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Adding simulation functions; creating networks from OmniPath
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RECeSS-EU-Project committed Feb 21, 2023
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633 changes: 316 additions & 317 deletions notebooks/NORDic Drug Repurposing (DR).ipynb
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425 changes: 210 additions & 215 deletions notebooks/NORDic Drug Simulation (DS).ipynb
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124 changes: 3 additions & 121 deletions notebooks/NORDic Network Identification (NI) Part I.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"NORDic==2.2.7\r\n"
"NORDic==2.3.0\r\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"--- DATA IMPORT ---\n",
"1. Import gene set from DisGeNET... <DISGENET> Retrieving genes... 1/1\n",
"... 7 genes imported.\n",
"2. Import network from STRING... ... 15 edges in model (including 0 directed edges) with a total of 6 non-isolated genes\n",
"3. Import experiments from LINCS L1000... \n",
"\t2 cell lines are considered (['NPC', 'SHSY5Y'])\n",
"\t6 genes available (convertable to EntrezIDs)\n",
"\t\t6/6 genes retrieved in LINCS L1000\n",
"<UTILS_EXP> Gene 1/6 Cell 1/2 Type 1/3\n",
"<UTILS_EXP> Gene 2/6 Cell 1/2 Type 1/3\n",
"<UTILS_EXP> Gene 3/6 Cell 1/2 Type 1/3\n",
"<UTILS_EXP> Gene 4/6 Cell 1/2 Type 1/3\n",
"<UTILS_EXP> Gene 5/6 Cell 1/2 Type 1/3\n",
"<UTILS_EXP> Gene 6/6 Cell 1/2 Type 1/3\n",
"<UTILS_EXP> Gene 1/6 Cell 1/2 Type 2/3\n",
"<UTILS_EXP> Gene 2/6 Cell 1/2 Type 2/3\n",
"<UTILS_EXP> Gene 3/6 Cell 1/2 Type 2/3\n",
"<UTILS_EXP> Gene 4/6 Cell 1/2 Type 2/3\n",
"<UTILS_EXP> Gene 5/6 Cell 1/2 Type 2/3\n",
"<UTILS_EXP> Gene 6/6 Cell 1/2 Type 2/3\n",
"<UTILS_EXP> Gene 1/6 Cell 1/2 Type 3/3\n",
"<UTILS_EXP> Gene 2/6 Cell 1/2 Type 3/3\n",
"<UTILS_EXP> Gene 3/6 Cell 1/2 Type 3/3\n",
"<UTILS_EXP> Gene 4/6 Cell 1/2 Type 3/3\n",
"<UTILS_EXP> Gene 5/6 Cell 1/2 Type 3/3\n",
"<UTILS_EXP> Gene 6/6 Cell 1/2 Type 3/3\n",
"<UTILS_EXP> Gene 1/6 Cell 2/2 Type 1/3\n",
"<UTILS_EXP> Gene 2/6 Cell 2/2 Type 1/3\n",
"\t<UTILS_EXP> (BDNF,SHSY5Y,trt_sh): 2\n",
"<UTILS_EXP> Gene 3/6 Cell 2/2 Type 1/3\n",
"<UTILS_EXP> Gene 4/6 Cell 2/2 Type 1/3\n",
"<UTILS_EXP> Gene 5/6 Cell 2/2 Type 1/3\n",
"<UTILS_EXP> Gene 6/6 Cell 2/2 Type 1/3\n",
"<UTILS_EXP> 0 experiments so far\n",
"\t<UTILS_EXP> Treatment BDNF (entrez_id 627)... <BioDBNet> 1/1\n",
"<LINCS> 2 TREATED experiments ('brew_prefix') (3 profiles 'distil_id' in average)\n",
"<LINCS> Selected distil_ss = 3.76598\n",
"<LINCS> 3 same-plate profiles\n",
"<LINCS> 18 CONTROL experiments ('brew_prefix') (5 profiles 'distil_id' in average)\n",
"<LINCS> Selected distil_ss = 3.75211\n",
"<LINCS> 3 same-plate profiles\n",
"<INTERFERENCE SCALE> KD Perturbed 627 = 1.01391 || Most stable control 7846 = 1.00000\n",
"<INTERFERENCE SCALE> -0.01391\n",
"... 5 genes, 6 profiles\n",
"<UTILS_EXP> 1 experiments so far\n",
"\t<UTILS_EXP> Duplicated treatment:BDNF, cell:SHSY5Y, type:trt_sh\n",
"<UTILS_EXP> Gene 1/6 Cell 2/2 Type 2/3\n",
"<UTILS_EXP> Gene 2/6 Cell 2/2 Type 2/3\n",
"<UTILS_EXP> Gene 3/6 Cell 2/2 Type 2/3\n",
"<UTILS_EXP> Gene 4/6 Cell 2/2 Type 2/3\n",
"<UTILS_EXP> Gene 5/6 Cell 2/2 Type 2/3\n",
"<UTILS_EXP> Gene 6/6 Cell 2/2 Type 2/3\n",
"<UTILS_EXP> Gene 1/6 Cell 2/2 Type 3/3\n",
"<UTILS_EXP> Gene 2/6 Cell 2/2 Type 3/3\n",
"<UTILS_EXP> Gene 3/6 Cell 2/2 Type 3/3\n",
"<UTILS_EXP> Gene 4/6 Cell 2/2 Type 3/3\n",
"<UTILS_EXP> Gene 5/6 Cell 2/2 Type 3/3\n",
"<UTILS_EXP> Gene 6/6 Cell 2/2 Type 3/3\n",
"\t\t1 unique experiments (including 1 with criterion thres_iscale > None, min_value None)\n",
"... 6 genes in 6 profiles (1 experiments)\n",
"\n",
"--- CONSTRAINT BUILDING ---\n",
"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",
"... score_STRING 0.000000\t6 genes (non isolated in PPI)\t60 edges in PPI\n",
"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",
"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",
"... 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",
"\n",
"--- INFER BOOLEAN NETWORK ---\n",
"1. Generate solutions from topological & dynamical constraints... ...<UTILS_GRN> Maximum possible #activators=5\n",
"<BONESIS> 30 interactions (maximum # of clauses = 3)\n",
"\n",
"<UTILS_GRN> 1 experiments\n",
" PHOX2B EDN3 RET GDNF BDNF ASCL1\n",
"Exp1_init 1 1 1 1 0 0\n",
"Exp1_final 1 1 1 0 0 0\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
" 0%| | 0/1 [00:00<?, ?it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Grounding...done in 0.0s\n",
"Found 1 solutions in 0.0s (first in 0.0s; rate 0.0s)"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"100%|████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 36.56it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"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",
"--- SELECTION OF OPTIMAL MODEL ---\n",
"A. Select an optimal model based on a topological criteria... ...1 solutions (1 unique solutions)\n",
"... 1 solutions (0/7 constant genes in average)\n",
"<MODEL VISUALIZATION> Minimal solution: 30 edges\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"<MODEL VISUALIZATION> Minimal solution: 30 edges\n",
"<MODEL VISUALIZATION> Maximal solution: 30 edges\n",
" 1\n",
"GTP 0.858009\n",
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