Add benchmarks and scripts to run them.

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`.

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

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

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

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)

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