From 9a763eba80e3c76566a00dbb00e8cc299ccc68fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20Huvar?= <492849@mail.muni.cz> Date: Sat, 30 Nov 2024 11:14:10 +0100 Subject: [PATCH] Add benchmarks and scripts to run them. --- README.md | 6 + .../celldivb}/celldivb_dataset.csv | 0 .../celldivb/celldivb_sketch.aeon} | 0 data/benchmarks/celldivb/metadata.txt | 2 + data/benchmarks/celldivb/model_concrete.aeon | 21 + .../eprotein}/eprotein_dataset.csv | 0 .../eprotein/eprotein_sketch.aeon} | 0 data/benchmarks/eprotein/metadata.txt | 2 + data/benchmarks/eprotein/model_concrete.aeon | 78 ++ .../etc}/etc_dataset.csv | 0 .../etc/etc_sketch.aeon} | 0 data/benchmarks/etc/metadata.txt | 2 + data/benchmarks/etc/model_concrete.aeon | 238 +++++ .../interferon/interferon_dataset.csv} | 0 .../interferon/interferon_sketch.aeon} | 0 data/benchmarks/interferon/metadata.txt | 2 + .../benchmarks/interferon/model_concrete.aeon | 311 +++++++ .../macrophage/macrophage_dataset.csv} | 0 .../macrophage/macrophage_sketch.aeon} | 0 data/benchmarks/macrophage/metadata.txt | 2 + .../benchmarks/macrophage/model_concrete.aeon | 854 ++++++++++++++++++ data/benchmarks/nsp4/metadata.txt | 2 + data/benchmarks/nsp4/model_concrete.aeon | 122 +++ .../nsp4}/nsp4_dataset.csv | 0 .../nsp4/nsp4_sketch.aeon} | 0 data/benchmarks/output_eval.txt | Bin 0 -> 4260 bytes data/benchmarks/readme.md | 25 + data/simple_dataset.csv | 4 - data/synthetic_cases/readme.md | 12 - run_performance_eval.py | 41 + src-tauri/Cargo.toml | 5 + src-tauri/src/analysis/inference_solver.rs | 4 +- src-tauri/src/analysis/mod.rs | 8 +- src-tauri/src/bin/run_inference.rs | 60 ++ src-tauri/src/logging.rs | 26 +- 35 files changed, 1802 insertions(+), 25 deletions(-) rename data/{synthetic_cases => benchmarks/celldivb}/celldivb_dataset.csv (100%) rename data/{synthetic_cases/celldivb-sketch.aeon => benchmarks/celldivb/celldivb_sketch.aeon} (100%) create mode 100644 data/benchmarks/celldivb/metadata.txt create mode 100644 data/benchmarks/celldivb/model_concrete.aeon rename data/{synthetic_cases => benchmarks/eprotein}/eprotein_dataset.csv (100%) rename data/{synthetic_cases/eprotein-sketch.aeon => benchmarks/eprotein/eprotein_sketch.aeon} (100%) create mode 100644 data/benchmarks/eprotein/metadata.txt create mode 100644 data/benchmarks/eprotein/model_concrete.aeon rename data/{synthetic_cases => benchmarks/etc}/etc_dataset.csv (100%) rename data/{synthetic_cases/etc-sketch.aeon => benchmarks/etc/etc_sketch.aeon} (100%) create mode 100644 data/benchmarks/etc/metadata.txt create mode 100644 data/benchmarks/etc/model_concrete.aeon rename data/{synthetic_cases/interferon-dataset.csv => benchmarks/interferon/interferon_dataset.csv} (100%) rename data/{synthetic_cases/interferon-sketch.aeon => benchmarks/interferon/interferon_sketch.aeon} (100%) create mode 100644 data/benchmarks/interferon/metadata.txt create mode 100644 data/benchmarks/interferon/model_concrete.aeon rename data/{synthetic_cases/macrophage-dataset.csv => benchmarks/macrophage/macrophage_dataset.csv} (100%) rename data/{synthetic_cases/macrophage-sketch.aeon => benchmarks/macrophage/macrophage_sketch.aeon} (100%) create mode 100644 data/benchmarks/macrophage/metadata.txt create mode 100644 data/benchmarks/macrophage/model_concrete.aeon create mode 100644 data/benchmarks/nsp4/metadata.txt create mode 100644 data/benchmarks/nsp4/model_concrete.aeon rename data/{synthetic_cases => benchmarks/nsp4}/nsp4_dataset.csv (100%) rename data/{synthetic_cases/nsp4-sketch.aeon => benchmarks/nsp4/nsp4_sketch.aeon} (100%) create mode 100644 data/benchmarks/output_eval.txt create mode 100644 data/benchmarks/readme.md delete mode 100644 data/simple_dataset.csv delete mode 100644 data/synthetic_cases/readme.md create mode 100644 run_performance_eval.py create mode 100644 src-tauri/src/bin/run_inference.rs diff --git a/README.md b/README.md index 0d9e50f3..baf99c96 100644 --- a/README.md +++ b/README.md @@ -79,3 +79,9 @@ We also utilize an end-to-end Selenium-based testing framework. Note that these You can follow this [detailed tutorial](https://jonaskruckenberg.github.io/tauri-docs-wip/development/testing.html) for setup. In short, you should install `tauri-driver` (with `cargo install tauri-driver`), and then you will need either `WebKitWebDriver` on Linux or `Microsoft Edge Driver` on Windows (make sure that you have updated Microsoft Edge too). The mocha test runner can be installed with `npm install mocha chai selenium-webdriver`. To run the tests, first build the app with `cargo tauri build` and then use `npx mocha` (you might need a longer timeout, like `npx mocha --timeout 10000`). The framework was tested on Windows with `Microsoft Edge WebDriver` version `130.0.2849.89`. + +### Benchmarks + +The benchmark models, results, and more details are in `data/benchmarks`. +There is also a README with further instructions, you can follow it. +Tldr, to run the performance benchmarks, you can use python and execute them all with `python3 run_performance_eval.py`. diff --git a/data/synthetic_cases/celldivb_dataset.csv b/data/benchmarks/celldivb/celldivb_dataset.csv similarity index 100% rename from data/synthetic_cases/celldivb_dataset.csv rename to data/benchmarks/celldivb/celldivb_dataset.csv diff --git a/data/synthetic_cases/celldivb-sketch.aeon b/data/benchmarks/celldivb/celldivb_sketch.aeon similarity index 100% rename from data/synthetic_cases/celldivb-sketch.aeon rename to data/benchmarks/celldivb/celldivb_sketch.aeon diff --git a/data/benchmarks/celldivb/metadata.txt b/data/benchmarks/celldivb/metadata.txt new file mode 100644 index 00000000..75659fe8 --- /dev/null +++ b/data/benchmarks/celldivb/metadata.txt @@ -0,0 +1,2 @@ +Publication: https://doi.org/10.1007/978-3-319-53150-2_1 +Source: http://ginsim.org/model/C_crescentus \ No newline at end of file diff --git a/data/benchmarks/celldivb/model_concrete.aeon b/data/benchmarks/celldivb/model_concrete.aeon new file mode 100644 index 00000000..9a72e186 --- /dev/null +++ b/data/benchmarks/celldivb/model_concrete.aeon @@ -0,0 +1,21 @@ +DivL -? CckA +CckA -? ChpT +CpdR -? ClpXP_RcdA +ChpT -? CpdR +ChpT -? CtrAb +ClpXP_RcdA -? CtrAb +DivK -? DivJ +PleC -? DivJ +DivJ -? DivK +PleC -? DivK +DivK -? DivL +DivK -? PleC +$CckA: DivL +$ChpT: CckA +$ClpXP_RcdA: !CpdR +$CpdR: ChpT +$CtrAb: (ChpT & !ClpXP_RcdA) +$DivJ: (DivK & !PleC) +$DivK: (!PleC & DivJ) +$DivL: !DivK +$PleC: !DivK diff --git a/data/synthetic_cases/eprotein_dataset.csv b/data/benchmarks/eprotein/eprotein_dataset.csv similarity index 100% rename from data/synthetic_cases/eprotein_dataset.csv rename to data/benchmarks/eprotein/eprotein_dataset.csv diff --git a/data/synthetic_cases/eprotein-sketch.aeon b/data/benchmarks/eprotein/eprotein_sketch.aeon similarity index 100% rename from data/synthetic_cases/eprotein-sketch.aeon rename to data/benchmarks/eprotein/eprotein_sketch.aeon diff --git a/data/benchmarks/eprotein/metadata.txt b/data/benchmarks/eprotein/metadata.txt new file mode 100644 index 00000000..7440c57e --- /dev/null +++ b/data/benchmarks/eprotein/metadata.txt @@ -0,0 +1,2 @@ +Publication: https://doi.org/10.1038/s41597-020-0477-8 +Source: https://git-r3lab.uni.lu/covid/models/-/blob/4ed915a55687f626f9e7b3d4ada249cbaa5945b8/Executable%20Modules/SBML_qual_build/sbml/E_protein_stable.sbml diff --git a/data/benchmarks/eprotein/model_concrete.aeon b/data/benchmarks/eprotein/model_concrete.aeon new file mode 100644 index 00000000..f4492918 --- /dev/null +++ b/data/benchmarks/eprotein/model_concrete.aeon @@ -0,0 +1,78 @@ +csa2_histone_complex_nucleus -> csa1_histone_complex_nucleus +BRD4 -> csa1_histone_complex_nucleus +BRD2 -> csa1_histone_complex_nucleus +H4C14 -> csa2_histone_complex_nucleus +H4_16 -> csa2_histone_complex_nucleus +H4C1 -> csa2_histone_complex_nucleus +H3C15 -> csa2_histone_complex_nucleus +H3C1 -> csa2_histone_complex_nucleus +H4C9 -> csa2_histone_complex_nucleus +H2BC21 -> csa2_histone_complex_nucleus +H2A -> csa2_histone_complex_nucleus +MPP5 -> CRB3_PALS1_PATJ_complex_complex +CRB3 -> CRB3_PALS1_PATJ_complex_complex +PATJ -> CRB3_PALS1_PATJ_complex_complex +ASIC1 -> ASIC1_trimer_H__STOML3_complex +STOML3 -> ASIC1_trimer_H__STOML3_complex +E_cell -| ASIC1_trimer_H__STOML3_complex +E_cell -| ATP1A_ATP1B_FXYDs_complex +MPP5 -> E_PALS1_complex +E_cell -> E_PALS1_complex +CDK9 -> P_TEFb_complex +BRD4 -> P_TEFb_complex +CCNT1 -> P_TEFb_complex +BRD4 -> BRD4 +E_nucleus -| BRD4 +TBP -> TBP +BRD2 -> TBP +BRD2 -> BRD2 +JQ_1_simple_molecule -| BRD2 +E_nucleus -| BRD2 +H__ion -> ASIC1 +PATJ -> PATJ +CRB3 -> CRB3 +MPP5 -> MPP5 +ATP1A_ATP1B_FXYDs_complex -> K__ion +ATP1A_ATP1B_FXYDs_complex -> Na__ion +ATP1A_ATP1B_FXYDs_complex -> Activity_of_sodium_channels_phenotype +STOML3 -| Activity_of_sodium_channels_phenotype +ASIC1_trimer_H__STOML3_complex -> Activity_of_sodium_channels_phenotype +CRB3_PALS1_PATJ_complex_complex -> Maintenance_of_tight_junction_phenotype +E_PALS1_complex -> Maintenance_of_tight_junction_phenotype +P_TEFb_complex -> RNA_Polymerase_II_dependent_Transcription__phenotype +csa1_histone_complex_nucleus -> Chromatin_organization_phenotype +$ASIC1: H__ion +$ASIC1_trimer_H__STOML3_complex: ((ASIC1 & STOML3) & !E_cell) +$ATP1A_ATP1B_FXYDs_complex: !E_cell +$Activity_of_sodium_channels_phenotype: ((ATP1A_ATP1B_FXYDs_complex | !STOML3) | ASIC1_trimer_H__STOML3_complex) +$BRD2: ((BRD2 & !JQ_1_simple_molecule) & !E_nucleus) +$BRD4: (BRD4 & !E_nucleus) +$CCNT1: true +$CDK9: true +$CRB3: CRB3 +$CRB3_PALS1_PATJ_complex_complex: ((MPP5 & CRB3) & PATJ) +$Chromatin_organization_phenotype: csa1_histone_complex_nucleus +$E_PALS1_complex: (MPP5 & E_cell) +$E_cell: true +$E_nucleus: true +$H2A: true +$H2BC21: true +$H3C1: true +$H3C15: true +$H4C1: true +$H4C14: true +$H4C9: true +$H4_16: true +$H__ion: true +$JQ_1_simple_molecule: true +$K__ion: ATP1A_ATP1B_FXYDs_complex +$MPP5: MPP5 +$Maintenance_of_tight_junction_phenotype: (CRB3_PALS1_PATJ_complex_complex | E_PALS1_complex) +$Na__ion: ATP1A_ATP1B_FXYDs_complex +$PATJ: PATJ +$P_TEFb_complex: ((CDK9 & BRD4) | (CCNT1 & BRD4)) +$RNA_Polymerase_II_dependent_Transcription__phenotype: P_TEFb_complex +$STOML3: true +$TBP: (TBP & BRD2) +$csa1_histone_complex_nucleus: ((BRD4 | BRD2) & csa2_histone_complex_nucleus) +$csa2_histone_complex_nucleus: (((((((H4C14 & H4_16) & H4C1) & H3C15) & H3C1) & H4C9) & H2BC21) & H2A) diff --git a/data/synthetic_cases/etc_dataset.csv b/data/benchmarks/etc/etc_dataset.csv similarity index 100% rename from data/synthetic_cases/etc_dataset.csv rename to data/benchmarks/etc/etc_dataset.csv diff --git a/data/synthetic_cases/etc-sketch.aeon b/data/benchmarks/etc/etc_sketch.aeon similarity index 100% rename from data/synthetic_cases/etc-sketch.aeon rename to data/benchmarks/etc/etc_sketch.aeon diff --git a/data/benchmarks/etc/metadata.txt b/data/benchmarks/etc/metadata.txt new file mode 100644 index 00000000..77173d5a --- /dev/null +++ b/data/benchmarks/etc/metadata.txt @@ -0,0 +1,2 @@ +Publication: https://doi.org/10.1038/s41597-020-0477-8 +Source: https://git-r3lab.uni.lu/covid/models/-/blob/4ed915a55687f626f9e7b3d4ada249cbaa5945b8/Executable%20Modules/SBML_qual_build/sbml/ETC_stable.sbml diff --git a/data/benchmarks/etc/model_concrete.aeon b/data/benchmarks/etc/model_concrete.aeon new file mode 100644 index 00000000..db79f608 --- /dev/null +++ b/data/benchmarks/etc/model_concrete.aeon @@ -0,0 +1,238 @@ +$Orf9c:false +$NDUFA1:!Orf9c +Orf9c -| NDUFA1 +$Complex_1_complex:((Complex_1_complex & (NADH_simple_molecule | (NDUFA1 & (NDUFB9 & (OXPHOS_factors_complex & csa98_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix))))) | (!Complex_1_complex & (NDUFA1 & (NDUFB9 & (OXPHOS_factors_complex & csa98_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix))))) +NDUFA1 -> Complex_1_complex +NDUFB9 -> Complex_1_complex +csa98_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix -> Complex_1_complex +OXPHOS_factors_complex -> Complex_1_complex +NADH_simple_molecule -> Complex_1_complex +Complex_1_complex -> Complex_1_complex +$NDUFB9:!Orf9c +Orf9c -| NDUFB9 +$csa98_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix:true +$OXPHOS_factors_complex:(ACAD9 & (ECSIT & NDUFAF7)) +ACAD9 -> OXPHOS_factors_complex +ECSIT -> OXPHOS_factors_complex +NDUFAF7 -> OXPHOS_factors_complex +$NADH_simple_molecule:false +$ACAD9:!Orf9c +Orf9c -| ACAD9 +$ECSIT:!Orf9c +Orf9c -| ECSIT +$NDUFAF7:!Nsp7 +Nsp7 -| NDUFAF7 +$mt_DNA_gene:((Mt_DNA_repair_complex & (damaged_mt_DNA_gene | (!mt_DNA_damage_phenotype & mt_DNA_replication_phenotype))) | (!Mt_DNA_repair_complex & ((Mt_dNTP_pool_complex & (damaged_mt_DNA_gene | (!mt_DNA_damage_phenotype & mt_DNA_replication_phenotype))) | (!Mt_dNTP_pool_complex & ((TFAM & (damaged_mt_DNA_gene | (!mt_DNA_damage_phenotype & mt_DNA_replication_phenotype))) | (!TFAM & (!mt_DNA_damage_phenotype & mt_DNA_replication_phenotype))))))) +mt_DNA_damage_phenotype -| mt_DNA_gene +mt_DNA_replication_phenotype -> mt_DNA_gene +damaged_mt_DNA_gene -> mt_DNA_gene +TFAM -> mt_DNA_gene +Mt_DNA_repair_complex -> mt_DNA_gene +Mt_dNTP_pool_complex -> mt_DNA_gene +$mt_mRNA_rna:((MT_transcription_complex & (!damaged_mt_DNA_gene & mt_DNA_gene)) | (!MT_transcription_complex & (TFAM & (!damaged_mt_DNA_gene & mt_DNA_gene)))) +mt_DNA_gene -> mt_mRNA_rna +TFAM -> mt_mRNA_rna +MT_transcription_complex -> mt_mRNA_rna +damaged_mt_DNA_gene -| mt_mRNA_rna +$TFAM:false +$MT_transcription_complex:false +$damaged_mt_DNA_gene:(mt_DNA_damage_phenotype & mt_DNA_gene) +mt_DNA_gene -> damaged_mt_DNA_gene +mt_DNA_damage_phenotype -> damaged_mt_DNA_gene +$csa60_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix:((Mt_ribosomal_proteins_complex & mt_mRNA_rna) | (!Mt_ribosomal_proteins_complex & ((Mt_translation_complex & mt_mRNA_rna) | (!Mt_translation_complex & (Nsp8_affected_Mt_ribosomal_proteins_complex & mt_mRNA_rna))))) +mt_mRNA_rna -> csa60_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix +Mt_translation_complex -> csa60_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix +Mt_ribosomal_proteins_complex -> csa60_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix +Nsp8_affected_Mt_ribosomal_proteins_complex -> csa60_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix +$Mt_translation_complex:false +$Mt_ribosomal_proteins_complex:false +$Nsp8_affected_Mt_ribosomal_proteins_complex:!Nsp8 +Nsp8 -| Nsp8_affected_Mt_ribosomal_proteins_complex +$Nsp8:false +$Nsp7:false +$SIRT3:false +$csa24_complex_2_complex_mitochondrial_matrix:((Complex_1_complex & (OXPHOS_factors_complex | (SIRT3 | (csa84_complex_2_complex_mitochondrial_matrix & sa219_Q_simple_molecule_mitochondrial_matrix)))) | (!Complex_1_complex & (OXPHOS_factors_complex | SIRT3))) +SIRT3 -> csa24_complex_2_complex_mitochondrial_matrix +OXPHOS_factors_complex -> csa24_complex_2_complex_mitochondrial_matrix +csa84_complex_2_complex_mitochondrial_matrix -> csa24_complex_2_complex_mitochondrial_matrix +sa219_Q_simple_molecule_mitochondrial_matrix -> csa24_complex_2_complex_mitochondrial_matrix +Complex_1_complex -> csa24_complex_2_complex_mitochondrial_matrix +$csa84_complex_2_complex_mitochondrial_matrix:(TCA_phenotype & csa24_complex_2_complex_mitochondrial_matrix) +csa24_complex_2_complex_mitochondrial_matrix -> csa84_complex_2_complex_mitochondrial_matrix +TCA_phenotype -> csa84_complex_2_complex_mitochondrial_matrix +$sa219_Q_simple_molecule_mitochondrial_matrix:false +$TCA_phenotype:false +$csa103_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix:false +$complex_3_complex:((Complex_1_complex & ((OXPHOS_factors_complex & (csa103_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix | sa219_Q_simple_molecule_mitochondrial_matrix)) | (!OXPHOS_factors_complex & sa219_Q_simple_molecule_mitochondrial_matrix))) | (!Complex_1_complex & (OXPHOS_factors_complex & csa103_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix))) +csa103_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix -> complex_3_complex +OXPHOS_factors_complex -> complex_3_complex +Complex_1_complex -> complex_3_complex +sa219_Q_simple_molecule_mitochondrial_matrix -> complex_3_complex +$H__ion_mitochondrial_matrix:(ATP_Synthase_complex | ((Complex_1_complex & ((Fe3__ion & ((H_2_O_2__simple_molecule & (NADH_simple_molecule | (hydroxide_simple_molecule | superoxide_simple_molecule))) | (!H_2_O_2__simple_molecule & (NADH_simple_molecule | superoxide_simple_molecule)))) | (!Fe3__ion & ((H_2_O_2__simple_molecule & (NADH_simple_molecule | hydroxide_simple_molecule)) | (!H_2_O_2__simple_molecule & NADH_simple_molecule))))) | (!Complex_1_complex & ((Fe3__ion & ((H_2_O_2__simple_molecule & (hydroxide_simple_molecule | superoxide_simple_molecule)) | (!H_2_O_2__simple_molecule & superoxide_simple_molecule))) | (!Fe3__ion & (H_2_O_2__simple_molecule & hydroxide_simple_molecule)))))) +ATP_Synthase_complex -> H__ion_mitochondrial_matrix +H_2_O_2__simple_molecule -> H__ion_mitochondrial_matrix +hydroxide_simple_molecule -> H__ion_mitochondrial_matrix +NADH_simple_molecule -> H__ion_mitochondrial_matrix +Complex_1_complex -> H__ion_mitochondrial_matrix +superoxide_simple_molecule -> H__ion_mitochondrial_matrix +Fe3__ion -> H__ion_mitochondrial_matrix +$H__ion_mitochondrion:((Complex_1_complex & (H__ion_mitochondrial_matrix | complex_3_complex)) | (!Complex_1_complex & complex_3_complex)) +H__ion_mitochondrial_matrix -> H__ion_mitochondrion +Complex_1_complex -> H__ion_mitochondrion +O_2__simple_molecule ->? H__ion_mitochondrion +sa13_Cyt_C_mitochondrial_matrix ->? H__ion_mitochondrion +sa255_QH_2__simple_molecule_mitochondrial_matrix ->? H__ion_mitochondrion +complex_3_complex -> H__ion_mitochondrion +$O_2__simple_molecule:(Fe3__ion & superoxide_simple_molecule) +superoxide_simple_molecule -> O_2__simple_molecule +Fe3__ion -> O_2__simple_molecule +$sa13_Cyt_C_mitochondrial_matrix:false +$sa255_QH_2__simple_molecule_mitochondrial_matrix:false +$ATP_Synthase_complex:((ATP5MG & (H__ion_mitochondrion | !Nsp6)) | (!ATP5MG & H__ion_mitochondrion)) +H__ion_mitochondrion -> ATP_Synthase_complex +ATP5MG -> ATP_Synthase_complex +Nsp6 -| ATP_Synthase_complex +$ATP5MG:true +$Nsp6:true +$complex_4_complex:((OXPHOS_factors_complex & ((complex_3_complex & (csa103_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix | sa253_Cyt_C_mitochondrial_matrix)) | (!complex_3_complex & csa103_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix))) | (!OXPHOS_factors_complex & (complex_3_complex & sa253_Cyt_C_mitochondrial_matrix))) +csa103_mtDNA_encoded_OXPHOS_units_complex_mitochondrial_matrix -> complex_4_complex +OXPHOS_factors_complex -> complex_4_complex +complex_3_complex -> complex_4_complex +sa253_Cyt_C_mitochondrial_matrix -> complex_4_complex +$sa253_Cyt_C_mitochondrial_matrix:(H__ion_mitochondrial_matrix & (O_2__simple_molecule & (complex_3_complex & (sa13_Cyt_C_mitochondrial_matrix & sa255_QH_2__simple_molecule_mitochondrial_matrix)))) +O_2__simple_molecule -> sa253_Cyt_C_mitochondrial_matrix +sa13_Cyt_C_mitochondrial_matrix -> sa253_Cyt_C_mitochondrial_matrix +H__ion_mitochondrial_matrix -> sa253_Cyt_C_mitochondrial_matrix +sa255_QH_2__simple_molecule_mitochondrial_matrix -> sa253_Cyt_C_mitochondrial_matrix +complex_3_complex -> sa253_Cyt_C_mitochondrial_matrix +$paraquat_dication_complex:(O_2__simple_molecule & paraquat_simple_molecule) +paraquat_simple_molecule -> paraquat_dication_complex +O_2__simple_molecule -> paraquat_dication_complex +$paraquat_simple_molecule:((Complex_1_complex & paraquat_dication_complex) | (!Complex_1_complex & (paraquat_dication_complex & superoxide_simple_molecule))) +paraquat_dication_complex -> paraquat_simple_molecule +Complex_1_complex -> paraquat_simple_molecule +superoxide_simple_molecule -> paraquat_simple_molecule +$superoxide_simple_molecule:((H_2_O_2__simple_molecule & (O_2__simple_molecule | hydroxide_simple_molecule)) | (!H_2_O_2__simple_molecule & O_2__simple_molecule)) +H_2_O_2__simple_molecule -> superoxide_simple_molecule +hydroxide_simple_molecule -> superoxide_simple_molecule +O_2__simple_molecule -> superoxide_simple_molecule +paraquat_simple_molecule ->? superoxide_simple_molecule +$Fe3__ion:(Fe2__ion & (H_2_O_2__simple_molecule | hydroxide_simple_molecule)) +H_2_O_2__simple_molecule -> Fe3__ion +Fe2__ion -> Fe3__ion +hydroxide_simple_molecule -> Fe3__ion +$mt_DNA_damage_phenotype:true +$mt_DNA_replication_phenotype:(Mt_dNTP_pool_complex | (Mt_replication_complex | TFAM)) +TFAM -> mt_DNA_replication_phenotype +Mt_replication_complex -> mt_DNA_replication_phenotype +Mt_dNTP_pool_complex -> mt_DNA_replication_phenotype +$Mt_DNA_repair_complex:false +$Mt_dNTP_pool_complex:true +$MT_tRNAs_complex:((Mt_tRNA_synthetase_complex & mt_DNA_gene) | (!Mt_tRNA_synthetase_complex & (TRMT1 & mt_DNA_gene))) +mt_DNA_gene -> MT_tRNAs_complex +Mt_tRNA_synthetase_complex -> MT_tRNAs_complex +TRMT1 -> MT_tRNAs_complex +$Mt_tRNA_synthetase_complex:false +$TRMT1:false +$TIMM29:false +$TIM22_complex_complex:(!Nsp4 & TIMM29) +TIMM29 -> TIM22_complex_complex +Nsp4 -| TIM22_complex_complex +$Nsp4:false +$TIM9_TIM10_complex_complex:!Nsp4 +Nsp4 -| TIM9_TIM10_complex_complex +$NAD__simple_molecule:(Complex_1_complex & NADH_simple_molecule) +NADH_simple_molecule -> NAD__simple_molecule +Complex_1_complex -> NAD__simple_molecule +$sa6_Q_simple_molecule_mitochondrial_matrix:(H__ion_mitochondrial_matrix & (O_2__simple_molecule & (complex_3_complex & (sa13_Cyt_C_mitochondrial_matrix & sa255_QH_2__simple_molecule_mitochondrial_matrix)))) +O_2__simple_molecule -> sa6_Q_simple_molecule_mitochondrial_matrix +sa13_Cyt_C_mitochondrial_matrix -> sa6_Q_simple_molecule_mitochondrial_matrix +H__ion_mitochondrial_matrix -> sa6_Q_simple_molecule_mitochondrial_matrix +sa255_QH_2__simple_molecule_mitochondrial_matrix -> sa6_Q_simple_molecule_mitochondrial_matrix +complex_3_complex -> sa6_Q_simple_molecule_mitochondrial_matrix +$H_2_O_2__simple_molecule:(H__ion_mitochondrial_matrix & ((SOD1 & superoxide_simple_molecule) | (!SOD1 & (SOD2 & superoxide_simple_molecule)))) +superoxide_simple_molecule -> H_2_O_2__simple_molecule +H__ion_mitochondrial_matrix -> H_2_O_2__simple_molecule +SOD1 -> H_2_O_2__simple_molecule +SOD2 -> H_2_O_2__simple_molecule +$hydroxide_simple_molecule:(Fe2__ion & H_2_O_2__simple_molecule) +H_2_O_2__simple_molecule -> hydroxide_simple_molecule +Fe2__ion -> hydroxide_simple_molecule +$SOD1:true +$SOD2:SIRT3 +SIRT3 -> SOD2 +$Fe2__ion:(Fe3__ion & superoxide_simple_molecule) +superoxide_simple_molecule -> Fe2__ion +Fe3__ion -> Fe2__ion +$O__2__endsuper__simple_molecule:(H__ion_mitochondrial_matrix & (O_2__simple_molecule & (complex_3_complex & (sa13_Cyt_C_mitochondrial_matrix & sa255_QH_2__simple_molecule_mitochondrial_matrix)))) +O_2__simple_molecule -> O__2__endsuper__simple_molecule +sa13_Cyt_C_mitochondrial_matrix -> O__2__endsuper__simple_molecule +H__ion_mitochondrial_matrix -> O__2__endsuper__simple_molecule +sa255_QH_2__simple_molecule_mitochondrial_matrix -> O__2__endsuper__simple_molecule +complex_3_complex -> O__2__endsuper__simple_molecule +$ADP_simple_molecule:false +$ATP_simple_molecule:(ADP_simple_molecule & ((ATP_Synthase_complex & Pi_simple_molecule) | (!ATP_Synthase_complex & (H__ion_mitochondrial_matrix & Pi_simple_molecule)))) +ADP_simple_molecule -> ATP_simple_molecule +Pi_simple_molecule -> ATP_simple_molecule +ATP_Synthase_complex -> ATP_simple_molecule +H__ion_mitochondrial_matrix -> ATP_simple_molecule +$Pi_simple_molecule:false +$sa220_QH_2__simple_molecule_mitochondrial_matrix:(Complex_1_complex & (csa84_complex_2_complex_mitochondrial_matrix & sa219_Q_simple_molecule_mitochondrial_matrix)) +csa84_complex_2_complex_mitochondrial_matrix -> sa220_QH_2__simple_molecule_mitochondrial_matrix +sa219_Q_simple_molecule_mitochondrial_matrix -> sa220_QH_2__simple_molecule_mitochondrial_matrix +Complex_1_complex -> sa220_QH_2__simple_molecule_mitochondrial_matrix +$H_2_O_simple_molecule:((CAT & H_2_O_2__simple_molecule) | (!CAT & ((GPX1 & (H_2_O_2__simple_molecule & ((PRDX_complex & (TXN2 | (glutathione_simple_molecule | hydroxide_simple_molecule))) | (!PRDX_complex & (glutathione_simple_molecule | hydroxide_simple_molecule))))) | (!GPX1 & ((GPX4 & (H_2_O_2__simple_molecule & ((PRDX_complex & (TXN2 | (glutathione_simple_molecule | hydroxide_simple_molecule))) | (!PRDX_complex & (glutathione_simple_molecule | hydroxide_simple_molecule))))) | (!GPX4 & (H_2_O_2__simple_molecule & ((PRDX_complex & (TXN2 | hydroxide_simple_molecule)) | (!PRDX_complex & hydroxide_simple_molecule))))))))) +H_2_O_2__simple_molecule -> H_2_O_simple_molecule +TXN2 -> H_2_O_simple_molecule +PRDX_complex -> H_2_O_simple_molecule +glutathione_simple_molecule -> H_2_O_simple_molecule +GPX4 -> H_2_O_simple_molecule +GPX1 -> H_2_O_simple_molecule +CAT -> H_2_O_simple_molecule +hydroxide_simple_molecule -> H_2_O_simple_molecule +$TXN2:((H_2_O_2__simple_molecule & ((NADPH_simple_molecule & ((PRDX_complex & TXN2) | (!PRDX_complex & (TXN2 & TXNRD2)))) | (!NADPH_simple_molecule & (PRDX_complex & TXN2)))) | (!H_2_O_2__simple_molecule & (NADPH_simple_molecule & (TXN2 & TXNRD2)))) +H_2_O_2__simple_molecule -> TXN2 +TXN2 -> TXN2 +PRDX_complex -> TXN2 +NADPH_simple_molecule -> TXN2 +TXNRD2 -> TXN2 +$PRDX_complex:false +$glutathione_simple_molecule:(GSR & (NADPH_simple_molecule & glutathione_disulfide_simple_molecule)) +glutathione_disulfide_simple_molecule -> glutathione_simple_molecule +NADPH_simple_molecule -> glutathione_simple_molecule +GSR -> glutathione_simple_molecule +$GPX4:true +$GPX1:false +$CAT:false +$NADPH_simple_molecule:true +$TXNRD2:true +$glutathione_disulfide_simple_molecule:((GPX1 & (H_2_O_2__simple_molecule & glutathione_simple_molecule)) | (!GPX1 & (GPX4 & (H_2_O_2__simple_molecule & glutathione_simple_molecule)))) +H_2_O_2__simple_molecule -> glutathione_disulfide_simple_molecule +glutathione_simple_molecule -> glutathione_disulfide_simple_molecule +GPX4 -> glutathione_disulfide_simple_molecule +GPX1 -> glutathione_disulfide_simple_molecule +$GSR:false +$ROS_simple_molecule:(H_2_O_2__simple_molecule | (hydroxide_simple_molecule | superoxide_simple_molecule)) +superoxide_simple_molecule -> ROS_simple_molecule +hydroxide_simple_molecule -> ROS_simple_molecule +H_2_O_2__simple_molecule -> ROS_simple_molecule +$HO_simple_molecule:(Fe2__ion & (H_2_O_2__simple_molecule | hydroxide_simple_molecule)) +H_2_O_2__simple_molecule -> HO_simple_molecule +Fe2__ion -> HO_simple_molecule +hydroxide_simple_molecule -> HO_simple_molecule +$NADP____simple_molecule:((GSR & (NADPH_simple_molecule & ((TXN2 & (TXNRD2 | glutathione_disulfide_simple_molecule)) | (!TXN2 & glutathione_disulfide_simple_molecule)))) | (!GSR & (NADPH_simple_molecule & (TXN2 & TXNRD2)))) +glutathione_disulfide_simple_molecule -> NADP____simple_molecule +NADPH_simple_molecule -> NADP____simple_molecule +GSR -> NADP____simple_molecule +TXN2 -> NADP____simple_molecule +TXNRD2 -> NADP____simple_molecule +$Mt_replication_complex:false +$TOM_complex_complex:false +$precursor_protein_N_terminus_binding:(!Orf9b & (TIM22_complex_complex | (TIM23_complex_complex | (TIM9_TIM10_complex_complex | TOM_complex_complex)))) +TOM_complex_complex -> precursor_protein_N_terminus_binding +TIM22_complex_complex -> precursor_protein_N_terminus_binding +Orf9b -| precursor_protein_N_terminus_binding +TIM23_complex_complex -> precursor_protein_N_terminus_binding +TIM9_TIM10_complex_complex -> precursor_protein_N_terminus_binding +$Orf9b:false +$TIM23_complex_complex:false diff --git a/data/synthetic_cases/interferon-dataset.csv b/data/benchmarks/interferon/interferon_dataset.csv similarity index 100% rename from data/synthetic_cases/interferon-dataset.csv rename to data/benchmarks/interferon/interferon_dataset.csv diff --git a/data/synthetic_cases/interferon-sketch.aeon b/data/benchmarks/interferon/interferon_sketch.aeon similarity index 100% rename from data/synthetic_cases/interferon-sketch.aeon rename to data/benchmarks/interferon/interferon_sketch.aeon diff --git a/data/benchmarks/interferon/metadata.txt b/data/benchmarks/interferon/metadata.txt new file mode 100644 index 00000000..a7bdb9c4 --- /dev/null +++ b/data/benchmarks/interferon/metadata.txt @@ -0,0 +1,2 @@ +Publication: https://doi.org/10.1038/s41597-020-0477-8 +Source: https://git-r3lab.uni.lu/covid/models/-/blob/4ed915a55687f626f9e7b3d4ada249cbaa5945b8/Executable%20Modules/SBML_qual_build/sbml/Interferon1_stable.sbml diff --git a/data/benchmarks/interferon/model_concrete.aeon b/data/benchmarks/interferon/model_concrete.aeon new file mode 100644 index 00000000..581975df --- /dev/null +++ b/data/benchmarks/interferon/model_concrete.aeon @@ -0,0 +1,311 @@ +$IFNAR_complex:true +$IFNA1_IFNAR_complex:((IFNAR_complex & sa5_IFNA1_extracellular_space) & sa31_IFNA1_extracellular_space) +IFNAR_complex -> IFNA1_IFNAR_complex +sa5_IFNA1_extracellular_space -> IFNA1_IFNAR_complex +sa31_IFNA1_extracellular_space -> IFNA1_IFNAR_complex +$sa5_IFNA1_extracellular_space:true +$sa31_IFNA1_extracellular_space:IFNA1_cell +IFNA1_cell -> sa31_IFNA1_extracellular_space +$IRAK1_4:true +$TLR4_TRIF_TRAM_complex:(IRAK1_4 & TRIF) +IRAK1_4 -> TLR4_TRIF_TRAM_complex +TRIF -> TLR4_TRIF_TRAM_complex +$TRIF:true +$IFNB1_IFNAR_complex:((IFNAR_complex & sa3_IFNB1_extracellular_space) & sa27_IFNB1_extracellular_space) +IFNAR_complex -> IFNB1_IFNAR_complex +sa3_IFNB1_extracellular_space -> IFNB1_IFNAR_complex +sa27_IFNB1_extracellular_space -> IFNB1_IFNAR_complex +$sa3_IFNB1_extracellular_space:true +$sa27_IFNB1_extracellular_space:IFNB1_cell +IFNB1_cell -> sa27_IFNB1_extracellular_space +$STAT1_phosphorylated:(((((!Nsp1 & !Orf7b) & !Orf3a) & !M) & !Nsp6) & !Nsp13) +Nsp1 -| STAT1_phosphorylated +Orf7b -| STAT1_phosphorylated +Orf3a -| STAT1_phosphorylated +M -| STAT1_phosphorylated +Nsp6 -| STAT1_phosphorylated +Nsp13 -| STAT1_phosphorylated +$STAT1_2_IRF9_complex:((((((TREML4 | JAK1_TYK2_complex) & STAT1_phosphorylated) & IRF9) & STAT2_phosphorylated) & !Orf6) & !Nsp5) +STAT1_phosphorylated -> STAT1_2_IRF9_complex +IRF9 -> STAT1_2_IRF9_complex +STAT2_phosphorylated -> STAT1_2_IRF9_complex +Orf6 -| STAT1_2_IRF9_complex +TREML4 -> STAT1_2_IRF9_complex +JAK1_TYK2_complex -> STAT1_2_IRF9_complex +Nsp5 -| STAT1_2_IRF9_complex +$IRF9:true +$STAT2_phosphorylated:(((!Orf7a & !Orf7b) & !Nsp6) & !Nsp13) +Orf7a -| STAT2_phosphorylated +Orf7b -| STAT2_phosphorylated +Nsp6 -| STAT2_phosphorylated +Nsp13 -| STAT2_phosphorylated +$Orf6:true +$TREML4:true +$JAK1_TYK2_complex:(((IFNA1_IFNAR_complex | IFNB1_IFNAR_complex) & JAK1) & TYK2) +JAK1 -> JAK1_TYK2_complex +TYK2 -> JAK1_TYK2_complex +IFNA1_IFNAR_complex -> JAK1_TYK2_complex +IFNB1_IFNAR_complex -> JAK1_TYK2_complex +$Nsp5:true +$ISRE_complex:(STAT1_2_IRF9_complex & !Orf6) +STAT1_2_IRF9_complex -> ISRE_complex +Orf6 -| ISRE_complex +$JAK1:true +$TYK2:true +$JUN:true +$AP_1_complex_cell:(((E | MAPK8_14_complex) & JUN) & FOS) +JUN -> AP_1_complex_cell +FOS -> AP_1_complex_cell +E -> AP_1_complex_cell +MAPK8_14_complex -> AP_1_complex_cell +$FOS:true +$E:true +$MAPK8_14_complex:(((TBK1 | MAP3K7) & MAPK14) & MAPK8) +MAPK14 -> MAPK8_14_complex +MAPK8 -> MAPK8_14_complex +TBK1 -> MAPK8_14_complex +MAP3K7 -> MAPK8_14_complex +$csa42_IkB_p50_p65_complex_cell:(csa41_IkB_p50_p65_complex_cell & IKKa_IKKb_NEMO_complex) +csa41_IkB_p50_p65_complex_cell -> csa42_IkB_p50_p65_complex_cell +IKKa_IKKb_NEMO_complex -> csa42_IkB_p50_p65_complex_cell +$p50_p65_complex_cell:csa42_IkB_p50_p65_complex_cell +csa42_IkB_p50_p65_complex_cell -> p50_p65_complex_cell +$OAS1_cell_active:(OAS1_cell & !Nsp15) +OAS1_cell -> OAS1_cell_active +Nsp15 -| OAS1_cell_active +$OAS1_EIF2AK_complex:(((OAS1_cell_active & OAS3_cell_active) & EIF2AK) & OAS2_cell_active) +OAS1_cell_active -> OAS1_EIF2AK_complex +OAS3_cell_active -> OAS1_EIF2AK_complex +EIF2AK -> OAS1_EIF2AK_complex +OAS2_cell_active -> OAS1_EIF2AK_complex +$OAS3_cell_active:(OAS3_cell & !Nsp15) +OAS3_cell -> OAS3_cell_active +Nsp15 -| OAS3_cell_active +$EIF2AK:(EIF2AK_rna | !Nsp15) +EIF2AK_rna -> EIF2AK +Nsp15 -| EIF2AK +$OAS2_cell_active:(OAS2_cell & !Nsp15) +OAS2_cell -> OAS2_cell_active +Nsp15 -| OAS2_cell_active +$TBK1:(((IKBKE | STING1_ubiquitinated) | MAVS) & !Nsp13) +IKBKE -> TBK1 +STING1_ubiquitinated -> TBK1 +MAVS -> TBK1 +Nsp13 -| TBK1 +$TBK1_IKBKE_complex:(((((TRAF3 | NAP1) | Azithromycin_drug) & TBK1) & IKBKE) & !Nsp3) +TBK1 -> TBK1_IKBKE_complex +IKBKE -> TBK1_IKBKE_complex +TRAF3 -> TBK1_IKBKE_complex +Nsp3 -| TBK1_IKBKE_complex +NAP1 -> TBK1_IKBKE_complex +Azithromycin_drug -> TBK1_IKBKE_complex +$IKBKE:(TBK1 & !Nsp3) +Nsp3 -| IKBKE +TBK1 -> IKBKE +$TRAF3:(MYD88_TRAM_complex & !Nsp3) +MYD88_TRAM_complex -> TRAF3 +Nsp3 -| TRAF3 +$Nsp3:true +$NAP1:TLR4_TRIF_TRAM_complex +TLR4_TRIF_TRAM_complex -> NAP1 +$Azithromycin_drug:true +$MYD88:true +$MYD88_TRAM_complex:(((((TREML4 | TLR7) | TLR9) | Viral_dsRNA_rna_endosome) & MYD88) & IRAK1_4) +MYD88 -> MYD88_TRAM_complex +IRAK1_4 -> MYD88_TRAM_complex +TREML4 -> MYD88_TRAM_complex +TLR7 -> MYD88_TRAM_complex +TLR9 -> MYD88_TRAM_complex +Viral_dsRNA_rna_endosome -> MYD88_TRAM_complex +$TLR7:true +$TLR9:true +$Viral_dsRNA_rna_endosome:true +$TRAF3_TBK1_IKBKE_complex_cell_active:((TRAF3_TBK1_IKBKE_complex_cell & STING1_ubiquitinated) & !pp1ab) +TRAF3_TBK1_IKBKE_complex_cell -> TRAF3_TBK1_IKBKE_complex_cell_active +STING1_ubiquitinated -> TRAF3_TBK1_IKBKE_complex_cell_active +pp1ab -| TRAF3_TBK1_IKBKE_complex_cell_active +$TRAF3_TANK_TBK1_IKKepsilon_complex:((((TLR3_TRIF_complex | MAVS) & TRAF3_TBK1_IKBKE_complex_cell_active) & TANK) & !M) +TRAF3_TBK1_IKBKE_complex_cell_active -> TRAF3_TANK_TBK1_IKKepsilon_complex +TANK -> TRAF3_TANK_TBK1_IKKepsilon_complex +TLR3_TRIF_complex -> TRAF3_TANK_TBK1_IKKepsilon_complex +MAVS -> TRAF3_TANK_TBK1_IKKepsilon_complex +M -| TRAF3_TANK_TBK1_IKKepsilon_complex +$TANK:true +$TLR3_TRIF_complex:((Viral_dsRNA_rna_endosome | Azithromycin_drug) & TRIF) +TRIF -> TLR3_TRIF_complex +Viral_dsRNA_rna_endosome -> TLR3_TRIF_complex +Azithromycin_drug -> TLR3_TRIF_complex +$MAVS:((RIG1_MDA5_complex & !Orf9b) & !ITCH) +RIG1_MDA5_complex -> MAVS +Orf9b -| MAVS +ITCH -| MAVS +$M:true +$TRAF3_TBK1_IKBKE_complex_cell:((TBK1_IKBKE_complex & TRAF3) & !pp1ab) +TBK1_IKBKE_complex -> TRAF3_TBK1_IKBKE_complex_cell +TRAF3 -> TRAF3_TBK1_IKBKE_complex_cell +pp1ab -| TRAF3_TBK1_IKBKE_complex_cell +$pp1ab:true +$STING1_ubiquitinated:(MAVS & !pp1ab) +MAVS -> STING1_ubiquitinated +pp1ab -| STING1_ubiquitinated +$DDX58_ubiquitinated:((((TRIM25 | RNF135) | Azithromycin_drug) & !N) & !Nsp5) +N -| DDX58_ubiquitinated +TRIM25 -> DDX58_ubiquitinated +RNF135 -> DDX58_ubiquitinated +Nsp5 -| DDX58_ubiquitinated +Azithromycin_drug -> DDX58_ubiquitinated +$RIG1_MDA5_complex:(((((((((DDX58_ubiquitinated & IFIH1) & Viral_dsRNA_rna_cell) & !N) & !Nsp10) & !Nsp14) & !Nsp16) & !Nsp15) & !M) & !Nsp15) +DDX58_ubiquitinated -> RIG1_MDA5_complex +IFIH1 -> RIG1_MDA5_complex +Viral_dsRNA_rna_cell -> RIG1_MDA5_complex +N -| RIG1_MDA5_complex +Nsp10 -| RIG1_MDA5_complex +Nsp14 -| RIG1_MDA5_complex +Nsp16 -| RIG1_MDA5_complex +Nsp15 -| RIG1_MDA5_complex +M -| RIG1_MDA5_complex +$IFIH1:(Azithromycin_drug & !Nsp15) +Nsp15 -| IFIH1 +Azithromycin_drug -> IFIH1 +$Viral_dsRNA_rna_cell:(((Viral_dsRNA_rna_cell & Viral_replication_phenotype) & !sa31_IFNA1_extracellular_space) & !sa27_IFNB1_extracellular_space) +Viral_dsRNA_rna_cell -> Viral_dsRNA_rna_cell +Viral_replication_phenotype -> Viral_dsRNA_rna_cell +sa31_IFNA1_extracellular_space -| Viral_dsRNA_rna_cell +sa27_IFNB1_extracellular_space -| Viral_dsRNA_rna_cell +$N:true +$Nsp10:true +$Nsp14:true +$Nsp16:true +$Nsp15:true +$NLRP3_inflammasome_complex:((E | p50_p65_complex_nucleus) & !MNS_drug) +E -> NLRP3_inflammasome_complex +p50_p65_complex_nucleus -> NLRP3_inflammasome_complex +MNS_drug -| NLRP3_inflammasome_complex +$p50_p65_complex_nucleus:p50_p65_complex_cell +p50_p65_complex_cell -> p50_p65_complex_nucleus +$MNS_drug:true +$MAPK14:true +$MAPK8:true +$MAP3K7:TRAF6_ubiquitinated +TRAF6_ubiquitinated -> MAP3K7 +$AP_1_complex_nucleus:AP_1_complex_cell +AP_1_complex_cell -> AP_1_complex_nucleus +$TLR3_TRIF_RIPK1_complex:(TLR3_TRIF_complex & RIP1) +TLR3_TRIF_complex -> TLR3_TRIF_RIPK1_complex +RIP1 -> TLR3_TRIF_RIPK1_complex +$RIP1:true +$TAB1:true +$TAB1_2_TRAF6_TAK1_complex:((((TAB1 & TAB2) & TRAF6_ubiquitinated) & TAK1) & TLR3_TRIF_RIPK1_complex) +TAB1 -> TAB1_2_TRAF6_TAK1_complex +TAB2 -> TAB1_2_TRAF6_TAK1_complex +TRAF6_ubiquitinated -> TAB1_2_TRAF6_TAK1_complex +TAK1 -> TAB1_2_TRAF6_TAK1_complex +TLR3_TRIF_RIPK1_complex -> TAB1_2_TRAF6_TAK1_complex +$TAB2:true +$TRAF6_ubiquitinated:((MYD88_TRAM_complex & !Nsp3) & !ITCH) +MYD88_TRAM_complex -> TRAF6_ubiquitinated +Nsp3 -| TRAF6_ubiquitinated +ITCH -| TRAF6_ubiquitinated +$TAK1:true +$NEMO:true +$IKKa_IKKb_NEMO_complex:(((NEMO & IKKa) & IKKb) & TAB1_2_TRAF6_TAK1_complex) +NEMO -> IKKa_IKKb_NEMO_complex +IKKa -> IKKa_IKKb_NEMO_complex +IKKb -> IKKa_IKKb_NEMO_complex +TAB1_2_TRAF6_TAK1_complex -> IKKa_IKKb_NEMO_complex +$IKKa:true +$IKKb:true +$RELA:true +$csa41_IkB_p50_p65_complex_cell:((RELA & NFKB1) & IkB) +RELA -> csa41_IkB_p50_p65_complex_cell +NFKB1 -> csa41_IkB_p50_p65_complex_cell +IkB -> csa41_IkB_p50_p65_complex_cell +$NFKB1:true +$IkB:true +$IRF3_homodimer_complex_cell:(((((((((MAVS | TRAF3_TANK_TBK1_IKKepsilon_complex) & IRF3) & !Nsp3) & !N) & !Orf8_complex) & !Orf6) & !pp1ab) & !Nsp6) & !Nsp15) +IRF3 -> IRF3_homodimer_complex_cell +Nsp3 -| IRF3_homodimer_complex_cell +N -| IRF3_homodimer_complex_cell +Orf8_complex -| IRF3_homodimer_complex_cell +Orf6 -| IRF3_homodimer_complex_cell +pp1ab -| IRF3_homodimer_complex_cell +MAVS -> IRF3_homodimer_complex_cell +TRAF3_TANK_TBK1_IKKepsilon_complex -> IRF3_homodimer_complex_cell +Nsp6 -| IRF3_homodimer_complex_cell +Nsp15 -| IRF3_homodimer_complex_cell +$IRF3_homodimer_complex_nucleus:(IRF3_homodimer_complex_cell & !Orf6) +IRF3_homodimer_complex_cell -> IRF3_homodimer_complex_nucleus +Orf6 -| IRF3_homodimer_complex_nucleus +$IRF3:true +$Orf8_complex:true +$Nsp6:true +$IRF7:true +$IRF7_homodimer_complex:(IRF7 & TRAF3_TANK_TBK1_IKKepsilon_complex) +IRF7 -> IRF7_homodimer_complex +TRAF3_TANK_TBK1_IKKepsilon_complex -> IRF7_homodimer_complex +$ISG15:ISG15_rna +ISG15_rna -> ISG15 +$ISG15_Nsp3_complex:((ISG15 & Nsp3) & !GRL0617_drug) +ISG15 -> ISG15_Nsp3_complex +Nsp3 -> ISG15_Nsp3_complex +GRL0617_drug -| ISG15_Nsp3_complex +$GRL0617_drug:true +$IFNB1_rna:((((AP_1_complex_nucleus & p50_p65_complex_nucleus) & IRF3_homodimer_complex_nucleus) & IRF7_homodimer_complex) & Azithromycin_drug) +AP_1_complex_nucleus -> IFNB1_rna +p50_p65_complex_nucleus -> IFNB1_rna +IRF3_homodimer_complex_nucleus -> IFNB1_rna +IRF7_homodimer_complex -> IFNB1_rna +Azithromycin_drug -> IFNB1_rna +$IFNB1_cell:IFNB1_rna +IFNB1_rna -> IFNB1_cell +$IFNA1_rna:((AP_1_complex_nucleus & p50_p65_complex_nucleus) & IRF7_homodimer_complex) +AP_1_complex_nucleus -> IFNA1_rna +p50_p65_complex_nucleus -> IFNA1_rna +IRF7_homodimer_complex -> IFNA1_rna +$IFNA1_cell:IFNA1_rna +IFNA1_rna -> IFNA1_cell +$OAS1_rna:(ISRE_complex & IRF3_homodimer_complex_nucleus) +ISRE_complex -> OAS1_rna +IRF3_homodimer_complex_nucleus -> OAS1_rna +$EIF2AK_rna:(ISRE_complex & IRF3_homodimer_complex_nucleus) +ISRE_complex -> EIF2AK_rna +IRF3_homodimer_complex_nucleus -> EIF2AK_rna +$OAS1_cell:OAS1_rna +OAS1_rna -> OAS1_cell +$ITCH:Orf9b +Orf9b -> ITCH +$Nsp13:true +$Nsp1:true +$Orf7b:true +$Orf3a:true +$Orf7a:true +$OAS2_rna:(ISRE_complex & IRF3_homodimer_complex_nucleus) +ISRE_complex -> OAS2_rna +IRF3_homodimer_complex_nucleus -> OAS2_rna +$OAS2_cell:OAS2_rna +OAS2_rna -> OAS2_cell +$OAS3_rna:(ISRE_complex & IRF3_homodimer_complex_nucleus) +ISRE_complex -> OAS3_rna +IRF3_homodimer_complex_nucleus -> OAS3_rna +$OAS3_cell:OAS3_rna +OAS3_rna -> OAS3_cell +$ISG_expression_antiviral_response_phenotype:((((p50_p65_complex_nucleus | OAS1_EIF2AK_complex) | !Nsp3) | ISG15) | Azithromycin_drug) +p50_p65_complex_nucleus -> ISG_expression_antiviral_response_phenotype +OAS1_EIF2AK_complex -> ISG_expression_antiviral_response_phenotype +Nsp3 -| ISG_expression_antiviral_response_phenotype +ISG15 -> ISG_expression_antiviral_response_phenotype +Azithromycin_drug -> ISG_expression_antiviral_response_phenotype +$Orf9b:true +$TRIM25:true +$RNF135:true +$Viral_replication_phenotype:true +$Proinflammatory_cytokine_expression_Inflammation_phenotype:(p50_p65_complex_nucleus | NLRP3_inflammasome_complex) +p50_p65_complex_nucleus -> Proinflammatory_cytokine_expression_Inflammation_phenotype +NLRP3_inflammasome_complex -> Proinflammatory_cytokine_expression_Inflammation_phenotype +$type_I_IFN_response_phenotype:(sa31_IFNA1_extracellular_space | sa27_IFNB1_extracellular_space) +sa31_IFNA1_extracellular_space -> type_I_IFN_response_phenotype +sa27_IFNB1_extracellular_space -> type_I_IFN_response_phenotype +$IkB_phosphorylated:csa42_IkB_p50_p65_complex_cell +csa42_IkB_p50_p65_complex_cell -> IkB_phosphorylated +$ISG15_rna:ISRE_complex +ISRE_complex -> ISG15_rna diff --git a/data/synthetic_cases/macrophage-dataset.csv b/data/benchmarks/macrophage/macrophage_dataset.csv similarity index 100% rename from data/synthetic_cases/macrophage-dataset.csv rename to data/benchmarks/macrophage/macrophage_dataset.csv diff --git a/data/synthetic_cases/macrophage-sketch.aeon b/data/benchmarks/macrophage/macrophage_sketch.aeon similarity index 100% rename from data/synthetic_cases/macrophage-sketch.aeon rename to data/benchmarks/macrophage/macrophage_sketch.aeon diff --git a/data/benchmarks/macrophage/metadata.txt b/data/benchmarks/macrophage/metadata.txt new file mode 100644 index 00000000..4a2cd3b8 --- /dev/null +++ b/data/benchmarks/macrophage/metadata.txt @@ -0,0 +1,2 @@ +Publication: https://doi.org/10.1186/1752-0509-2-36 +Source: https://research.cellcollective.org/?dashboard=true#module/1582:1/signaling-in-macrophage-activation/1 diff --git a/data/benchmarks/macrophage/model_concrete.aeon b/data/benchmarks/macrophage/model_concrete.aeon new file mode 100644 index 00000000..c6cc5d84 --- /dev/null +++ b/data/benchmarks/macrophage/model_concrete.aeon @@ -0,0 +1,854 @@ +$IPARP:(PARP & (CASP7nucleus | CASP3nucleus)) +CASP7nucleus -> IPARP +CASP3nucleus -> IPARP +PARP -> IPARP +$Inactive_DNA_Repair:IPARP +IPARP -> Inactive_DNA_Repair +$TRADD:External_Activator +External_Activator -> TRADD +$TNF_TNFRSF1A_FADD_TRADD:(TNF_TNFRSF1A & (TRADD & FADD)) +TRADD -> TNF_TNFRSF1A_FADD_TRADD +FADD -> TNF_TNFRSF1A_FADD_TRADD +TNF_TNFRSF1A -> TNF_TNFRSF1A_FADD_TRADD +$FADD:External_Activator +External_Activator -> FADD +$TNF_TNFRSF1A:TNF_BAG4_TNFRSF1A +TNF_BAG4_TNFRSF1A -> TNF_TNFRSF1A +$TNFRSF1B:External_Activator +External_Activator -> TNFRSF1B +$TNF_TNFRSF1B:(TNF & TNFRSF1B) +TNFRSF1B -> TNF_TNFRSF1B +TNF -> TNF_TNFRSF1B +$TNF:true +$External_Activator:true +$PRKRA:External_Activator +External_Activator -> PRKRA +$TICAM1:External_Activator +External_Activator -> TICAM1 +$TLR4_TICAM1_TICAM2:(TLR4 & (TICAM1 & TICAM2)) +TICAM1 -> TLR4_TICAM1_TICAM2 +TLR4 -> TLR4_TICAM1_TICAM2 +TICAM2 -> TLR4_TICAM1_TICAM2 +$TLR4:LPS +LPS -> TLR4 +$TICAM2:External_Activator +External_Activator -> TICAM2 +$BAK1:Mitochondrial_Activator +Mitochondrial_Activator -> BAK1 +$DIABLOcytoplasm:(DIABLOmitochondria & ((BAK1 | tBID) | BAX)) +BAK1 -> DIABLOcytoplasm +DIABLOmitochondria -> DIABLOcytoplasm +tBID -> DIABLOcytoplasm +BAX -> DIABLOcytoplasm +$DIABLOmitochondria:Mitochondrial_Activator +Mitochondrial_Activator -> DIABLOmitochondria +$tBID:(BID & (CASP2 | CASP8)) +BID -> tBID +CASP2 -> tBID +CASP8 -> tBID +$BAX:Mitochondrial_Activator +Mitochondrial_Activator -> BAX +$TLR3_TICAM1_TICAM2_RIPK1:(TLR3_TICAM1_TICAM2 & RIPK1) +TLR3_TICAM1_TICAM2 -> TLR3_TICAM1_TICAM2_RIPK1 +RIPK1 -> TLR3_TICAM1_TICAM2_RIPK1 +$TLR3_TICAM1_TICAM2_RIPK1_RIPK3:(TLR3_TICAM1_TICAM2_RIPK1 & RIPK3) +TLR3_TICAM1_TICAM2_RIPK1 -> TLR3_TICAM1_TICAM2_RIPK1_RIPK3 +RIPK3 -> TLR3_TICAM1_TICAM2_RIPK1_RIPK3 +$RIPK3:External_Activator +External_Activator -> RIPK3 +$CASP3cytoplasm:(ProCASP3 & ((Apoptosome | CASP8) | CASP4)) +Apoptosome -> CASP3cytoplasm +ProCASP3 -> CASP3cytoplasm +BIRC4cytoplasm -|? CASP3cytoplasm +BIRC2 -|? CASP3cytoplasm +CASP8 -> CASP3cytoplasm +CASP4 -> CASP3cytoplasm +$CASP3nucleus:CASP3cytoplasm +CASP3cytoplasm -> CASP3nucleus +$CFLAR:External_Activator +External_Activator -> CFLAR +$EIF2AK2_PRKRA:(EIF2AK2cytoplasm & PRKRA) +PRKRA -> EIF2AK2_PRKRA +EIF2AK2cytoplasm -> EIF2AK2_PRKRA +$TP53cytoplasm:EIF2AK2_PRKRA +EIF2AK2_PRKRA -> TP53cytoplasm +$ProCASP10:External_Activator +External_Activator -> ProCASP10 +$APAF1:External_Activator +External_Activator -> APAF1 +$TBK1:External_Activator +External_Activator -> TBK1 +$TRAF5:External_Activator +External_Activator -> TRAF5 +$TNFSF13B_TNFRSF17_TRAF5:(TNFSF13B_TNFRSF17 & TRAF5) +TRAF5 -> TNFSF13B_TNFRSF17_TRAF5 +TNFSF13B_TNFRSF17 -> TNFSF13B_TNFRSF17_TRAF5 +$TNFSF13B_TNFRSF17:(TNFSF13B & TNFRSF17) +TNFSF13B -> TNFSF13B_TNFRSF17 +TNFRSF17 -> TNFSF13B_TNFRSF17 +$RPS6KA5:External_Activator +External_Activator -> RPS6KA5 +$RELAp65_NFKB1p50cytoplasm:(NFKBIA_RELAp65_NFKB1p50 & (((((RPS6KA5 | CHUK) | PRKCZ) | TBK1) | MAP3K7) | IKBKB)) +RPS6KA5 -> RELAp65_NFKB1p50cytoplasm +CHUK -> RELAp65_NFKB1p50cytoplasm +PRKCZ -> RELAp65_NFKB1p50cytoplasm +TBK1 -> RELAp65_NFKB1p50cytoplasm +NFKBIA_RELAp65_NFKB1p50 -> RELAp65_NFKB1p50cytoplasm +MAP3K7 -> RELAp65_NFKB1p50cytoplasm +IKBKB -> RELAp65_NFKB1p50cytoplasm +$CHUK:External_Activator +External_Activator -> CHUK +$PRKCZ:External_Activator +External_Activator -> PRKCZ +$NFKBIA_RELAp65_NFKB1p50:((IKBKG_CHUK_IKBKB & ((RELA_p65 & NFKBIA) & NFKB1_p50)) | (TNF_IKBKG_Complex & ((RELA_p65 & NFKBIA) & NFKB1_p50))) +RELA_p65 -> NFKBIA_RELAp65_NFKB1p50 +NFKBIA -> NFKBIA_RELAp65_NFKB1p50 +NFKB1_p50 -> NFKBIA_RELAp65_NFKB1p50 +TNF_IKBKG_Complex -> NFKBIA_RELAp65_NFKB1p50 +IKBKG_CHUK_IKBKB -> NFKBIA_RELAp65_NFKB1p50 +$MAP3K7:External_Activator +External_Activator -> MAP3K7 +$IKBKB:External_Activator +External_Activator -> IKBKB +$TNFSF13B:true +$TNFRSF17:External_Activator +External_Activator -> TNFRSF17 +$TLR7:External_Activator +External_Activator -> TLR7 +$TLR7_TLR7:(TLR7 & ssRNA) +TLR7 -> TLR7_TLR7 +ssRNA -> TLR7_TLR7 +$ssRNA:Virus +Virus -> ssRNA +$IRF3_IRF3cytoplasm:IRF3 +IRF3 -> IRF3_IRF3cytoplasm +$IRF3_IRF3nucleus:IRF3_IRF3cytoplasm +IRF3_IRF3cytoplasm -> IRF3_IRF3nucleus +$TP53nucleus:TP53cytoplasm +TP53cytoplasm -> TP53nucleus +$BBC3gene:TP53nucleus +TP53nucleus -> BBC3gene +$RELAp65_NFBK1p50nucleus:RELAp65_NFKB1p50cytoplasm +RELAp65_NFKB1p50cytoplasm -> RELAp65_NFBK1p50nucleus +$TRAF2gene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> TRAF2gene +$FASLG_FAS_FADD_FAF1_DAXX:(FASLG_FAS & ((FADD & FAF1) & DAXX)) +FADD -> FASLG_FAS_FADD_FAF1_DAXX +FAF1 -> FASLG_FAS_FADD_FAF1_DAXX +DAXX -> FASLG_FAS_FADD_FAF1_DAXX +FASLG_FAS -> FASLG_FAS_FADD_FAF1_DAXX +$FASLG_FAS_FADD_FAF1_DAXX_CFLAR:(FASLG_FAS_FADD_FAF1_DAXX & CFLAR) +FASLG_FAS_FADD_FAF1_DAXX -> FASLG_FAS_FADD_FAF1_DAXX_CFLAR +CFLAR -> FASLG_FAS_FADD_FAF1_DAXX_CFLAR +$STAT1_STAT1nucleus_p2:STAT1_STAT1nucleus_p1 +PTP -|? STAT1_STAT1nucleus_p2 +STAT1_STAT1nucleus_p1 -> STAT1_STAT1nucleus_p2 +$IRF1gene:STAT1_STAT1nucleus_p2 +STAT1_STAT1nucleus_p2 -> IRF1gene +$NFKB2p100_NFKB2p100_Ub:(NFKB2p100_NFKB2p100cytoplasm & Ub) +Ub -> NFKB2p100_NFKB2p100_Ub +NFKB2p100_NFKB2p100cytoplasm -> NFKB2p100_NFKB2p100_Ub +$NFKB2p52_NFKB2p52cytoplasm:(NFKB2p100_NFKB2p100_Ub & Proteasome) +NFKB2p100_NFKB2p100_Ub -> NFKB2p52_NFKB2p52cytoplasm +Proteasome -> NFKB2p52_NFKB2p52cytoplasm +$Proteasome:External_Activator +External_Activator -> Proteasome +$TRAF3:External_Activator +External_Activator -> TRAF3 +$CD40_CD40LG_TRAF3:(CD40_CD40LG & TRAF3) +TRAF3 -> CD40_CD40LG_TRAF3 +CD40_CD40LG -> CD40_CD40LG_TRAF3 +$CD40_CD40LG:(CD40 & CD40LG) +CD40 -> CD40_CD40LG +CD40LG -> CD40_CD40LG +$Mitochondrial_Activator:true +$BAD:Mitochondrial_Activator +Mitochondrial_Activator -> BAD +$IRF3_IRF7nucleus:IRF3_IRF7cytoplasm +IRF3_IRF7cytoplasm -> IRF3_IRF7nucleus +$CXCL10gene:((CBP & (IRF3_IRF7nucleus | IRF3_IRF3nucleus)) | ISGF3nucleus) +IRF3_IRF7nucleus -> CXCL10gene +ISGF3nucleus -> CXCL10gene +CBP -> CXCL10gene +IRF3_IRF3nucleus -> CXCL10gene +$ISGF3nucleus:ISGF3cytoplasm +ISGF3cytoplasm -> ISGF3nucleus +$CBP:(EP300 & CREBBP) +EP300 -> CBP +CREBBP -> CBP +$FASgene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> FASgene +$IFIT2gene:((CBP & (IRF3_IRF7nucleus | IRF3_IRF3nucleus)) | ISGF3nucleus) +IRF3_IRF7nucleus -> IFIT2gene +ISGF3nucleus -> IFIT2gene +CBP -> IFIT2gene +IRF3_IRF3nucleus -> IFIT2gene +$TLR9:External_Activator +External_Activator -> TLR9 +$IRF1_IRF1nucleus:IRF1_IRF1cytoplasm +IRF1_IRF1cytoplasm -> IRF1_IRF1nucleus +$IRF2gene:IRF1_IRF1nucleus +IRF1_IRF1nucleus -> IRF2gene +$TRAF2cytoplasm:External_Activator +External_Activator -> TRAF2cytoplasm +$TNF_TNFRSF1B_TRAF2:(TNF_TNFRSF1B & TRAF2cytoplasm) +TRAF2cytoplasm -> TNF_TNFRSF1B_TRAF2 +TNF_TNFRSF1B -> TNF_TNFRSF1B_TRAF2 +$dsRNA:Virus +Virus -> dsRNA +$TLR3_TLR3:(dsRNA & TLR3) +dsRNA -> TLR3_TLR3 +TLR3 -> TLR3_TLR3 +$TLR3:External_Activator +External_Activator -> TLR3 +$ISGF3cytoplasm:(STAT1_STAT2 & IRF9) +STAT1_STAT2 -> ISGF3cytoplasm +IRF9 -> ISGF3cytoplasm +$APAF1_CYCS:(APAF1 & CYCScytoplasm) +APAF1 -> APAF1_CYCS +CYCScytoplasm -> APAF1_CYCS +$CYCScytoplasm:(CYCSmytochondria & ((BAK1 | tBID) | BAX)) +BAK1 -> CYCScytoplasm +tBID -> CYCScytoplasm +CYCSmytochondria -> CYCScytoplasm +BAX -> CYCScytoplasm +$NFKB2p52_NFKB2p52nucleus:NFKB2p52_NFKB2p52cytoplasm +NFKB2p52_NFKB2p52cytoplasm -> NFKB2p52_NFKB2p52nucleus +$BIRC2:External_Activator +External_Activator -> BIRC2 +$IRF3_IRF7cytoplasm:(IRF3 & IRF7) +IRF7 -> IRF3_IRF7cytoplasm +IRF3 -> IRF3_IRF7cytoplasm +$IFNGR:(IFNG & ((IFNGR1 & IFNGR2) & JAK2)) +PTPN2 -|? IFNGR +IFNGR1 -> IFNGR +IFNGR2 -> IFNGR +SOCS3 -|? IFNGR +SOCS1 -|? IFNGR +JAK2 -> IFNGR +IFNG -> IFNGR +$STAT1:IFNGR +IFNGR -> STAT1 +$TLR6:External_Activator +External_Activator -> TLR6 +$APAF1gene:TP53nucleus +TP53nucleus -> APAF1gene +$TLR7_MYD88_TRAF6_IRF5:((TLR7_TLR7 & (TRAF6 & MYD88)) & !IRF5) +TLR7_TLR7 -> TLR7_MYD88_TRAF6_IRF5 +IRF5 -| TLR7_MYD88_TRAF6_IRF5 +TRAF6 -> TLR7_MYD88_TRAF6_IRF5 +MYD88 -> TLR7_MYD88_TRAF6_IRF5 +$IRF5:((Virus | TLR9_MYD88_TRAF6_IRF5) | TLR7_MYD88_TRAF6_IRF5) +TLR9_MYD88_TRAF6_IRF5 -> IRF5 +Virus -> IRF5 +TLR7_MYD88_TRAF6_IRF5 -> IRF5 +$TRAF6:External_Activator +External_Activator -> TRAF6 +$MYD88:External_Activator +External_Activator -> MYD88 +$IFNAR1:External_Activator +External_Activator -> IFNAR1 +$TLR5_MYD88_IRAK1_IRAK4_TRAF6:(TLR5_MYD88_IRAK1_IRAK4 & TRAF6) +TRAF6 -> TLR5_MYD88_IRAK1_IRAK4_TRAF6 +TLR5_MYD88_IRAK1_IRAK4 -> TLR5_MYD88_IRAK1_IRAK4_TRAF6 +$TLR5_MYD88_IRAK1_IRAK4:(TLR5_TLR5 & ((IRAK1 & IRAK4) & MYD88)) +IRAK1 -> TLR5_MYD88_IRAK1_IRAK4 +IRAK4 -> TLR5_MYD88_IRAK1_IRAK4 +TLR5_TLR5 -> TLR5_MYD88_IRAK1_IRAK4 +MYD88 -> TLR5_MYD88_IRAK1_IRAK4 +$IRF1_IRF1_Activator:true +$PKC:IRF1_IRF1_Activator +IRF1_IRF1_Activator -> PKC +$IRAK4:External_Activator +External_Activator -> IRAK4 +$Ub:External_Activator +External_Activator -> Ub +$TLR5:External_Activator +External_Activator -> TLR5 +$IRF2:IRF2_Activator +IRF2_Activator -> IRF2 +$IRF8:(IRF2 | IRF1_IRF1nucleus) +IRF2 -> IRF8 +IRF1_IRF1nucleus -> IRF8 +$ENDOGcytoplasm:(tBID & ENDOGmitochondria) +tBID -> ENDOGcytoplasm +ENDOGmitochondria -> ENDOGcytoplasm +$ENDOGmitochondria:Mitochondrial_Activator +Mitochondrial_Activator -> ENDOGmitochondria +$TLR7_MYD88_IRAK1_IRAK4_TRAF6:(TLR7_MYD88_IRAK1_IRAK4 & TRAF6) +TRAF6 -> TLR7_MYD88_IRAK1_IRAK4_TRAF6 +TLR7_MYD88_IRAK1_IRAK4 -> TLR7_MYD88_IRAK1_IRAK4_TRAF6 +$TLR7_MYD88_IRAK1_IRAK4:(TLR7_TLR7 & ((IRAK1 & IRAK4) & MYD88)) +IRAK1 -> TLR7_MYD88_IRAK1_IRAK4 +TLR7_TLR7 -> TLR7_MYD88_IRAK1_IRAK4 +IRAK4 -> TLR7_MYD88_IRAK1_IRAK4 +MYD88 -> TLR7_MYD88_IRAK1_IRAK4 +$TLR3_TICAM1_TICAM2:(TLR3_TLR3 & (TICAM1 & TICAM2)) +TLR3_TLR3 -> TLR3_TICAM1_TICAM2 +TICAM1 -> TLR3_TICAM1_TICAM2 +TICAM2 -> TLR3_TICAM1_TICAM2 +$EIF2S1:EIF2AK2gene +EIF2AK2gene -> EIF2S1 +$Inactivation_of_Protein_Synthesis:EIF2S1 +EIF2S1 -> Inactivation_of_Protein_Synthesis +$TLR9_MYD88_IRAK1_IRAK4_TRAF6:(TLR9_MYD88_IRAK1_IRAK4 & TRAF6) +TLR9_MYD88_IRAK1_IRAK4 -> TLR9_MYD88_IRAK1_IRAK4_TRAF6 +TRAF6 -> TLR9_MYD88_IRAK1_IRAK4_TRAF6 +$TLR9_MYD88_TRAF6:TLR9_MYD88_IRAK1_IRAK4_TRAF6 +TLR9_MYD88_IRAK1_IRAK4_TRAF6 -> TLR9_MYD88_TRAF6 +$Apoptosis:(((DNA_Fragmentation | Inactive_DNA_Repair) | Inactivation_of_Protein_Synthesis) | Cell_Shrinkage) +Inactivation_of_Protein_Synthesis -> Apoptosis +Inactive_DNA_Repair -> Apoptosis +Cell_Shrinkage -> Apoptosis +DNA_Fragmentation -> Apoptosis +$Cell_Shrinkage:(cLMNA | cGAS2) +cLMNA -> Cell_Shrinkage +cGAS2 -> Cell_Shrinkage +$DNA_Fragmentation:(Fragmented_DNAnucleus | IDFFA) +IDFFA -> DNA_Fragmentation +Fragmented_DNAnucleus -> DNA_Fragmentation +$IFNGR2:External_Activator +External_Activator -> IFNGR2 +$TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4:(TLR2_TLR6 & (((IRAK1 & IRAK4) & TOLLIP) & MYD88)) +TLR2_TLR6 -> TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4 +IRAK1 -> TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4 +IRAK4 -> TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4 +TOLLIP -> TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4 +MYD88 -> TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4 +$TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4_TRAF6:(TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4 & TRAF6) +TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4 -> TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4_TRAF6 +TRAF6 -> TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4_TRAF6 +$STAT1_STAT2:(STAT1 & STAT2) +STAT1 -> STAT1_STAT2 +STAT2 -> STAT1_STAT2 +$STAT2:IFNAR +IFNAR -> STAT2 +$ICAM1gene:STAT1_STAT1nucleus_p2 +STAT1_STAT1nucleus_p2 -> ICAM1gene +$IRF5_IRF5nucleus:IRF5_IRF5cytoplasm +IRF5_IRF5cytoplasm -> IRF5_IRF5nucleus +$BAK1gene:IRF5_IRF5nucleus +IRF5_IRF5nucleus -> BAK1gene +$ILIB:true +$ILIB_IL1R1:(ILIB & IL1R1) +ILIB -> ILIB_IL1R1 +IL1R1 -> ILIB_IL1R1 +$IL1R1:External_Activator +External_Activator -> IL1R1 +$TNFRSF10B:External_Activator +External_Activator -> TNFRSF10B +$TNFSF10:true +$TNFSF10_TNFRSF10A:(TNFSF10 & TNFRSF10A) +TNFSF10 -> TNFSF10_TNFRSF10A +TNFRSF10A -> TNFSF10_TNFRSF10A +$TNFRSF10A:External_Activator +External_Activator -> TNFRSF10A +$IRAK1:External_Activator +External_Activator -> IRAK1 +$BIRC3gene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> BIRC3gene +$IFNAR2:External_Activator +External_Activator -> IFNAR2 +$TNFSF10_TNFSF10B:(TNFSF10 & TNFRSF10B) +TNFSF10 -> TNFSF10_TNFSF10B +TNFRSF10B -> TNFSF10_TNFSF10B +$TYK2:External_Activator +External_Activator -> TYK2 +$IL12Bgene:IRF1_IRF1nucleus +IRF1_IRF1nucleus -> IL12Bgene +$TNF_IKBKG_Complex:(TNF_TNFRSF1A_FADD_TRADD_TRAF2_RIPK1 & ((CHUK & IKBKG) & IKBKB)) +CHUK -> TNF_IKBKG_Complex +IKBKG -> TNF_IKBKG_Complex +TNF_TNFRSF1A_FADD_TRADD_TRAF2_RIPK1 -> TNF_IKBKG_Complex +IKBKB -> TNF_IKBKG_Complex +$IKBKG:External_Activator +External_Activator -> IKBKG +$TNF_TNFRSF1A_FADD_TRADD_TRAF2_RIPK1:(TNF_TNFRSF1A_FADD_TRADD & (RIPK1 & TRAF2cytoplasm)) +RIPK1 -> TNF_TNFRSF1A_FADD_TRADD_TRAF2_RIPK1 +TRAF2cytoplasm -> TNF_TNFRSF1A_FADD_TRADD_TRAF2_RIPK1 +TNF_TNFRSF1A_FADD_TRADD -> TNF_TNFRSF1A_FADD_TRADD_TRAF2_RIPK1 +$CASP3_Activator:true +$ProCASP3:CASP3_Activator +CASP3_Activator -> ProCASP3 +$ATF2:External_Activator +External_Activator -> ATF2 +$IFNB1gene:((((((RELAp65_NFBK1p50nucleus & (((ATF2 & IRF3_IRF7nucleus) & CBP) & IRF3_IRF3nucleus)) | IRF5_IRF5nucleus) | STAT1_STAT1nucleus_p2) | IRF3_IRF3nucleus) | ISGF3nucleus) | IRF1_IRF1nucleus) +ATF2 ->? IFNB1gene +IRF5_IRF5nucleus -> IFNB1gene +IRF2 -|? IFNB1gene +IRF3_IRF7nucleus ->? IFNB1gene +ISGF3nucleus -> IFNB1gene +CBP ->? IFNB1gene +RELAp65_NFBK1p50nucleus ->? IFNB1gene +IRF3_IRF3nucleus -> IFNB1gene +STAT1_STAT1nucleus_p2 -> IFNB1gene +IRF1_IRF1nucleus -> IFNB1gene +$STAT1_STAT1_IRF9nucleus:STAT1_STAT1_IRF9cytoplasm +STAT1_STAT1_IRF9cytoplasm -> STAT1_STAT1_IRF9nucleus +$IFR5gene:(STAT1_STAT1_IRF9nucleus | TP53nucleus) +STAT1_STAT1_IRF9nucleus -> IFR5gene +TP53nucleus -> IFR5gene +$IRF5_IRF7cytoplasm:IRF5 +IRF5 -> IRF5_IRF7cytoplasm +$IRF5_IRF7nucleus:IRF5_IRF7cytoplasm +IRF5_IRF7cytoplasm -> IRF5_IRF7nucleus +$TOLLIP:External_Activator +External_Activator -> TOLLIP +$TNFSF10_TNFSF10B_FADD:(TNFSF10_TNFSF10B & FADD) +FADD -> TNFSF10_TNFSF10B_FADD +TNFSF10_TNFSF10B -> TNFSF10_TNFSF10B_FADD +$CASP8:(ProCASP8 & (((FASLG_FAS_FADD_FAF1_DAXX_CFLAR | FASLG_FAS_FADD_FAF1_DAXX) | TNFSF10_TNFRSF10A_FADD) | TNFSF10_TNFSF10B_FADD)) +FASLG_FAS_FADD_FAF1_DAXX_CFLAR -> CASP8 +FASLG_FAS_FADD_FAF1_DAXX -> CASP8 +TNFSF10_TNFRSF10A_FADD -> CASP8 +ProCASP8 -> CASP8 +TNFSF10_TNFSF10B_FADD -> CASP8 +$TNFSF10_TNFRSF10A_FADD:(TNFSF10_TNFRSF10A & FADD) +TNFSF10_TNFRSF10A -> TNFSF10_TNFRSF10A_FADD +FADD -> TNFSF10_TNFRSF10A_FADD +$ProCASP8:External_Activator +External_Activator -> ProCASP8 +$BAG4:(External_Activator | TNF_BAG4_TNFRSF1A) +TNF_BAG4_TNFRSF1A -> BAG4 +External_Activator -> BAG4 +$BAG4_TNFRSF1A:(BAG4 & TNFRSF1A) +BAG4 -> BAG4_TNFRSF1A +TNFRSF1A -> BAG4_TNFRSF1A +$TNFRSF1A:External_Activator +External_Activator -> TNFRSF1A +$RIPK1:External_Activator +External_Activator -> RIPK1 +$RELB:External_Activator +External_Activator -> RELB +$CASP6cytoplasm:(ProCASP6 & CASP9) +CASP9 -> CASP6cytoplasm +ProCASP6 -> CASP6cytoplasm +$CASP6nucleus:CASP6cytoplasm +CASP6cytoplasm -> CASP6nucleus +$TNF_BAG4_TNFRSF1A:(TNF & BAG4_TNFRSF1A) +BAG4_TNFRSF1A -> TNF_BAG4_TNFRSF1A +TNF -> TNF_BAG4_TNFRSF1A +$LPS:Bacteria +Bacteria -> LPS +$IL15gene:IRF1_IRF1nucleus +IRF1_IRF1nucleus -> IL15gene +$CXCL9gene:STAT1_STAT1nucleus_p2 +STAT1_STAT1nucleus_p2 -> CXCL9gene +$CASP9:CASP6_Activator +CASP6_Activator -> CASP9 +$Apoptosome:(APAF1_CYCS & CASP9) +CASP9 -> Apoptosome +APAF1_CYCS -> Apoptosome +$IFNAR:((IFNB1 & (((IFNAR2 & IFNAR1) & TYK2) & JAK1)) | (IFNA & (((IFNAR2 & IFNAR1) & TYK2) & JAK1))) +IFNAR2 -> IFNAR +IFNAR1 -> IFNAR +IFNA -> IFNAR +TYK2 -> IFNAR +IFNB1 -> IFNAR +JAK1 -> IFNAR +$PSMB9gene:(IRF2 | IRF1_IRF1nucleus) +IRF2 -> PSMB9gene +IRF1_IRF1nucleus -> PSMB9gene +$NFKB2p100_RELB_Ub:(NFKB2p100_RELBcytoplasm & Ub) +NFKB2p100_RELBcytoplasm -> NFKB2p100_RELB_Ub +Ub -> NFKB2p100_RELB_Ub +$NFKB2p52_RELBcytoplasm:(NFKB2p100_RELB_Ub & Proteasome) +NFKB2p100_RELB_Ub -> NFKB2p52_RELBcytoplasm +Proteasome -> NFKB2p52_RELBcytoplasm +$IKBKE_TBK1:(TLR4_TICAM1_TICAM2 & (TBK1 & IKBKE)) +TLR4_TICAM1_TICAM2 -> IKBKE_TBK1 +TBK1 -> IKBKE_TBK1 +IKBKE -> IKBKE_TBK1 +$IRF3:(IKBKE_TBK1 | TLR3_TICAM1_TICAM2_TBK1) +IKBKE_TBK1 -> IRF3 +TLR3_TICAM1_TICAM2_TBK1 -> IRF3 +$TLR3_TICAM1_TICAM2_TBK1:(TLR3_TICAM1_TICAM2 & TBK1) +TLR3_TICAM1_TICAM2 -> TLR3_TICAM1_TICAM2_TBK1 +TBK1 -> TLR3_TICAM1_TICAM2_TBK1 +$G1P2gene:((((IRF1_IRF1nucleus & ((SPI1 & IRF8) & IRF4)) | (CBP & (IRF3_IRF7nucleus | IRF3_IRF3nucleus))) | (IRF2 & ((SPI1 & IRF8) & IRF4))) | ISGF3nucleus) +IRF2 -> G1P2gene +IRF3_IRF7nucleus -> G1P2gene +SPI1 -> G1P2gene +ISGF3nucleus -> G1P2gene +IRF8 -> G1P2gene +CBP -> G1P2gene +IRF3_IRF3nucleus -> G1P2gene +IRF4 -> G1P2gene +IRF1_IRF1nucleus -> G1P2gene +$SPI1:External_Activator +External_Activator -> SPI1 +$IRF4:External_Activator +External_Activator -> IRF4 +$BID:External_Activator +External_Activator -> BID +$CASP2:(ProCASP2 & Fragmented_DNAcytoplasm) +ProCASP2 -> CASP2 +Fragmented_DNAcytoplasm -> CASP2 +$TNFSF10gene:(IRF1_IRF1nucleus | IRF5_IRF5nucleus) +IRF5_IRF5nucleus -> TNFSF10gene +IRF1_IRF1nucleus -> TNFSF10gene +$CIITAgene:(IRF2 | IRF1_IRF1nucleus) +IRF2 -> CIITAgene +IRF1_IRF1nucleus -> CIITAgene +$EIF2AK2gene:(ISGF3nucleus | IRF1_IRF1nucleus) +ISGF3nucleus -> EIF2AK2gene +IRF1_IRF1nucleus -> EIF2AK2gene +$CREBBP:External_Activator +External_Activator -> CREBBP +$SOCS1:External_Activator +External_Activator -> SOCS1 +$JAK2:External_Activator +External_Activator -> JAK2 +$IRF1_IRF1cytoplasm:IRF1cytoplasm +IRF1cytoplasm -> IRF1_IRF1cytoplasm +$RELA_NFKB1_Activator:true +$RELA_p65:RELA_NFKB1_Activator +RELA_NFKB1_Activator -> RELA_p65 +$ENDOGnucleus:ENDOGcytoplasm +ENDOGcytoplasm -> ENDOGnucleus +$Fragmented_DNAnucleus:(DNA & (ENDOGnucleus | PDCD8nucleus)) +ENDOGnucleus -> Fragmented_DNAnucleus +PDCD8nucleus -> Fragmented_DNAnucleus +DNA -> Fragmented_DNAnucleus +$PDCD8nucleus:PDCD8cytoplasm +PDCD8cytoplasm -> PDCD8nucleus +$DNA:External_Activator +External_Activator -> DNA +$BIRC4gene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> BIRC4gene +$LMNA:External_Activator +External_Activator -> LMNA +$IRF3_IRF5cytoplasm:IRF5 +IRF5 -> IRF3_IRF5cytoplasm +$IRF3_IRF5nucleus:IRF3_IRF5cytoplasm +IRF3_IRF5cytoplasm -> IRF3_IRF5nucleus +$PTP:External_Activator +External_Activator -> PTP +$MAP3K7IP2:External_Activator +External_Activator -> MAP3K7IP2 +$Virus:true +$Viral_Bacterial_CpG:(Bacteria | Virus) +Virus -> Viral_Bacterial_CpG +Bacteria -> Viral_Bacterial_CpG +$Bacteria:true +$HIST2H4gene:(IRF2 | IRF1_IRF1nucleus) +IRF2 -> HIST2H4gene +IRF1_IRF1nucleus -> HIST2H4gene +$IRF5_IRF5cytoplasm:IRF5 +IRF5 -> IRF5_IRF5cytoplasm +$TIRAP:External_Activator +External_Activator -> TIRAP +$TLR9_TLR9:(TLR9 & Viral_Bacterial_CpG) +TLR9 -> TLR9_TLR9 +Viral_Bacterial_CpG -> TLR9_TLR9 +$IRF9:External_Activator +External_Activator -> IRF9 +$RIPK1gene:IRF5_IRF5nucleus +IRF5_IRF5nucleus -> RIPK1gene +$CYBBgene:(IRF8 & SPI1) +SPI1 -> CYBBgene +IRF8 -> CYBBgene +$SP100gene:IRF5_IRF5nucleus +IRF5_IRF5nucleus -> SP100gene +$IRAK2:External_Activator +External_Activator -> IRAK2 +$Triacyl_Lipopeptides:Bacteria +Bacteria -> Triacyl_Lipopeptides +$TLR9_MYD88_TRAF6_IRF5:((TLR9_TLR9 & (TRAF6 & MYD88)) & !IRF5) +IRF5 -| TLR9_MYD88_TRAF6_IRF5 +TRAF6 -> TLR9_MYD88_TRAF6_IRF5 +MYD88 -> TLR9_MYD88_TRAF6_IRF5 +TLR9_TLR9 -> TLR9_MYD88_TRAF6_IRF5 +$CASP7cytoplasm:(ProCASP7 & ((Apoptosome | CASP8) | CASP10)) +Apoptosome -> CASP7cytoplasm +BIRC4cytoplasm -|? CASP7cytoplasm +CASP8 -> CASP7cytoplasm +ProCASP7 -> CASP7cytoplasm +CASP10 -> CASP7cytoplasm +$CASP7nucleus:CASP7cytoplasm +CASP7cytoplasm -> CASP7nucleus +$FAS:External_Activator +External_Activator -> FAS +$IKBKE:External_Activator +External_Activator -> IKBKE +$BCL3_NFKB2p52_NFKB2p52:(BCL3 & NFKB2p52_NFKB2p52nucleus) +NFKB2p52_NFKB2p52nucleus -> BCL3_NFKB2p52_NFKB2p52 +BCL3 -> BCL3_NFKB2p52_NFKB2p52 +$BCL3:External_Activator +External_Activator -> BCL3 +$EP300:External_Activator +External_Activator -> EP300 +$OAS1gene:(((IRF1_IRF1nucleus | ISGF3nucleus) | IRF5_IRF5nucleus) | IRF8) +IRF5_IRF5nucleus -> OAS1gene +ISGF3nucleus -> OAS1gene +IRF8 -> OAS1gene +IRF1_IRF1nucleus -> OAS1gene +$IFNA:true +$IFNA_IFNA:IFNA +IFNA -> IFNA_IFNA +$NFKB2p52_RELBnucleus:NFKB2p52_RELBcytoplasm +NFKB2p52_RELBcytoplasm -> NFKB2p52_RELBnucleus +$NFKB2p100:External_Activator +External_Activator -> NFKB2p100 +$IDFFA:(DFFA & CASP3nucleus) +CASP3nucleus -> IDFFA +DFFA -> IDFFA +$DFFA:External_Activator +External_Activator -> DFFA +$BCL2A1:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> BCL2A1 +$TLR5_TLR5:(TLR5 & Flagellin) +TLR5 -> TLR5_TLR5 +Flagellin -> TLR5_TLR5 +$BIRC4cytoplasm:!(DIABLOcytoplasm | HTRA2cytoplasm) +DIABLOcytoplasm -| BIRC4cytoplasm +HTRA2cytoplasm -| BIRC4cytoplasm +$ProCASP7:CASP7_Activator +CASP7_Activator -> ProCASP7 +$CASP10:(ProCASP10 & TNF_TNFRSF1A_FADD_TRADD) +ProCASP10 -> CASP10 +TNF_TNFRSF1A_FADD_TRADD -> CASP10 +$STAT1_STAT1_IRF9cytoplasm:(STAT1 & IRF9) +STAT1 -> STAT1_STAT1_IRF9cytoplasm +IRF9 -> STAT1_STAT1_IRF9cytoplasm +$PLSCR1gene:IRF5_IRF5nucleus +IRF5_IRF5nucleus -> PLSCR1gene +$BCL2:Mitochondrial_Activator +Mitochondrial_Activator -> BCL2 +$Flagellin:Bacteria +Bacteria -> Flagellin +$MDM2gene:TP53nucleus +TP53nucleus -> MDM2gene +$HTRA2mitochondria:Mitochondrial_Activator +Mitochondrial_Activator -> HTRA2mitochondria +$HTRA2cytoplasm:(tBID & HTRA2mitochondria) +HTRA2mitochondria -> HTRA2cytoplasm +tBID -> HTRA2cytoplasm +$ProCASP6:CASP6_Activator +CASP6_Activator -> ProCASP6 +$CYCSmytochondria:Mitochondrial_Activator +Mitochondrial_Activator -> CYCSmytochondria +$ProCASP4:External_Activator +External_Activator -> ProCASP4 +$CASP4:ProCASP4 +ProCASP4 -> CASP4 +$HLA_Bgene:IRF8 +IRF2 -|? HLA_Bgene +IRF8 -> HLA_Bgene +$CASP3gene:(IRF5_IRF5nucleus | CASP3cytoplasm) +IRF5_IRF5nucleus -> CASP3gene +CASP3cytoplasm -> CASP3gene +$GAS2:External_Activator +External_Activator -> GAS2 +$MAP3K14:((TNFSF13B_TNFRSF17_TRAF5 | CD40_CD40LG_TRAF3) | TNF_TNFRSF1B_TRAF2) +TNFSF13B_TNFRSF17_TRAF5 -> MAP3K14 +TNF_TNFRSF1B_TRAF2 -> MAP3K14 +CD40_CD40LG_TRAF3 -> MAP3K14 +$IRF1cytoplasm:((PKC | CKII) | PKA) +CKII -> IRF1cytoplasm +PKA -> IRF1cytoplasm +PKC -> IRF1cytoplasm +$NFKBIA:(RELA_NFKB1_Activator | NFKBIA_RELAp65_NFKB1p50) +Ub -|? NFKBIA +RELA_NFKB1_Activator -> NFKBIA +NFKBIA_RELAp65_NFKB1p50 -> NFKBIA +$NFKB1_p50:RELA_NFKB1_Activator +RELA_NFKB1_Activator -> NFKB1_p50 +$IKBKG_CHUK_IKBKB:((IKBKG & ((CHUK & MAP3K7IP1_MAP3K7IP2_MAP3K7) & IKBKB)) | (TLR3_TICAM1_TICAM2_RIPK1_RIPK3 & ((CHUK & IKBKG) & IKBKB))) +CHUK -> IKBKG_CHUK_IKBKB +IKBKG -> IKBKG_CHUK_IKBKB +TLR3_TICAM1_TICAM2_RIPK1_RIPK3 -> IKBKG_CHUK_IKBKB +MAP3K7IP1_MAP3K7IP2_MAP3K7 -> IKBKG_CHUK_IKBKB +IKBKB -> IKBKG_CHUK_IKBKB +$cLMNA:(LMNA & CASP6nucleus) +CASP6nucleus -> cLMNA +LMNA -> cLMNA +$NFKB2p100_RELBcytoplasm:(NFKB2p100 & (CHUK_CHUK & RELB)) +CHUK_CHUK -> NFKB2p100_RELBcytoplasm +NFKB2p100 -> NFKB2p100_RELBcytoplasm +RELB -> NFKB2p100_RELBcytoplasm +$PRKRAgene:IRF5_IRF5nucleus +IRF5_IRF5nucleus -> PRKRAgene +$JAK1:External_Activator +External_Activator -> JAK1 +$ProCASP1:External_Activator +External_Activator -> ProCASP1 +$Diacyl_Lipopeptides:Bacteria +Bacteria -> Diacyl_Lipopeptides +$FASLG_FAS:(FASLG & FAS) +FAS -> FASLG_FAS +FASLG -> FASLG_FAS +$FASLG:true +$ProCASP2:External_Activator +External_Activator -> ProCASP2 +$Fragmented_DNAcytoplasm:DNA_Fragmentation +DNA_Fragmentation -> Fragmented_DNAcytoplasm +$BCL2L1_BAD:(BCL2L1mitochondria & BAD) +BAD -> BCL2L1_BAD +BCL2L1mitochondria -> BCL2L1_BAD +$BCL2L1mitochondria:Mitochondrial_Activator +Mitochondrial_Activator -> BCL2L1mitochondria +$ILIB_IL1R1_MYD88_IRAK1_IRAK4:(ILIB_IL1R1 & ((IRAK1 & IRAK4) & MYD88)) +IRAK1 -> ILIB_IL1R1_MYD88_IRAK1_IRAK4 +ILIB_IL1R1 -> ILIB_IL1R1_MYD88_IRAK1_IRAK4 +IRAK4 -> ILIB_IL1R1_MYD88_IRAK1_IRAK4 +MYD88 -> ILIB_IL1R1_MYD88_IRAK1_IRAK4 +$CKII:IRF1_IRF1_Activator +IRF1_IRF1_Activator -> CKII +$FASLGgene:(TP53nucleus | IRF1_IRF1nucleus) +TP53nucleus -> FASLGgene +IRF1_IRF1nucleus -> FASLGgene +$STAT1_STAT1cytoplasm:(STAT1 & PRKCD) +STAT1 -> STAT1_STAT1cytoplasm +PRKCD -> STAT1_STAT1cytoplasm +$PRKCD:External_Activator +External_Activator -> PRKCD +$PKA:IRF1_IRF1_Activator +IRF1_IRF1_Activator -> PKA +$TRAF1gene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> TRAF1gene +$ILIB_IL1R1_MYD88_IRAK1_IRAK4_TRAF6:(ILIB_IL1R1_MYD88_IRAK1_IRAK4 & TRAF6) +TRAF6 -> ILIB_IL1R1_MYD88_IRAK1_IRAK4_TRAF6 +ILIB_IL1R1_MYD88_IRAK1_IRAK4 -> ILIB_IL1R1_MYD88_IRAK1_IRAK4_TRAF6 +$SOCS3:External_Activator +External_Activator -> SOCS3 +$MAP3K7IP1_MAP3K7IP2_MAP3K7:(((((((TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4_TRAF6 & ((MAP3K7IP2 & MAP3K7) & MAP3K7IP1)) | (TLR3_TICAM1_TICAM2_TRAF6 & ((MAP3K7IP2 & MAP3K7) & MAP3K7IP1))) | (TLR7_MYD88_IRAK1_IRAK4_TRAF6 & ((MAP3K7IP2 & MAP3K7) & MAP3K7IP1))) | (TLR5_MYD88_IRAK1_IRAK4_TRAF6 & ((MAP3K7IP2 & MAP3K7) & MAP3K7IP1))) | (TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4_TRAF6 & ((MAP3K7IP2 & MAP3K7) & MAP3K7IP1))) | (TLR9_MYD88_IRAK1_IRAK4_TRAF6 & ((MAP3K7IP2 & MAP3K7) & MAP3K7IP1))) | (ILIB_IL1R1_MYD88_IRAK1_IRAK4_TRAF6 & ((MAP3K7IP2 & MAP3K7) & MAP3K7IP1))) +MAP3K7IP2 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +TLR9_MYD88_IRAK1_IRAK4_TRAF6 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4_TRAF6 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +TLR3_TICAM1_TICAM2_TRAF6 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +TLR5_MYD88_IRAK1_IRAK4_TRAF6 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +TLR2_TLR6_TOLLIP_MYD88_IRAK1_IRAK4_TRAF6 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +TLR7_MYD88_IRAK1_IRAK4_TRAF6 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +MAP3K7 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +MAP3K7IP1 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +ILIB_IL1R1_MYD88_IRAK1_IRAK4_TRAF6 -> MAP3K7IP1_MAP3K7IP2_MAP3K7 +$PARP:External_Activator +External_Activator -> PARP +$PTPN2:External_Activator +External_Activator -> PTPN2 +$PDCD8cytoplasm:(tBID & PDCD8mitochondria) +tBID -> PDCD8cytoplasm +PDCD8mitochondria -> PDCD8cytoplasm +$PDCD8_HSPA1A:(PDCD8cytoplasm & HSPA1A) +PDCD8cytoplasm -> PDCD8_HSPA1A +HSPA1A -> PDCD8_HSPA1A +$HSPA1A:External_Activator +External_Activator -> HSPA1A +$NFKB2p100_NFKB2p100cytoplasm:(NFKB2p100 & IKBKG_CHUK_IKBKB) +NFKB2p100 -> NFKB2p100_NFKB2p100cytoplasm +IKBKG_CHUK_IKBKB -> NFKB2p100_NFKB2p100cytoplasm +$BCL2L1gene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> BCL2L1gene +$FAF1:External_Activator +External_Activator -> FAF1 +$DAXX:External_Activator +External_Activator -> DAXX +$IRF7:IKBKE_TBK1 +IKBKE_TBK1 -> IRF7 +$cGAS2:(GAS2 & CASP3nucleus) +CASP3nucleus -> cGAS2 +GAS2 -> cGAS2 +$EIF2AK2cytoplasm:dsRNA +dsRNA -> EIF2AK2cytoplasm +$TLR9_MYD88_IRAK1_IRAK4:(TLR9_TLR9 & ((IRAK1 & IRAK4) & MYD88)) +IRAK1 -> TLR9_MYD88_IRAK1_IRAK4 +IRAK4 -> TLR9_MYD88_IRAK1_IRAK4 +MYD88 -> TLR9_MYD88_IRAK1_IRAK4 +TLR9_TLR9 -> TLR9_MYD88_IRAK1_IRAK4 +$IFNB1:true +$IFNB1_IFNB1:IFNB1 +IFNB1 -> IFNB1_IFNB1 +$IER3gene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> IER3gene +$PDCD8mitochondria:Mitochondrial_Activator +Mitochondrial_Activator -> PDCD8mitochondria +$TLR2:External_Activator +External_Activator -> TLR2 +$TLR1_TLR2:Triacyl_Lipopeptides +Triacyl_Lipopeptides -> TLR1_TLR2 +$TLR2_TLR6:(TLR2 & (Diacyl_Lipopeptides & TLR6)) +TLR2 -> TLR2_TLR6 +Diacyl_Lipopeptides -> TLR2_TLR6 +TLR6 -> TLR2_TLR6 +$IRF7_IRF7cytoplasm:IRF7 +IRF7 -> IRF7_IRF7cytoplasm +$TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4_TRAF6:(TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4 & TRAF6) +TRAF6 -> TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4_TRAF6 +TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4 -> TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4_TRAF6 +$TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4:(TLR1_TLR2 & ((((IRAK1 & IRAK2) & IRAK4) & TIRAP) & MYD88)) +TLR1_TLR2 -> TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4 +IRAK1 -> TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4 +IRAK2 -> TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4 +IRAK4 -> TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4 +TIRAP -> TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4 +MYD88 -> TLR1_TLR2_TIRAP_MYD88_IRAK2_IRAK1_IRAK4 +$TLR3_TICAM1_TICAM2_TRAF6:(TLR3_TICAM1_TICAM2 & TRAF6) +TLR3_TICAM1_TICAM2 -> TLR3_TICAM1_TICAM2_TRAF6 +TRAF6 -> TLR3_TICAM1_TICAM2_TRAF6 +$MAP3K7IP1:External_Activator +External_Activator -> MAP3K7IP1 +$CXCL11gene:IRF5_IRF5nucleus +IRF5_IRF5nucleus -> CXCL11gene +$CHUK_CHUK:(CHUK & MAP3K14) +CHUK -> CHUK_CHUK +MAP3K14 -> CHUK_CHUK +$TAP1gene:(IRF1_IRF1nucleus | IRF2) +IRF2 -> TAP1gene +IRF1_IRF1nucleus -> TAP1gene +$SOD2gene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> SOD2gene +$STAT1_STAT1nucleus_p1:STAT1_STAT1cytoplasm +STAT1_STAT1cytoplasm -> STAT1_STAT1nucleus_p1 +$CASP6_Activator:true +$CD40:External_Activator +External_Activator -> CD40 +$CD40LG:true +$GBP1gene:(IRF2 | IRF1_IRF1nucleus) +IRF2 -> GBP1gene +IRF1_IRF1nucleus -> GBP1gene +$CCL5gene:IRF1_IRF1nucleus +IRF1_IRF1nucleus -> CCL5gene +$PMAIPgene:IRF5_IRF5nucleus +IRF5_IRF5nucleus -> PMAIPgene +$IFNAgene:(((((((IRF3_IRF5nucleus | IRF5_IRF5nucleus) | IRF7_IRF7nucleus) | ISGF3nucleus) | IRF3_IRF3nucleus) | IRF1_IRF1nucleus) | IRF3_IRF7nucleus) | STAT1_STAT1_IRF9nucleus) +IRF5_IRF5nucleus -> IFNAgene +STAT1_STAT1_IRF9nucleus -> IFNAgene +IRF2 -|? IFNAgene +IRF3_IRF7nucleus -> IFNAgene +ISGF3nucleus -> IFNAgene +IRF3_IRF5nucleus -> IFNAgene +IRF3_IRF3nucleus -> IFNAgene +IRF7_IRF7nucleus -> IFNAgene +IRF1_IRF1nucleus -> IFNAgene +$IRF7_IRF7nucleus:IRF7_IRF7cytoplasm +IRF7_IRF7cytoplasm -> IRF7_IRF7nucleus +$IFNGR1:External_Activator +External_Activator -> IFNGR1 +$G1P3gene:IRF8 +IRF8 -> G1P3gene +$CFLARgene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> CFLARgene +$NOS2Agene:External_Activator +IRF2 -|? NOS2Agene +External_Activator -> NOS2Agene +$TNFRSF10Bgene:TP53nucleus +TP53nucleus -> TNFRSF10Bgene +$BCL2_BAX:(BCL2 & BAX) +BAX -> BCL2_BAX +BCL2 -> BCL2_BAX +$CASP1:(ProCASP1 & CASP4) +ProCASP1 -> CASP1 +CASP4 -> CASP1 +$IFIT1gene:IRF5_IRF5nucleus +IRF5_IRF5nucleus -> IFIT1gene +$BCL2A1gene:RELAp65_NFBK1p50nucleus +RELAp65_NFBK1p50nucleus -> BCL2A1gene +$IRF2_Activator:true +$STAT1gene:IRF1_IRF1nucleus +IRF1_IRF1nucleus -> STAT1gene +$IFNG:true +$CASP7_Activator:true +$IL1Bgene:(IRF8 & SPI1) +SPI1 -> IL1Bgene +IRF8 -> IL1Bgene diff --git a/data/benchmarks/nsp4/metadata.txt b/data/benchmarks/nsp4/metadata.txt new file mode 100644 index 00000000..7aab86c4 --- /dev/null +++ b/data/benchmarks/nsp4/metadata.txt @@ -0,0 +1,2 @@ +Publication: https://doi.org/10.1038/s41597-020-0477-8 +Source: https://git-r3lab.uni.lu/covid/models/-/blob/4ed915a55687f626f9e7b3d4ada249cbaa5945b8/Executable%20Modules/SBML_qual_build/sbml/Nsp4_Nsp6_stable.sbml diff --git a/data/benchmarks/nsp4/model_concrete.aeon b/data/benchmarks/nsp4/model_concrete.aeon new file mode 100644 index 00000000..d6469cb6 --- /dev/null +++ b/data/benchmarks/nsp4/model_concrete.aeon @@ -0,0 +1,122 @@ +$sa160_Nsp3_____rna:sa219_Nsp3_____rna +sa219_Nsp3_____rna -> sa160_Nsp3_____rna +$Nsp3:sa160_Nsp3_____rna +sa160_Nsp3_____rna -> Nsp3 +$Nsp3_Nsp4_Nsp6_complex:(Nsp3 & (Nsp4 & Nsp6)) +Nsp3 -> Nsp3_Nsp4_Nsp6_complex +Nsp6 -> Nsp3_Nsp4_Nsp6_complex +Nsp4 -> Nsp3_Nsp4_Nsp6_complex +$Nsp6:sa47_Nsp6_____rna +sa47_Nsp6_____rna -> Nsp6 +$Nsp4:sa3_Nsp4_____rna +sa3_Nsp4_____rna -> Nsp4 +$sa47_Nsp6_____rna:sa218_Nsp6_____rna +sa218_Nsp6_____rna -> sa47_Nsp6_____rna +$sa3_Nsp4_____rna:sa220_Nsp4_____rna +sa220_Nsp4_____rna -> sa3_Nsp4_____rna +$csa15_Nsp4_ALG11_complex_endoplasmic_reticulum:(Nsp4 & sa14_ALG11_endoplasmic_reticulum) +Nsp4 -> csa15_Nsp4_ALG11_complex_endoplasmic_reticulum +sa14_ALG11_endoplasmic_reticulum -> csa15_Nsp4_ALG11_complex_endoplasmic_reticulum +$sa14_ALG11_endoplasmic_reticulum:false +$csa2_Nsp4_IDE_complex_cell:(Nsp4 & sa8_IDE_cell) +Nsp4 -> csa2_Nsp4_IDE_complex_cell +sa8_IDE_cell -> csa2_Nsp4_IDE_complex_cell +$sa8_IDE_cell:false +$Nsp4_IDE_complex:csa2_Nsp4_IDE_complex_cell +csa2_Nsp4_IDE_complex_cell -> Nsp4_IDE_complex +$Nsp4_DNAJC11_complex:(DNAJC11 & Nsp4) +Nsp4 -> Nsp4_DNAJC11_complex +DNAJC11 -> Nsp4_DNAJC11_complex +$DNAJC11:false +$F_ATPase_Nsp6_complex:(F_ATPase_complex & Nsp6) +Nsp6 -> F_ATPase_Nsp6_complex +F_ATPase_complex -> F_ATPase_Nsp6_complex +$F_ATPase_complex:false +$Nsp4_NUP210_complex_endoplasmic_reticulum:(NUP210_endoplasmic_reticulum & Nsp4) +Nsp4 -> Nsp4_NUP210_complex_endoplasmic_reticulum +NUP210_endoplasmic_reticulum -> Nsp4_NUP210_complex_endoplasmic_reticulum +$NUP210_endoplasmic_reticulum:false +$Nsp4_NUP210_complex_nucleus:Nsp4_NUP210_complex_endoplasmic_reticulum +Nsp4_NUP210_complex_endoplasmic_reticulum -> Nsp4_NUP210_complex_nucleus +$Several_drugs_drug:false +$SIGMAR1_Drugs_complex:(SIGMAR1_endoplasmic_reticulum & Several_drugs_drug) +Several_drugs_drug -> SIGMAR1_Drugs_complex +SIGMAR1_endoplasmic_reticulum -> SIGMAR1_Drugs_complex +$SIGMAR1_endoplasmic_reticulum:false +$Nsp6_SIGMAR1_complex_endoplasmic_reticulum:(Nsp6 & SIGMAR1_endoplasmic_reticulum) +Nsp6 -> Nsp6_SIGMAR1_complex_endoplasmic_reticulum +SIGMAR1_endoplasmic_reticulum -> Nsp6_SIGMAR1_complex_endoplasmic_reticulum +$Nsp6_SIGMAR1_complex_nucleus:Nsp6_SIGMAR1_complex_endoplasmic_reticulum +Nsp6_SIGMAR1_complex_endoplasmic_reticulum -> Nsp6_SIGMAR1_complex_nucleus +$V_ATPase_Nsp6_complex_endoplasmic_reticulum:(Nsp6 & V_ATPase_complex_endoplasmic_reticulum) +Nsp6 -> V_ATPase_Nsp6_complex_endoplasmic_reticulum +V_ATPase_complex_endoplasmic_reticulum -> V_ATPase_Nsp6_complex_endoplasmic_reticulum +$V_ATPase_complex_endoplasmic_reticulum:(ATP6AP1 & V_type_space_proton_space_ATPase_complex) +V_type_space_proton_space_ATPase_complex -> V_ATPase_complex_endoplasmic_reticulum +ATP6AP1 -> V_ATPase_complex_endoplasmic_reticulum +$V_ATPase_Nsp6_complex_endosome:V_ATPase_Nsp6_complex_endoplasmic_reticulum +V_ATPase_Nsp6_complex_endoplasmic_reticulum -> V_ATPase_Nsp6_complex_endosome +$TIM_complex_Nsp4_complex:(Nsp4 & TOM_complex_complex) +Nsp4 -> TIM_complex_Nsp4_complex +TOM_complex_complex -> TIM_complex_Nsp4_complex +$TOM_complex_complex:false +$V_type_space_proton_space_ATPase_complex:false +$ATP6AP1:false +$NUP210_Selinexor_complex:(NUP210_endoplasmic_reticulum & Selinexor_drug) +NUP210_endoplasmic_reticulum -> NUP210_Selinexor_complex +Selinexor_drug -> NUP210_Selinexor_complex +$Selinexor_drug:false +$P_ATPase_Nsp6_complex:(Nsp6 & P_ATPase_complex) +Nsp6 -> P_ATPase_Nsp6_complex +P_ATPase_complex -> P_ATPase_Nsp6_complex +$P_ATPase_complex:false +$csa4_Nsp4_IDE_complex_cell:csa2_Nsp4_IDE_complex_cell +csa2_Nsp4_IDE_complex_cell -> csa4_Nsp4_IDE_complex_cell +$SLC6A15_Nsp6_complex:(Nsp6 & SLC6A15) +Nsp6 -> SLC6A15_Nsp6_complex +SLC6A15 -> SLC6A15_Nsp6_complex +$SLC6A15:false +$SLC6A15_Orf9c_complex:(Orf9c & SLC6A15) +SLC6A15 -> SLC6A15_Orf9c_complex +Orf9c -> SLC6A15_Orf9c_complex +$Orf9c:false +$SLC6A15_M_complex:(M & SLC6A15) +SLC6A15 -> SLC6A15_M_complex +M -> SLC6A15_M_complex +$M:false +$SLC6A15_Loratadine_complex:(Loratadine_drug & SLC6A15) +SLC6A15 -> SLC6A15_Loratadine_complex +Loratadine_drug -> SLC6A15_Loratadine_complex +$Loratadine_drug:false +$V_ATPase_complex_endosome:V_ATPase_complex_endoplasmic_reticulum +V_ATPase_complex_endoplasmic_reticulum -> V_ATPase_complex_endosome +$ATP6AP1_Bafilomycin_A1_complex:(ATP6AP1 & Bafilomycin_A1_drug) +ATP6AP1 -> ATP6AP1_Bafilomycin_A1_complex +Bafilomycin_A1_drug -> ATP6AP1_Bafilomycin_A1_complex +$Bafilomycin_A1_drug:false +$Nsp6_SIGMAR1_complex_cell:Nsp6_SIGMAR1_complex_endoplasmic_reticulum +Nsp6_SIGMAR1_complex_endoplasmic_reticulum -> Nsp6_SIGMAR1_complex_cell +$csa93_Nsp4_ALG11_complex_endoplasmic_reticulum:csa15_Nsp4_ALG11_complex_endoplasmic_reticulum +csa15_Nsp4_ALG11_complex_endoplasmic_reticulum -> csa93_Nsp4_ALG11_complex_endoplasmic_reticulum +$sa220_Nsp4_____rna:sa3_Nsp4_____rna +sa3_Nsp4_____rna -> sa220_Nsp4_____rna +$sa218_Nsp6_____rna:sa47_Nsp6_____rna +sa47_Nsp6_____rna -> sa218_Nsp6_____rna +$IDE_human_host:sa8_IDE_cell +sa8_IDE_cell -> IDE_human_host +$sa219_Nsp3_____rna:sa160_Nsp3_____rna +sa160_Nsp3_____rna -> sa219_Nsp3_____rna +$Plasma_membrane_organization_phenotype:Nsp3_Nsp4_Nsp6_complex +Nsp3_Nsp4_Nsp6_complex -> Plasma_membrane_organization_phenotype +$NUP210_nucleus:NUP210_endoplasmic_reticulum +NUP210_endoplasmic_reticulum -> NUP210_nucleus +$sa225_IDE_cell:sa8_IDE_cell +sa8_IDE_cell -> sa225_IDE_cell +$SIGMAR1_nucleus:SIGMAR1_endoplasmic_reticulum +SIGMAR1_endoplasmic_reticulum -> SIGMAR1_nucleus +$SIGMAR1_cell:SIGMAR1_endoplasmic_reticulum +SIGMAR1_endoplasmic_reticulum -> SIGMAR1_cell +$sa230_ALG11_endoplasmic_reticulum:sa14_ALG11_endoplasmic_reticulum +sa14_ALG11_endoplasmic_reticulum -> sa230_ALG11_endoplasmic_reticulum +$H__ion:V_type_space_proton_space_ATPase_complex +V_type_space_proton_space_ATPase_complex -> H__ion diff --git a/data/synthetic_cases/nsp4_dataset.csv b/data/benchmarks/nsp4/nsp4_dataset.csv similarity index 100% rename from data/synthetic_cases/nsp4_dataset.csv rename to data/benchmarks/nsp4/nsp4_dataset.csv diff --git a/data/synthetic_cases/nsp4-sketch.aeon b/data/benchmarks/nsp4/nsp4_sketch.aeon similarity index 100% rename from data/synthetic_cases/nsp4-sketch.aeon rename to data/benchmarks/nsp4/nsp4_sketch.aeon diff --git a/data/benchmarks/output_eval.txt b/data/benchmarks/output_eval.txt new file mode 100644 index 0000000000000000000000000000000000000000..60e779154949543bd2dec3d29fd3966cf30a5244 GIT binary patch literal 4260 zcmcgvYi`p(7@Xfo+`%V6e#CZ+1QJx0sGtE+dVt_0C6b*)4XxD612g+MO~A!*YRg(V zws*bXYi4IRzkj_&y?HppXI$b7F7OHG@bDGaxWYF+y=UJ9@7Qy}kt@8!3x2&ui4B%0 zFvU;a*I4n}yy`D7XYU*{_HA*;{+w@Hwguk`wgt;-dXp;}m#j#)%x18_s zx~JuW5t{uKZrH2X9(dpIt2KWWxqR-UOpv-3GUBAA=P5H6A612?{ca!g%n!UG1ror)&2dAgnahFt$9^b)nQ5RUF=#NPT`iS*PdA+Vq!ZUoLgf5 z7#Z4}-nh`jJVnyCzhm6nBh`f=hpM)sLTsvvJ(tO+GcF`b zn$lL-s&`kr9a4Sq zO=pjMP<@k5XkQBX8@6Vh5cgfhgMpbRO%dP4E5lkCBo*>8M*=q{CfLgBzUMXRTu8nt z8mma3UYpgfj$2s)?g9y@{WS$|8*EUF#=eTpCp@c5W~Y z=p&+L{{D+{7ls|~*d@=Vd36H+!RH%txQp#m*{doGX;oD$9yuP{nX3(xg_N;B9hk}D zue4M#`;0o_uT(ZBd$mJ|-BLQOG28FOd1>>>>>>>>> COMPILE RUST BINARIES", flush=True) +try: + subprocess.run(["cargo", "build", "--release", "--bin", "run-inference"], cwd=SOURCE_DIR, check=True) + print("Compilation completed successfully.\n", flush=True) +except subprocess.CalledProcessError as e: + print(f"Error during Rust compilation: {e}", file=sys.stderr, flush=True) + sys.exit(1) + +# Step 2: Run benchmarks +print(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>", flush=True) +print(">>>>>>>>>> START BENCHMARKS RUN", flush=True) +print(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", flush=True) + +for model in MODELS: + print("==========================", flush=True) + print(f"Model {model}", flush=True) + print("==========================\n", flush=True) + + model_dir = BENCH_DIR / model + aeon_file = model_dir / f"{model}_sketch.aeon" + + if not aeon_file.exists(): + print(f"File not found: {aeon_file}", file=sys.stderr, flush=True) + continue + + try: + subprocess.run([str(SOURCE_DIR / "target/release/run-inference"), str(aeon_file)], check=True) + except FileNotFoundError: + print(f"Executable not found: {SOURCE_DIR / 'target/release/run-inference'}", file=sys.stderr, flush=True) + except subprocess.CalledProcessError as e: + print(f"Error running inference for {model}: {e}", file=sys.stderr, flush=True) diff --git a/src-tauri/Cargo.toml b/src-tauri/Cargo.toml index 0e3ccfeb..3486a32f 100644 --- a/src-tauri/Cargo.toml +++ b/src-tauri/Cargo.toml @@ -11,11 +11,16 @@ readme = "README.md" [build-dependencies] tauri-build = { version = "1.5", features = [] } +[[bin]] +name = "run-inference" +path = "src/bin/run_inference.rs" + [dependencies] biodivine-lib-bdd = ">=0.5.22, <1.0.0" biodivine-lib-param-bn = ">=0.5.13, <1.0.0" biodivine-hctl-model-checker = ">=0.3.1, <1.0.0" chrono = "0.4.38" +clap = { version = "4.1.4", features = ["derive"] } csv = "1.3" lazy_static = "1.5.0" rand = "0.8.5" diff --git a/src-tauri/src/analysis/inference_solver.rs b/src-tauri/src/analysis/inference_solver.rs index 8577d8d5..fd8e35ef 100644 --- a/src-tauri/src/analysis/inference_solver.rs +++ b/src-tauri/src/analysis/inference_solver.rs @@ -480,9 +480,9 @@ impl InferenceSolver { Ok(()) } - /// Internal modular variant of the inference. You can choose which parts to select. + /// A modular variant of the inference. You can choose which parts to select. /// For example, you can only consider static properties, only dynamic properties, or all. - pub(crate) fn run_inference_modular( + pub fn run_inference_modular( &mut self, analysis_type: InferenceType, sketch: Sketch, diff --git a/src-tauri/src/analysis/mod.rs b/src-tauri/src/analysis/mod.rs index 25518b0e..8e9af294 100644 --- a/src-tauri/src/analysis/mod.rs +++ b/src-tauri/src/analysis/mod.rs @@ -2,6 +2,10 @@ pub mod analysis_state; /// Structures and utilities to track final results of inference. pub mod inference_results; +/// Structures and methods to run the whole inference process. +/// This module covers the general async workflow, the details regarding the actual +/// algorithms are in the module [crate::algorithms]. +pub mod inference_solver; /// Structures and utilities to track progress status of inference. pub mod inference_status; /// Enum with various supported analysis types. @@ -12,10 +16,6 @@ pub mod sampling_data; /// Utilities to sample and download networks. /// Some functionality is taken from our repository [biodivine-bn-classifier]. mod candidate_sampling; -/// Structures and methods to run the whole inference process. -/// This module covers the general async workflow, the details regarding the actual -/// algorithms are in the module [crate::algorithms]. -mod inference_solver; /// Utilities to download results. mod results_export; /// Utilities to explore canditate update functions. diff --git a/src-tauri/src/bin/run_inference.rs b/src-tauri/src/bin/run_inference.rs new file mode 100644 index 00000000..8dbf727f --- /dev/null +++ b/src-tauri/src/bin/run_inference.rs @@ -0,0 +1,60 @@ +use biodivine_sketchbook::analysis::inference_results::InferenceResults; +use biodivine_sketchbook::analysis::inference_solver::InferenceSolver; +use biodivine_sketchbook::analysis::inference_type::InferenceType; +use biodivine_sketchbook::logging; +use biodivine_sketchbook::sketchbook::Sketch; + +use clap::Parser; +use std::fs::File; +use std::io::Read; +use std::sync::mpsc; +use std::sync::mpsc::{Receiver, Sender}; + +/// Structure to collect CLI arguments +#[derive(Parser)] +#[clap( + author = "Ondřej Huvar", + about = "Run the inference of BNs from predefined sketch." +)] + +struct Arguments { + /// Path to a file with a model in aeon sketch format. + model_path: String, +} + +/// Wrapper to create an inference solver, run the inference on a given sketch, and return results. +pub fn get_inference_results(sketch: &Sketch) -> InferenceResults { + let (send_channel, rec_channel): (Sender, Receiver) = mpsc::channel(); + let mut solver = InferenceSolver::new(send_channel); + let results = + solver.run_inference_modular(InferenceType::FullInference, sketch.clone(), true, true); + loop { + if rec_channel.try_recv().is_err() { + break; + } + } + results.expect("The computation was not successful.") +} + +fn main() { + let args = Arguments::parse(); + // we disable logging since it would only overflow the output + logging::disable_logging(); + + // load the sketch + let mut sketch_file = + File::open(args.model_path.as_str()).expect("Provided file does not exist."); + let mut file_contents = String::new(); + sketch_file + .read_to_string(&mut file_contents) + .expect("Error reading provided file."); + let sketch = Sketch::from_aeon(&file_contents).expect("Error parsing the sketch."); + + let inference_results = get_inference_results(&sketch); + println!( + "Number of candidates: {}", + inference_results.num_sat_networks + ); + println!("Computation time: {}ms", inference_results.comp_time); + println!("{}", inference_results.summary_message); +} diff --git a/src-tauri/src/logging.rs b/src-tauri/src/logging.rs index 06698902..e13ed310 100644 --- a/src-tauri/src/logging.rs +++ b/src-tauri/src/logging.rs @@ -1,3 +1,21 @@ +use lazy_static::lazy_static; +use std::sync::atomic::{AtomicBool, Ordering}; + +// Logging enabled by default +lazy_static! { + static ref LOGGING_ENABLED: AtomicBool = AtomicBool::new(true); +} + +/// Check if logging is enabled. +pub fn is_logging_enabled() -> bool { + LOGGING_ENABLED.load(Ordering::SeqCst) +} + +/// Disable logging. +pub fn disable_logging() { + LOGGING_ENABLED.store(false, Ordering::SeqCst); +} + pub const DEBUG: u8 = 0; pub const INFO: u8 = 8; pub const WARNING: u8 = 16; @@ -23,9 +41,11 @@ pub const ERROR: u8 = 32; /// such log output. #[macro_export] macro_rules! log { - ($severity:tt,$($arg:tt)*) => {{ - print!("[level:{}][{}:{}] ", $severity, file!(), line!()); - println!($($arg)*); + ($severity:tt, $($arg:tt)*) => {{ + if $crate::logging::is_logging_enabled() { + print!("[level:{}][{}:{}] ", $severity, file!(), line!()); + println!($($arg)*); + } }}; }