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Adding simulation functions; creating networks from OmniPath
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‎notebooks/NORDic Drug Repurposing (DR).ipynb

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‎notebooks/NORDic Drug Simulation (DS).ipynb

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‎notebooks/NORDic Network Identification (NI) Part I.ipynb

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"name": "stdout",
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"NORDic==2.2.7\r\n"
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"NORDic==2.3.0\r\n"
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}
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"text": [
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"--- DATA IMPORT ---\n",
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"1. Import gene set from DisGeNET... <DISGENET> Retrieving genes... 1/1\n",
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"... 7 genes imported.\n",
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"2. Import network from STRING... ... 15 edges in model (including 0 directed edges) with a total of 6 non-isolated genes\n",
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"3. Import experiments from LINCS L1000... \n",
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"\t2 cell lines are considered (['NPC', 'SHSY5Y'])\n",
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"\t6 genes available (convertable to EntrezIDs)\n",
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"\t\t6/6 genes retrieved in LINCS L1000\n",
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"<UTILS_EXP> Gene 1/6 Cell 1/2 Type 1/3\n",
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"<UTILS_EXP> Gene 2/6 Cell 1/2 Type 1/3\n",
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"<UTILS_EXP> Gene 3/6 Cell 1/2 Type 1/3\n",
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"<UTILS_EXP> Gene 4/6 Cell 1/2 Type 1/3\n",
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"<UTILS_EXP> Gene 5/6 Cell 1/2 Type 1/3\n",
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"<UTILS_EXP> Gene 6/6 Cell 1/2 Type 1/3\n",
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"<UTILS_EXP> Gene 1/6 Cell 1/2 Type 2/3\n",
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"<UTILS_EXP> Gene 2/6 Cell 1/2 Type 2/3\n",
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"<UTILS_EXP> Gene 3/6 Cell 1/2 Type 2/3\n",
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"<UTILS_EXP> Gene 4/6 Cell 1/2 Type 2/3\n",
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"<UTILS_EXP> Gene 5/6 Cell 1/2 Type 2/3\n",
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"<UTILS_EXP> Gene 6/6 Cell 1/2 Type 2/3\n",
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"<UTILS_EXP> Gene 1/6 Cell 1/2 Type 3/3\n",
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"<UTILS_EXP> Gene 2/6 Cell 1/2 Type 3/3\n",
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"<UTILS_EXP> Gene 3/6 Cell 1/2 Type 3/3\n",
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"<UTILS_EXP> Gene 4/6 Cell 1/2 Type 3/3\n",
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"<UTILS_EXP> Gene 5/6 Cell 1/2 Type 3/3\n",
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"<UTILS_EXP> Gene 6/6 Cell 1/2 Type 3/3\n",
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"<UTILS_EXP> Gene 1/6 Cell 2/2 Type 1/3\n",
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"<UTILS_EXP> Gene 2/6 Cell 2/2 Type 1/3\n",
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"\t<UTILS_EXP> (BDNF,SHSY5Y,trt_sh): 2\n",
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"<UTILS_EXP> Gene 3/6 Cell 2/2 Type 1/3\n",
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"<UTILS_EXP> Gene 4/6 Cell 2/2 Type 1/3\n",
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"<UTILS_EXP> Gene 5/6 Cell 2/2 Type 1/3\n",
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"<UTILS_EXP> Gene 6/6 Cell 2/2 Type 1/3\n",
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"<UTILS_EXP> 0 experiments so far\n",
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"\t<UTILS_EXP> Treatment BDNF (entrez_id 627)... <BioDBNet> 1/1\n",
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"<LINCS> 2 TREATED experiments ('brew_prefix') (3 profiles 'distil_id' in average)\n",
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"<LINCS> Selected distil_ss = 3.76598\n",
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"<LINCS> 3 same-plate profiles\n",
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"<LINCS> 18 CONTROL experiments ('brew_prefix') (5 profiles 'distil_id' in average)\n",
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"<LINCS> Selected distil_ss = 3.75211\n",
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"<LINCS> 3 same-plate profiles\n",
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"<INTERFERENCE SCALE> KD Perturbed 627 = 1.01391 || Most stable control 7846 = 1.00000\n",
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"<INTERFERENCE SCALE> -0.01391\n",
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"... 5 genes, 6 profiles\n",
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"<UTILS_EXP> 1 experiments so far\n",
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"\t<UTILS_EXP> Duplicated treatment:BDNF, cell:SHSY5Y, type:trt_sh\n",
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"<UTILS_EXP> Gene 1/6 Cell 2/2 Type 2/3\n",
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"<UTILS_EXP> Gene 2/6 Cell 2/2 Type 2/3\n",
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"<UTILS_EXP> Gene 3/6 Cell 2/2 Type 2/3\n",
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"<UTILS_EXP> Gene 4/6 Cell 2/2 Type 2/3\n",
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"<UTILS_EXP> Gene 5/6 Cell 2/2 Type 2/3\n",
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"<UTILS_EXP> Gene 6/6 Cell 2/2 Type 2/3\n",
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"<UTILS_EXP> Gene 1/6 Cell 2/2 Type 3/3\n",
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"<UTILS_EXP> Gene 2/6 Cell 2/2 Type 3/3\n",
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"<UTILS_EXP> Gene 3/6 Cell 2/2 Type 3/3\n",
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"<UTILS_EXP> Gene 4/6 Cell 2/2 Type 3/3\n",
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"<UTILS_EXP> Gene 5/6 Cell 2/2 Type 3/3\n",
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"<UTILS_EXP> Gene 6/6 Cell 2/2 Type 3/3\n",
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"\t\t1 unique experiments (including 1 with criterion thres_iscale > None, min_value None)\n",
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"... 6 genes in 6 profiles (1 experiments)\n",
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"\n",
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"--- CONSTRAINT BUILDING ---\n",
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"1. Filtering out edges by minimum set of edges with highest score which preserve connectivity... ... 15 unique edges involving genes both in experiments (6 genes in total)\n",
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"... score_STRING 0.000000\t6 genes (non isolated in PPI)\t60 edges in PPI\n",
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"2. Build topological constraints from filtered edges using gene expression data... ...... 14 negative, 16 positive undirected interactions (30 edges in total), 6 non isolated genes in experiments\n",
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"3. Build dynamical constraints by binarization of experimental profiles... ...<UTILS_EXP> Cell SHSY5Y (1/1)... <UTILS_EXP> 303 (good) profiles | 50 (best) profiles (capped at 50 or min>=4) (distil_ss max=6.206, min=4.141)\n",
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"... 1 experiments on 1 cell lines and 6/6 genes (Frobenius norm signature matrix: 3.464, 5 possibly constant genes: 83.3%, 0 genes with undetermined status\n",
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"\n",
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"--- INFER BOOLEAN NETWORK ---\n",
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"1. Generate solutions from topological & dynamical constraints... ...<UTILS_GRN> Maximum possible #activators=5\n",
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"<BONESIS> 30 interactions (maximum # of clauses = 3)\n",
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"\n",
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"<UTILS_GRN> 1 experiments\n",
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" PHOX2B EDN3 RET GDNF BDNF ASCL1\n",
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"Exp1_init 1 1 1 1 0 0\n",
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"Exp1_final 1 1 1 0 0 0\n"
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]
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},
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"text": [
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" 0%| | 0/1 [00:00<?, ?it/s]"
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]
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},
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{
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"text": [
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"Grounding...done in 0.0s\n",
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"Found 1 solutions in 0.0s (first in 0.0s; rate 0.0s)"
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]
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"text": [
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"100%|████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 36.56it/s]"
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]
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},
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{
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"output_type": "stream",
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"text": [
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"1 solutions are already generated, and saved at MODELS/Ondine/SOLUTIONS-1_binthres=0.500_thresiscale=None_score=0.00_maxclause=3_{1,...1}.zip\n",
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"--- SELECTION OF OPTIMAL MODEL ---\n",
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"A. Select an optimal model based on a topological criteria... ...1 solutions (1 unique solutions)\n",
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"... 1 solutions (0/7 constant genes in average)\n",
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"<MODEL VISUALIZATION> Minimal solution: 30 edges\n"
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]
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"<MODEL VISUALIZATION> Minimal solution: 30 edges\n",
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"<MODEL VISUALIZATION> Maximal solution: 30 edges\n",
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" 1\n",
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"GTP 0.858009\n",

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