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Add model 238 #129

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Add model 238 #129

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29 changes: 29 additions & 0 deletions models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/README.md
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# \[238\] DNA-DAMAGE-INDUCED-FERROPTOSIS

- Variables: 33
- Inputs: 1
- Regulations: 89
- Publication: https://doi.org/10.3390/proteomes13010006
- Source: https://github.com/GuptaShan/A-Model-of-p53-and-ncRNAs-in-Ferroptosis
- Keywords: curated


### Modifications

The model is converted from the provided GINsim file but is otherwise unmodified.

### Model citation

```
@article{bbm-238,
title={DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance},
author={Gupta, Shantanu and Silveira, Daner A and Mombach, Jos{\'e} Carlos M and Hashimoto, Ronaldo F},
journal={Proteomes},
volume={13},
number={1},
pages={6},
year={2025},
publisher={MDPI}
}
```

14 changes: 14 additions & 0 deletions models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/metadata.json
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{
"id": 238,
"name": "DNA-DAMAGE-INDUCED-FERROPTOSIS",
"url-publication": "https://doi.org/10.3390/proteomes13010006",
"url-model": "https://github.com/GuptaShan/A-Model-of-p53-and-ncRNAs-in-Ferroptosis",
"keywords": [
"curated"
],
"variables": 33,
"inputs": 1,
"regulations": 89,
"notes": "### Modifications\n\nThe model is converted from the provided GINsim file but is otherwise unmodified.",
"bib": "@article{bbm-238,\n title={DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance},\n author={Gupta, Shantanu and Silveira, Daner A and Mombach, Jos{\\'e} Carlos M and Hashimoto, Ronaldo F},\n journal={Proteomes},\n volume={13},\n number={1},\n pages={6},\n year={2025},\n publisher={MDPI}\n}"
}
122 changes: 122 additions & 0 deletions models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.aeon
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v_DNA_damage -> v_ATM
v_Wip1 -| v_ATM
v_E2F1 -> v_ATM
v_ATM -> v_p38MAPK
v_Wip1 -| v_p38MAPK
v_ATM -| v_Mdm2
v_Wip1 -> v_Mdm2
v_p53 -> v_Mdm2
v_E2F1 -> v_Wip1
v_ATM -> v_p53
v_p38MAPK -> v_p53
v_Mdm2 -| v_p53
v_Wip1 -| v_p53
v_LncRNA_MALAT1 -| v_p53
v_p53_A -> v_p53_INP1
v_p53_K -> v_p53_INP1
v_Wip1 -| v_p53_A
v_p53 -> v_p53_A
v_p53_INP1 -| v_p53_A
v_p53_K -| v_p53_A
v_Sirt_1 -| v_p53_A
v_Wip1 -| v_p53_K
v_p53 -> v_p53_K
v_p53_A -| v_p53_K
v_Sirt_1 -| v_p53_K
v_Myc -> v_Cric_NOTCH1
v_Myc -> v_LncRNA_MALAT1
v_p53 -> v_miR_34c
v_Cric_NOTCH1 -| v_miR_34c
v_LncRNA_MALAT1 -| v_miR_34c
v_p38MAPK -> v_Myc
v_miR_34c -| v_Myc
v_p21 -| v_Myc
v_RB -| v_Myc
v_E2F1 -> v_Myc
v_xCT -> v_Myc
v_miR_34c -| v_SOX4
v_Myc -> v_SOX4
v_p38MAPK -> v_p21
v_p53_A -> v_p21
v_Myc -| v_p21
v_Caspase3 -| v_p21
v_ALOX15 -| v_p21
v_miR_34c -| v_cdk46_CycD
v_SOX4 -> v_cdk46_CycD
v_p21 -| v_cdk46_CycD
v_Cdc25 -> v_cdk46_CycD
v_ATM -| v_Cdc25
v_p38MAPK -| v_Cdc25
v_cdk46_CycD -| v_RB
v_ATM -> v_E2F1
v_Myc -> v_E2F1
v_Cdc25 -> v_E2F1
v_RB -| v_E2F1
v_Sirt_1 -| v_E2F1
v_miR_34c -| v_Sirt_1
v_E2F1 -> v_Sirt_1
v_p53_K -| v_BCL2
v_miR_34c -| v_BCL2
v_E2F1 -> v_BCL2
v_BIM -| v_BCL2
v_SAT1 -| v_BCL2
v_p53_K -> v_BIM
v_BCL2 -| v_BIM
v_Wip1 -| v_BAX
v_p53_K -> v_BAX
v_BCL2 -| v_BAX
v_BIM -> v_BAX
v_p21 -| v_Caspase3
v_BIM -> v_Caspase3
v_BAX -> v_Caspase3
v_xCT -| v_Caspase3
v_p53_K -> v_SAT1
v_ATM -| v_xCT
v_p53 -| v_xCT
v_Myc -> v_xCT
v_BIM -| v_xCT
v_xCT -> v_GSH
v_GSH -> v_GPX4
v_SAT1 -> v_ALOX15
v_GPX4 -| v_ALOX15
v_Mdm2 -> v_PROLIFERATION
v_LncRNA_MALAT1 -> v_DRUG_RESISTANCE
v_p21 -> v_FERROPTOSIS
v_BAX -> v_FERROPTOSIS
v_ALOX15 -> v_FERROPTOSIS
v_Caspase3 -> v_APOPTOSIS
v_p53_A -> v_SENESCENCE
v_p21 -> v_SENESCENCE
$v_ALOX15: v_SAT1 & !v_GPX4
$v_APOPTOSIS: v_Caspase3
$v_ATM: (v_DNA_damage & !v_Wip1) | (v_DNA_damage & v_Wip1 & v_E2F1)
$v_BAX: !v_Wip1 & v_p53_K & !v_BCL2 & v_BIM
$v_BCL2: !v_p53_K & !v_miR_34c & v_E2F1 & !v_BIM & !v_SAT1
$v_BIM: v_p53_K & !v_BCL2
$v_Caspase3: !v_p21 & v_BIM & v_BAX & !v_xCT
$v_Cdc25: !v_ATM & !v_p38MAPK
$v_Cric_NOTCH1: v_Myc
$v_DRUG_RESISTANCE: v_LncRNA_MALAT1
$v_E2F1: (!v_ATM & !v_Myc & !v_RB & !v_Sirt_1) | (!v_ATM & v_Myc) | (v_ATM & !v_Myc & !v_Cdc25 & !v_RB & !v_Sirt_1) | (v_ATM & !v_Myc & v_Cdc25 & !v_RB) | (v_ATM & v_Myc)
$v_FERROPTOSIS: v_p21 & v_BAX & v_ALOX15
$v_GPX4: v_GSH
$v_GSH: v_xCT
$v_LncRNA_MALAT1: v_Myc
$v_Mdm2: (!v_ATM & !v_Wip1 & v_p53) | (!v_ATM & v_Wip1)
$v_Myc: (!v_p38MAPK & !v_miR_34c) | (v_p38MAPK & !v_miR_34c) | (v_p38MAPK & v_miR_34c & !v_p21 & !v_RB & v_E2F1 & v_xCT)
$v_PROLIFERATION: v_Mdm2
$v_RB: !v_cdk46_CycD
$v_SAT1: v_p53_K
$v_SENESCENCE: v_p53_A & v_p21
$v_SOX4: !v_miR_34c & v_Myc
$v_Sirt_1: !v_miR_34c & v_E2F1
$v_Wip1: v_E2F1
$v_cdk46_CycD: !v_miR_34c | (v_miR_34c & v_SOX4 & !v_p21 & v_Cdc25)
$v_miR_34c: v_p53 & !v_Cric_NOTCH1 & !v_LncRNA_MALAT1
$v_p21: (!v_p38MAPK & v_p53_A & !v_Myc & !v_ALOX15) | (v_p38MAPK & !v_p53_A & !v_Caspase3) | (v_p38MAPK & v_p53_A & !v_Myc & !v_Caspase3) | (v_p38MAPK & v_p53_A & !v_Myc & v_Caspase3 & !v_ALOX15) | (v_p38MAPK & v_p53_A & v_Myc & !v_Caspase3)
$v_p38MAPK: v_ATM & !v_Wip1
$v_p53: (!v_ATM & v_p38MAPK & !v_Mdm2 & !v_Wip1) | (v_ATM & !v_p38MAPK & !v_LncRNA_MALAT1) | (v_ATM & v_p38MAPK & !v_Mdm2 & !v_Wip1) | (v_ATM & v_p38MAPK & !v_Mdm2 & v_Wip1 & !v_LncRNA_MALAT1) | (v_ATM & v_p38MAPK & v_Mdm2 & !v_LncRNA_MALAT1)
$v_p53_A: (!v_Wip1 & !v_p53 & !v_p53_INP1 & !v_p53_K & !v_Sirt_1) | (!v_Wip1 & v_p53 & !v_p53_K & !v_Sirt_1)
$v_p53_INP1: (!v_p53_A & v_p53_K) | v_p53_A
$v_p53_K: (!v_Wip1 & v_p53 & !v_p53_A) | (v_Wip1 & v_p53 & !v_p53_A & !v_Sirt_1)
$v_xCT: (!v_ATM & !v_p53) | (!v_ATM & v_p53 & v_Myc & !v_BIM) | (v_ATM & !v_p53)
34 changes: 34 additions & 0 deletions models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.bnet
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targets,factors
v_ALOX15, (v_SAT1 & !v_GPX4)
v_APOPTOSIS, v_Caspase3
v_ATM, ((v_DNA_damage & !v_Wip1) | ((v_DNA_damage & v_Wip1) & v_E2F1))
v_BAX, (((!v_Wip1 & v_p53_K) & !v_BCL2) & v_BIM)
v_BCL2, ((((!v_p53_K & !v_miR_34c) & v_E2F1) & !v_BIM) & !v_SAT1)
v_BIM, (v_p53_K & !v_BCL2)
v_Caspase3, (((!v_p21 & v_BIM) & v_BAX) & !v_xCT)
v_Cdc25, (!v_ATM & !v_p38MAPK)
v_Cric_NOTCH1, v_Myc
v_DRUG_RESISTANCE, v_LncRNA_MALAT1
v_E2F1, (((((((!v_ATM & !v_Myc) & !v_RB) & !v_Sirt_1) | (!v_ATM & v_Myc)) | ((((v_ATM & !v_Myc) & !v_Cdc25) & !v_RB) & !v_Sirt_1)) | (((v_ATM & !v_Myc) & v_Cdc25) & !v_RB)) | (v_ATM & v_Myc))
v_FERROPTOSIS, ((v_p21 & v_BAX) & v_ALOX15)
v_GPX4, v_GSH
v_GSH, v_xCT
v_LncRNA_MALAT1, v_Myc
v_Mdm2, (((!v_ATM & !v_Wip1) & v_p53) | (!v_ATM & v_Wip1))
v_Myc, (((!v_p38MAPK & !v_miR_34c) | (v_p38MAPK & !v_miR_34c)) | (((((v_p38MAPK & v_miR_34c) & !v_p21) & !v_RB) & v_E2F1) & v_xCT))
v_PROLIFERATION, v_Mdm2
v_RB, !v_cdk46_CycD
v_SAT1, v_p53_K
v_SENESCENCE, (v_p53_A & v_p21)
v_SOX4, (!v_miR_34c & v_Myc)
v_Sirt_1, (!v_miR_34c & v_E2F1)
v_Wip1, v_E2F1
v_cdk46_CycD, (!v_miR_34c | (((v_miR_34c & v_SOX4) & !v_p21) & v_Cdc25))
v_miR_34c, ((v_p53 & !v_Cric_NOTCH1) & !v_LncRNA_MALAT1)
v_p21, (((((((!v_p38MAPK & v_p53_A) & !v_Myc) & !v_ALOX15) | ((v_p38MAPK & !v_p53_A) & !v_Caspase3)) | (((v_p38MAPK & v_p53_A) & !v_Myc) & !v_Caspase3)) | ((((v_p38MAPK & v_p53_A) & !v_Myc) & v_Caspase3) & !v_ALOX15)) | (((v_p38MAPK & v_p53_A) & v_Myc) & !v_Caspase3))
v_p38MAPK, (v_ATM & !v_Wip1)
v_p53, (((((((!v_ATM & v_p38MAPK) & !v_Mdm2) & !v_Wip1) | ((v_ATM & !v_p38MAPK) & !v_LncRNA_MALAT1)) | (((v_ATM & v_p38MAPK) & !v_Mdm2) & !v_Wip1)) | ((((v_ATM & v_p38MAPK) & !v_Mdm2) & v_Wip1) & !v_LncRNA_MALAT1)) | (((v_ATM & v_p38MAPK) & v_Mdm2) & !v_LncRNA_MALAT1))
v_p53_A, (((((!v_Wip1 & !v_p53) & !v_p53_INP1) & !v_p53_K) & !v_Sirt_1) | (((!v_Wip1 & v_p53) & !v_p53_K) & !v_Sirt_1))
v_p53_INP1, ((!v_p53_A & v_p53_K) | v_p53_A)
v_p53_K, (((!v_Wip1 & v_p53) & !v_p53_A) | (((v_Wip1 & v_p53) & !v_p53_A) & !v_Sirt_1))
v_xCT, (((!v_ATM & !v_p53) | (((!v_ATM & v_p53) & v_Myc) & !v_BIM)) | (v_ATM & !v_p53))
1 change: 1 addition & 0 deletions models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.sbml
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1 change: 1 addition & 0 deletions models/summary.csv
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Expand Up @@ -236,3 +236,4 @@ ID, name, variables, inputs, regulations
235, BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE, 110, 7, 270
236, BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE, 109, 8, 263
237, COLORECTAL-TUMORIGENESIS-REVERSION-SWITCH, 17, 0, 44
238, DNA-DAMAGE-INDUCED-FERROPTOSIS, 33, 1, 89
Binary file added sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/A Boolean Model For Ferroptosis.zginml
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10 changes: 10 additions & 0 deletions sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/citation.bib
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@article{bbm-238,
title={DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance},
author={Gupta, Shantanu and Silveira, Daner A and Mombach, Jos{\'e} Carlos M and Hashimoto, Ronaldo F},
journal={Proteomes},
volume={13},
number={1},
pages={6},
year={2025},
publisher={MDPI}
}
7 changes: 7 additions & 0 deletions sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/metadata.json
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{
"id": 238,
"name": "DNA-DAMAGE-INDUCED-FERROPTOSIS",
"url-publication": "https://doi.org/10.3390/proteomes13010006",
"url-model": "https://github.com/GuptaShan/A-Model-of-p53-and-ncRNAs-in-Ferroptosis",
"keywords": ["curated"]
}
3 changes: 3 additions & 0 deletions sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/notes.md
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### Modifications

The model is converted from the provided GINsim file but is otherwise unmodified.
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