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
+