From 738e6ad7b87b046bd9b1a16d7287f920831f9ff0 Mon Sep 17 00:00:00 2001 From: Markta Opichalov Date: Sun, 24 Nov 2024 20:58:20 +0100 Subject: [PATCH 1/3] galaxy tools scripts for ebcsgen relocated --- Galaxy/tools/ebcsgen/.shed.yml | 57 + .../ebcsgen/ebcsgen_ctl_model_checking.py | 33 + .../ebcsgen/ebcsgen_ctl_model_checking.xml | 42 + Galaxy/tools/ebcsgen/ebcsgen_generate_ts.py | 43 + Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml | 58 + .../ebcsgen/ebcsgen_pctl_model_checking.py | 33 + .../ebcsgen/ebcsgen_pctl_model_checking.xml | 41 + .../ebcsgen_pctl_parameter_synthesis.py | 62 + .../ebcsgen_pctl_parameter_synthesis.xml | 78 ++ Galaxy/tools/ebcsgen/ebcsgen_sbml_export.py | 30 + Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml | 41 + Galaxy/tools/ebcsgen/ebcsgen_simulate.py | 51 + Galaxy/tools/ebcsgen/ebcsgen_simulate.xml | 96 ++ .../tools/ebcsgen/ebcsgen_static_analysis.py | 54 + .../tools/ebcsgen/ebcsgen_static_analysis.xml | 73 ++ Galaxy/tools/ebcsgen/macros.xml | 17 + .../ebcsgen/test-data/parametrised.bcsl.ts | 430 +++++++ .../test-data/pctl_model_checking.bcsl.ts | 75 ++ .../test-data/pctl_syntheisis_regions.csv | 941 ++++++++++++++++ .../ebcsgen/test-data/reduced.bcsl.model | 7 + .../ebcsgen/test-data/redundant.bcsl.model | 8 + .../test-data/repressilator.bcsl.model | 15 + .../tools/ebcsgen/test-data/simple.bcsl.model | 7 + Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts | 98 ++ .../ebcsgen/test-data/simulation_determ.csv | 1002 +++++++++++++++++ 25 files changed, 3392 insertions(+) create mode 100644 Galaxy/tools/ebcsgen/.shed.yml create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.py create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.xml create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_generate_ts.py create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.py create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.xml create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.py create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.xml create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_sbml_export.py create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_simulate.py create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_simulate.xml create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_static_analysis.py create mode 100644 Galaxy/tools/ebcsgen/ebcsgen_static_analysis.xml create mode 100644 Galaxy/tools/ebcsgen/macros.xml create mode 100644 Galaxy/tools/ebcsgen/test-data/parametrised.bcsl.ts create mode 100644 Galaxy/tools/ebcsgen/test-data/pctl_model_checking.bcsl.ts create mode 100644 Galaxy/tools/ebcsgen/test-data/pctl_syntheisis_regions.csv create mode 100644 Galaxy/tools/ebcsgen/test-data/reduced.bcsl.model create mode 100644 Galaxy/tools/ebcsgen/test-data/redundant.bcsl.model create mode 100644 Galaxy/tools/ebcsgen/test-data/repressilator.bcsl.model create mode 100644 Galaxy/tools/ebcsgen/test-data/simple.bcsl.model create mode 100644 Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts create mode 100644 Galaxy/tools/ebcsgen/test-data/simulation_determ.csv diff --git a/Galaxy/tools/ebcsgen/.shed.yml b/Galaxy/tools/ebcsgen/.shed.yml new file mode 100644 index 0000000..60166cf --- /dev/null +++ b/Galaxy/tools/ebcsgen/.shed.yml @@ -0,0 +1,57 @@ +owner: sybila +remote_repository_url: "https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen" +homepage_url: "https://github.com/sybila/eBCSgen" +categories: + - Systems Biology +repositories: + ebcsgen_generate_transition_system: + description: "Generate transition system of the given BCSL model." + include: + - ebcsgen_generate_ts.xml + - ebcsgen_generate_ts.py + - test-data/simple.bcsl.model + - macros.xml + ebcsgen_pctl_model_checking: + description: "Explicit PCTL model checking of given transition system." + include: + - ebcsgen_pctl_model_checking.xml + - ebcsgen_pctl_model_checking.py + - test-data/pctl_model_checking.bcsl.ts + - macros.xml + ebcsgen_simulation: + description: "Simulation of the given BCSL model." + include: + - ebcsgen_simulate.xml + - ebcsgen_simulate.py + - test-data/repressilator.bcsl.model + - test-data/simulation_determ.csv + - macros.xml + ebcsgen_ctl_model_checking: + description: "Explicit CTL model checking of given transition system." + include: + - ebcsgen_ctl_model_checking.xml + - ebcsgen_ctl_model_checking.py + - test-data/simple.bcsl.ts + - macros.xml + ebcsgen_pctl_parameter_synthesis: + description: "PCTL parameter synthesis of given parametric transition system." + include: + - ebcsgen_pctl_parameter_synthesis.xml + - ebcsgen_pctl_parameter_synthesis.py + - test-data/parametrised.bcsl.ts + - macros.xml + ebcsgen_sbml_export: + description: "Export given BCSL model to SBML with usage of SBML-multi package." + include: + - ebcsgen_sbml_export.xml + - ebcsgen_sbml_export.py + - test-data/simple.bcsl.model + - macros.xml + ebcsgen_static_analysis: + description: "Run static analysis techniques on given BCSL model." + include: + - ebcsgen_static_analysis.xml + - ebcsgen_static_analysis.py + - test-data/redundant.bcsl.model + - test-data/reduced.bcsl.model + - macros.xml diff --git a/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.py b/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.py new file mode 100644 index 0000000..74c8cfe --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.py @@ -0,0 +1,33 @@ +import argparse + +from eBCSgen.Analysis.CTL import CTL +from eBCSgen.Errors.FormulaParsingError import FormulaParsingError +from eBCSgen.Errors.InvalidInputError import InvalidInputError +from eBCSgen.Parsing.ParseBCSL import load_TS_from_json +from eBCSgen.Parsing.ParseCTLformula import CTLparser + +args_parser = argparse.ArgumentParser(description='Model checking') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') + +required.add_argument('--transition_file', required=True) +required.add_argument('--output', type=str, required=True) +required.add_argument('--formula', type=str, required=True) + +args = args_parser.parse_args() + +ts = load_TS_from_json(args.transition_file) + +if len(ts.params) != 0: + raise InvalidInputError("Provided transition system is parametrised - model checking cannot be executed.") + +formula = CTLparser().parse(args.formula) +if formula.success: + result, states = CTL.model_checking(ts, formula) + output = 'Result: {}\nNumber of satisfying states: {}'.format(result, len(states)) + f = open(args.output, "w") + f.write(output) + f.close() +else: + raise FormulaParsingError(formula.data, args.formula) diff --git a/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.xml b/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.xml new file mode 100644 index 0000000..ec1b92a --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.xml @@ -0,0 +1,42 @@ + + - explicit CTL model checking of transition system + + macros.xml + + + + sybila/ebcsgen:v@TOOL_VERSION@ + + + + python3 ${__tool_directory__}/ebcsgen_ctl_model_checking.py + --transition_file '$transition_file' + --formula '$formula' + --output '$output' + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.py b/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.py new file mode 100644 index 0000000..55ee60a --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.py @@ -0,0 +1,43 @@ +import argparse + +from eBCSgen.Errors.ModelParsingError import ModelParsingError +from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError +from eBCSgen.Parsing.ParseBCSL import Parser + +import numpy as np + + +args_parser = argparse.ArgumentParser(description='Transition system generating') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') +optional = args_parser.add_argument_group('optional arguments') + +required.add_argument('--model', type=str, required=True) +required.add_argument('--output', type=str, required=True) +required.add_argument('--direct', required=True) + +optional.add_argument('--max_time', type=float, default=np.inf) +optional.add_argument('--max_size', type=float, default=np.inf) +optional.add_argument('--bound', type=int, default=None) + +args = args_parser.parse_args() + +model_parser = Parser("model") +model_str = open(args.model, "r").read() + +model = model_parser.parse(model_str) +if model.success: + if eval(args.direct): + ts = model.data.generate_direct_transition_system(args.max_time, + args.max_size, + args.bound) + ts.change_to_vector_backend() + else: + vm = model.data.to_vector_model(args.bound) + ts = vm.generate_transition_system(None, args.max_time, args.max_size) + ts.save_to_json(args.output, model.data.params) +else: + if "error" in model.data: + raise UnspecifiedParsingError(model.data["error"]) + raise ModelParsingError(model.data, model_str) diff --git a/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml b/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml new file mode 100644 index 0000000..62e8748 --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml @@ -0,0 +1,58 @@ + + - generate transition system of the given model + + macros.xml + + + + sybila/ebcsgen:v@TOOL_VERSION@ + + + python3 ${__tool_directory__}/ebcsgen_generate_ts.py + --model '$model' + --output '$output' + --direct '$network_free_choice' + #if $adv.bound != "": + --bound '$adv.bound' + #end if + #if $adv.max_time != "": + --max_time '$adv.max_time' + #end if + #if $adv.max_size != "": + --max_size '$adv.max_size' + #end if + + + + + + + + +
+ + + +
+
+ + + + + + + + + + + + + + + + + + + +
diff --git a/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.py b/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.py new file mode 100644 index 0000000..66629bf --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.py @@ -0,0 +1,33 @@ +import argparse + +from eBCSgen.Analysis.PCTL import PCTL +from eBCSgen.Errors.FormulaParsingError import FormulaParsingError +from eBCSgen.Errors.InvalidInputError import InvalidInputError +from eBCSgen.Parsing.ParseBCSL import load_TS_from_json +from eBCSgen.Parsing.ParsePCTLformula import PCTLparser + + +args_parser = argparse.ArgumentParser(description='Model checking') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') + +required.add_argument('--transition_file', required=True) +required.add_argument('--output', type=str, required=True) +required.add_argument('--formula', type=str, required=True) + +args = args_parser.parse_args() + +ts = load_TS_from_json(args.transition_file) + +if len(ts.params) != 0: + raise InvalidInputError("Provided transition system is parametrised - model checking cannot be executed.") + +formula = PCTLparser().parse(args.formula) +if formula.success: + result = PCTL.model_checking(ts, formula) + f = open(args.output, "w") + f.write(result.decode("utf-8")) + f.close() +else: + raise FormulaParsingError(formula.data, args.formula) diff --git a/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.xml b/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.xml new file mode 100644 index 0000000..e96fbb2 --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.xml @@ -0,0 +1,41 @@ + + - explicit PCTL model checking of transition system + + macros.xml + + + + sybila/ebcsgen:v@TOOL_VERSION@ + + + + python3 ${__tool_directory__}/ebcsgen_pctl_model_checking.py + --transition_file '$transition_file' + --output '$output' + --formula '$formula' + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.py b/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.py new file mode 100644 index 0000000..0996d78 --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.py @@ -0,0 +1,62 @@ +import argparse + +from eBCSgen.Analysis.PCTL import PCTL +from eBCSgen.Errors.FormulaParsingError import FormulaParsingError +from eBCSgen.Errors.InvalidInputError import InvalidInputError +from eBCSgen.Parsing.ParseBCSL import load_TS_from_json +from eBCSgen.Parsing.ParsePCTLformula import PCTLparser + + +class FakeFile: + def __init__(self, content): + self.content = content.decode("utf-8") + + def read(self): + return self.content + + +args_parser = argparse.ArgumentParser(description='Parameter synthesis') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') +optional = args_parser.add_argument_group('optional arguments') + +required.add_argument('--transition_file', required=True) +required.add_argument('--output', type=str, required=True) +required.add_argument('--formula', type=str, required=True) +optional.add_argument('--region', type=str) + +args = args_parser.parse_args() + +if args.region: + region = args.region.replace("=", "<=") +else: + region = None + +ts = load_TS_from_json(args.transition_file) + +if len(ts.params) == 0: + raise InvalidInputError("Provided model is not parametrised - parameter synthesis cannot be executed.") + +if "?" not in args.formula: + if not region: + params = set() + else: + params = {param.split("<=")[1] for param in region.split(",")} + + undefined = set(ts.params) - params + if undefined: + raise InvalidInputError("Intervals undefined for parameters: {}.".format(", ".join(undefined))) + +formula = PCTLparser().parse(args.formula) +if formula.success: + result = PCTL.parameter_synthesis(ts, formula, region) + if "?" not in args.formula: + result = FakeFile(result) + df = PCTL.process_output(result) + df.to_csv(args.output, index=False) + else: + with open(args.output, "w") as f: + f.write(result.decode("utf-8")) +else: + raise FormulaParsingError(formula.data, args.formula) diff --git a/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.xml b/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.xml new file mode 100644 index 0000000..96d7498 --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.xml @@ -0,0 +1,78 @@ + + - PCTL parameter synthesis of given parametric transition system + + macros.xml + + + + sybila/ebcsgen:v@TOOL_VERSION@ + + + + python3 ${__tool_directory__}/ebcsgen_pctl_parameter_synthesis.py + --transition_file '$transition_file' + #if len($regions) > 0: + --output '$output_regions' + #else: + --output '$output_sample' + #end if + --formula '$formula' + + #set parameters = ",".join([str($s.from) + "=" + str($s.param) + "=" + str($s.to) for $s in $regions]) + #if $parameters: + --region '$parameters' + #end if + + + + + + + + + + + + + + + + + + + + "?" not in formula + + + "?" in formula + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.py b/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.py new file mode 100644 index 0000000..a7639d8 --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.py @@ -0,0 +1,30 @@ +import argparse + +from eBCSgen.Errors.ModelParsingError import ModelParsingError +from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError +from eBCSgen.Parsing.ParseBCSL import Parser + +import libsbml + + +args_parser = argparse.ArgumentParser(description='Export SBML model with usage of SBML-multi package') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') + +required.add_argument('--model', type=str, required=True) +required.add_argument('--output', type=str, required=True) + +args = args_parser.parse_args() + +model_parser = Parser("model") +model_str = open(args.model, "r").read() + +model = model_parser.parse(model_str) +if model.success: + document = model.data.export_sbml() + libsbml.writeSBMLToFile(document, args.output) +else: + if "error" in model.data: + raise UnspecifiedParsingError(model.data["error"]) + raise ModelParsingError(model.data, model_str) diff --git a/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml b/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml new file mode 100644 index 0000000..b9707e0 --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml @@ -0,0 +1,41 @@ + + - export given BCSL model to SBML employing multi package + + macros.xml + + + + sybila/ebcsgen:v@TOOL_VERSION@ + + + + python3 ${__tool_directory__}/ebcsgen_sbml_export.py + --model '$model' + --output '$output' + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Galaxy/tools/ebcsgen/ebcsgen_simulate.py b/Galaxy/tools/ebcsgen/ebcsgen_simulate.py new file mode 100644 index 0000000..bb42ac3 --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_simulate.py @@ -0,0 +1,51 @@ +import argparse + +from eBCSgen.Errors import UnspecifiedParsingError +from eBCSgen.Errors.InvalidInputError import InvalidInputError +from eBCSgen.Errors.ModelParsingError import ModelParsingError +from eBCSgen.Errors.RatesNotSpecifiedError import RatesNotSpecifiedError +from eBCSgen.Parsing.ParseBCSL import Parser + + +args_parser = argparse.ArgumentParser(description='Simulation') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') + +required.add_argument('--model', type=str, required=True) +required.add_argument('--output', type=str, required=True) +required.add_argument('--deterministic', required=True) +required.add_argument('--direct', required=True) +required.add_argument('--runs', type=int, required=True) +required.add_argument('--max_time', type=float, required=True) +required.add_argument('--volume', type=float, required=True) +required.add_argument('--step', type=float, required=True) + +args = args_parser.parse_args() + +model_parser = Parser("model") +model_str = open(args.model, "r").read() + +model = model_parser.parse(model_str) + +if model.success: + if len(model.data.params) != 0: + raise InvalidInputError("Provided model is parametrised - simulation cannot be executed.") + if not model.data.all_rates: + raise RatesNotSpecifiedError("Some rules do not have rates specified - simulation cannot be executed.") + + if eval(args.deterministic): + vm = model.data.to_vector_model() + df = vm.deterministic_simulation(args.max_time, args.volume, args.step) + else: + if eval(args.direct): + df = model.data.network_free_simulation(args.max_time) + else: + vm = model.data.to_vector_model() + df = vm.stochastic_simulation(args.max_time, args.runs) + + df.to_csv(args.output, index=None, header=True) +else: + if "error" in model.data: + raise UnspecifiedParsingError(model.data["error"]) + raise ModelParsingError(model.data, model_str) diff --git a/Galaxy/tools/ebcsgen/ebcsgen_simulate.xml b/Galaxy/tools/ebcsgen/ebcsgen_simulate.xml new file mode 100644 index 0000000..751a58f --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_simulate.xml @@ -0,0 +1,96 @@ + + - simulate given model + + macros.xml + + + + sybila/ebcsgen:v@TOOL_VERSION@ + + + python3 ${__tool_directory__}/ebcsgen_simulate.py + --model '$model' + --output '$output' + --deterministic '$type.deterministic_choice' + #if $type.deterministic_choice == "True": + --direct False + --runs 1 + --volume '$type.volume' + --step '$type.step' + #else: + --direct '$type.network_free_choice' + --runs '$type.num_of_runs' + --volume 1 + --step 0.01 + #end if + --max_time '$max_time' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + +
+ + +
+ + + +
+ + + + + + + +
+ + +
+ + + +
+ + + + + + + +
+
+
diff --git a/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.py b/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.py new file mode 100644 index 0000000..2425ddf --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.py @@ -0,0 +1,54 @@ +import argparse + +from eBCSgen.Errors.ComplexParsingError import ComplexParsingError +from eBCSgen.Errors.ModelParsingError import ModelParsingError +from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError +from eBCSgen.Parsing.ParseBCSL import Parser + + +def save_model(model, filename): + f = open(filename, "w") + f.write(repr(model)) + f.close() + + +args_parser = argparse.ArgumentParser(description='Static analysis') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') +optional = args_parser.add_argument_group('optional arguments') + +required.add_argument('--model', type=str, required=True) +required.add_argument('--output', type=str, required=True) +required.add_argument('--method', type=str, required=True) +optional.add_argument('--complex') + +args = args_parser.parse_args() + +model_parser = Parser("model") +model_str = open(args.model, "r").read() +model = model_parser.parse(model_str) + +if model.success: + if args.method == "reduce": + model.data.reduce_context() + save_model(model.data, args.output) + elif args.method == "eliminate": + model.data.eliminate_redundant() + save_model(model.data, args.output) + else: + complex_parser = Parser("rate_complex") + complex = complex_parser.parse(args.complex) + if complex.success: + result = model.data.static_non_reachability(complex.data.children[0]) + f = open(args.output, "w") + s = "can possibly" if result else "cannot" + message = "The given agent\n\t{}\n{} be reached in the model.".format(complex.data.children[0], s) + f.write(message) + f.close() + else: + raise ComplexParsingError(complex.data, args.complex) +else: + if "error" in model.data: + raise UnspecifiedParsingError(model.data["error"]) + raise ModelParsingError(model.data, model_str) diff --git a/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.xml b/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.xml new file mode 100644 index 0000000..6d61ea7 --- /dev/null +++ b/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.xml @@ -0,0 +1,73 @@ + + - run static analysis techniques on given BCSL model + + macros.xml + + + + sybila/ebcsgen:v@TOOL_VERSION@ + + + + python3 ${__tool_directory__}/ebcsgen_static_analysis.py + --model '$model' + --output '$output' + --method '$Method.method' + #if $Method.method == "reach": + --complex '$Method.complex' + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Galaxy/tools/ebcsgen/macros.xml b/Galaxy/tools/ebcsgen/macros.xml new file mode 100644 index 0000000..4f2b643 --- /dev/null +++ b/Galaxy/tools/ebcsgen/macros.xml @@ -0,0 +1,17 @@ + + 2.1.0 + + + + + + + + diff --git a/Galaxy/tools/ebcsgen/test-data/parametrised.bcsl.ts b/Galaxy/tools/ebcsgen/test-data/parametrised.bcsl.ts new file mode 100644 index 0000000..068ae6e --- /dev/null +++ b/Galaxy/tools/ebcsgen/test-data/parametrised.bcsl.ts @@ -0,0 +1,430 @@ +{ + "bound": 1, + "parameters": [ + "param_sig", + "param_block" + ], + "nodes": { + "1": "(0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0)", + "2": "(0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1)", + "3": "(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0)", + "4": "(0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0)", + "5": "(0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0)", + "6": "(0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0)", + "7": "(0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0)", + "8": "(0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0)", + "9": "(0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1)", + "10": 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0.6, + "t": 6 + }, + { + "s": 28, + "p": "(0.4)/(1.0*param_sig + 0.55)", + "t": 14 + } + ] +} \ No newline at end of file diff --git a/Galaxy/tools/ebcsgen/test-data/pctl_model_checking.bcsl.ts b/Galaxy/tools/ebcsgen/test-data/pctl_model_checking.bcsl.ts new file mode 100644 index 0000000..2887b17 --- /dev/null +++ b/Galaxy/tools/ebcsgen/test-data/pctl_model_checking.bcsl.ts @@ -0,0 +1,75 @@ +{ + "nodes": { + "1": "(inf, inf, inf)", + "2": "(1, 2, 0)", + "3": "(0, 1, 0)", + "4": "(0, 2, 0)", + "5": "(2, 1, 0)", + "6": "(2, 2, 0)", + "7": "(1, 1, 0)" + }, + "edges": [ + { + "s": 7, + "t": 3, + "p": 0.8 + }, + { + "s": 3, + "t": 4, + "p": 1.0 + }, + { + "s": 5, + "t": 7, + "p": 0.9855072463768116 + }, + { + "s": 1, + "t": 1, + "p": 1 + }, + { + "s": 2, + "t": 1, + "p": 0.2 + }, + { + "s": 5, + "t": 6, + "p": 0.014492753623188406 + }, + { + "s": 6, + "t": 1, + "p": 0.014492753623188406 + }, + { + "s": 6, + "t": 2, + "p": 0.9855072463768116 + }, + { + "s": 4, + "t": 1, + "p": 1.0 + }, + { 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+387/1280,1567/5120,1501/2560,753/1280,Unknown +1567/5120,793/2560,1501/2560,753/1280,Unknown diff --git a/Galaxy/tools/ebcsgen/test-data/reduced.bcsl.model b/Galaxy/tools/ebcsgen/test-data/reduced.bcsl.model new file mode 100644 index 0000000..bfaa940 --- /dev/null +++ b/Galaxy/tools/ebcsgen/test-data/reduced.bcsl.model @@ -0,0 +1,7 @@ +#! rules +P()::cell => P()::out @ 1.0 + +#! inits +1 P()::cell + +#! definitions diff --git a/Galaxy/tools/ebcsgen/test-data/redundant.bcsl.model b/Galaxy/tools/ebcsgen/test-data/redundant.bcsl.model new file mode 100644 index 0000000..a90384a --- /dev/null +++ b/Galaxy/tools/ebcsgen/test-data/redundant.bcsl.model @@ -0,0 +1,8 @@ +#! rules +r1_S ~ P(S{i})::cell => P(S{a})::cell +r1_T ~ P(T{i})::cell => P(T{a})::cell +r2 ~ P()::cell => P()::out +r1_X ~ P(T{i})::cell => P(T{a})::cell + +#! inits +1 P(S{i},T{i})::cell \ No newline at end of file diff --git a/Galaxy/tools/ebcsgen/test-data/repressilator.bcsl.model b/Galaxy/tools/ebcsgen/test-data/repressilator.bcsl.model new file mode 100644 index 0000000..f4df1f9 --- /dev/null +++ b/Galaxy/tools/ebcsgen/test-data/repressilator.bcsl.model @@ -0,0 +1,15 @@ +#! rules +X()::rep => @ k1*[X()::rep] +Y()::rep => @ k2*[Y()::rep] +Z()::rep => @ k1*[Z()::rep] + => X()::rep @ 5**4/(5**4+[Z()::rep]**4) + => Y()::rep @ 5**4/(5**4+[X()::rep]**4) + => Z()::rep @ 5**4/(5**4+[Y()::rep]**4) + +#! inits +1 X()::rep +1 Y()::rep + +#! definitions +k1 = 0.05 +k2 = 0.12 diff --git a/Galaxy/tools/ebcsgen/test-data/simple.bcsl.model b/Galaxy/tools/ebcsgen/test-data/simple.bcsl.model new file mode 100644 index 0000000..b05d773 --- /dev/null +++ b/Galaxy/tools/ebcsgen/test-data/simple.bcsl.model @@ -0,0 +1,7 @@ +#! rules +r1_S ~ P(S{i})::cell => P(S{a})::cell +r1_T ~ P(T{i})::cell => P(T{a})::cell +r2 ~ P()::cell => P()::out + +#! inits +1 P(S{i},T{i})::cell \ No newline at end of file diff --git a/Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts b/Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts new file mode 100644 index 0000000..2c1b6f8 --- /dev/null +++ b/Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts @@ -0,0 +1,98 @@ +{ + "nodes": { + "1": "(0, 0, 0, 0, 0, 1, 0, 0)", + "2": "(0, 0, 1, 0, 0, 0, 0, 0)", + "3": "(1, 0, 0, 0, 0, 0, 0, 0)", + "4": "(0, 0, 0, 1, 0, 0, 0, 0)", + "5": "(0, 0, 0, 0, 0, 0, 1, 0)", + "6": "(0, 0, 0, 0, 0, 0, 0, 1)", + "7": "(0, 0, 0, 0, 1, 0, 0, 0)", + "8": "(0, 1, 0, 0, 0, 0, 0, 0)" + }, + "edges": [ + { + "s": 8, + "t": 8, + "p": 1, + "label": "\u03b5" + }, + { + "s": 3, + "t": 8, + "p": 1.0, + "label": "r2" + }, + { + "s": 5, + "t": 6, + "p": 0.3333333333333333, + "label": "r2" + }, + { + "s": 6, + "t": 6, + "p": 1, + "label": "\u03b5" + }, + { + "s": 2, + "t": 3, + "p": 0.5, + "label": "r1_T" + }, + { + "s": 7, + "t": 1, + "p": 0.5, + "label": "r2" + }, + { + "s": 5, + "t": 2, + "p": 0.3333333333333333, + "label": "r1_S" + }, + { + "s": 7, + "t": 3, + "p": 0.5, + "label": "r1_S" + }, + { + "s": 4, + 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+99.60000000000001,3.4521732785060646,6.952497334776885,6.490563276628219 +99.7,3.461002415678205,6.950485623255075,6.479252567391758 +99.80000000000001,3.469921672936583,6.948343092814243,6.468018137967923 +99.9,3.4789303599793704,6.9460691328601945,6.45686088366796 +100.0,3.4880277673576505,6.943663138605678,6.445781705157098 From d57c478a81e7943ccefbcd6d5a815e796f80c67b Mon Sep 17 00:00:00 2001 From: Markta Opichalov Date: Mon, 9 Dec 2024 07:11:10 +0100 Subject: [PATCH 2/3] removed all xml files and test data as per the feedback --- .../ebcsgen/ebcsgen_ctl_model_checking.xml | 42 - Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml | 58 - .../ebcsgen/ebcsgen_pctl_model_checking.xml | 41 - .../ebcsgen_pctl_parameter_synthesis.xml | 78 -- Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml | 41 - Galaxy/tools/ebcsgen/ebcsgen_simulate.xml | 96 -- .../tools/ebcsgen/ebcsgen_static_analysis.xml | 73 -- Galaxy/tools/ebcsgen/macros.xml | 17 - .../ebcsgen/test-data/parametrised.bcsl.ts | 430 ------- .../test-data/pctl_model_checking.bcsl.ts | 75 -- .../test-data/pctl_syntheisis_regions.csv | 941 ---------------- .../ebcsgen/test-data/reduced.bcsl.model | 7 - .../ebcsgen/test-data/redundant.bcsl.model | 8 - .../test-data/repressilator.bcsl.model | 15 - .../tools/ebcsgen/test-data/simple.bcsl.model | 7 - Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts | 98 -- .../ebcsgen/test-data/simulation_determ.csv | 1002 ----------------- 17 files changed, 3029 deletions(-) delete mode 100644 Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.xml delete mode 100644 Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml delete mode 100644 Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.xml delete mode 100644 Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.xml delete mode 100644 Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml delete mode 100644 Galaxy/tools/ebcsgen/ebcsgen_simulate.xml delete mode 100644 Galaxy/tools/ebcsgen/ebcsgen_static_analysis.xml delete mode 100644 Galaxy/tools/ebcsgen/macros.xml delete mode 100644 Galaxy/tools/ebcsgen/test-data/parametrised.bcsl.ts delete mode 100644 Galaxy/tools/ebcsgen/test-data/pctl_model_checking.bcsl.ts delete mode 100644 Galaxy/tools/ebcsgen/test-data/pctl_syntheisis_regions.csv delete mode 100644 Galaxy/tools/ebcsgen/test-data/reduced.bcsl.model delete mode 100644 Galaxy/tools/ebcsgen/test-data/redundant.bcsl.model delete mode 100644 Galaxy/tools/ebcsgen/test-data/repressilator.bcsl.model delete mode 100644 Galaxy/tools/ebcsgen/test-data/simple.bcsl.model delete mode 100644 Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts delete mode 100644 Galaxy/tools/ebcsgen/test-data/simulation_determ.csv diff --git a/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.xml b/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.xml deleted file mode 100644 index ec1b92a..0000000 --- a/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - explicit CTL model checking of transition system - - macros.xml - - - - sybila/ebcsgen:v@TOOL_VERSION@ - - - - python3 ${__tool_directory__}/ebcsgen_ctl_model_checking.py - --transition_file '$transition_file' - --formula '$formula' - --output '$output' - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml b/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml deleted file mode 100644 index 62e8748..0000000 --- a/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - generate transition system of the given model - - macros.xml - - - - sybila/ebcsgen:v@TOOL_VERSION@ - - - python3 ${__tool_directory__}/ebcsgen_generate_ts.py - --model '$model' - --output '$output' - --direct '$network_free_choice' - #if $adv.bound != "": - --bound '$adv.bound' - #end if - #if $adv.max_time != "": - --max_time '$adv.max_time' - #end if - #if $adv.max_size != "": - --max_size '$adv.max_size' - #end if - - - - - - - - -
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diff --git a/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.xml b/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.xml deleted file mode 100644 index e96fbb2..0000000 --- a/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.xml +++ /dev/null @@ -1,41 +0,0 @@ - - - explicit PCTL model checking of transition system - - macros.xml - - - - sybila/ebcsgen:v@TOOL_VERSION@ - - - - python3 ${__tool_directory__}/ebcsgen_pctl_model_checking.py - --transition_file '$transition_file' - --output '$output' - --formula '$formula' - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.xml b/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.xml deleted file mode 100644 index 96d7498..0000000 --- a/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.xml +++ /dev/null @@ -1,78 +0,0 @@ - - - PCTL parameter synthesis of given parametric transition system - - macros.xml - - - - sybila/ebcsgen:v@TOOL_VERSION@ - - - - python3 ${__tool_directory__}/ebcsgen_pctl_parameter_synthesis.py - --transition_file '$transition_file' - #if len($regions) > 0: - --output '$output_regions' - #else: - --output '$output_sample' - #end if - --formula '$formula' - - #set parameters = ",".join([str($s.from) + "=" + str($s.param) + "=" + str($s.to) for $s in $regions]) - #if $parameters: - --region '$parameters' - #end if - - - - - - - - - - - - - - - - - - - - "?" not in formula - - - "?" in formula - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml b/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml deleted file mode 100644 index b9707e0..0000000 --- a/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.xml +++ /dev/null @@ -1,41 +0,0 @@ - - - export given BCSL model to SBML employing multi package - - macros.xml - - - - sybila/ebcsgen:v@TOOL_VERSION@ - - - - python3 ${__tool_directory__}/ebcsgen_sbml_export.py - --model '$model' - --output '$output' - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Galaxy/tools/ebcsgen/ebcsgen_simulate.xml b/Galaxy/tools/ebcsgen/ebcsgen_simulate.xml deleted file mode 100644 index 751a58f..0000000 --- a/Galaxy/tools/ebcsgen/ebcsgen_simulate.xml +++ /dev/null @@ -1,96 +0,0 @@ - - - simulate given model - - macros.xml - - - - sybila/ebcsgen:v@TOOL_VERSION@ - - - python3 ${__tool_directory__}/ebcsgen_simulate.py - --model '$model' - --output '$output' - --deterministic '$type.deterministic_choice' - #if $type.deterministic_choice == "True": - --direct False - --runs 1 - --volume '$type.volume' - --step '$type.step' - #else: - --direct '$type.network_free_choice' - --runs '$type.num_of_runs' - --volume 1 - --step 0.01 - #end if - --max_time '$max_time' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - -
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-
-
diff --git a/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.xml b/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.xml deleted file mode 100644 index 6d61ea7..0000000 --- a/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.xml +++ /dev/null @@ -1,73 +0,0 @@ - - - run static analysis techniques on given BCSL model - - macros.xml - - - - sybila/ebcsgen:v@TOOL_VERSION@ - - - - python3 ${__tool_directory__}/ebcsgen_static_analysis.py - --model '$model' - --output '$output' - --method '$Method.method' - #if $Method.method == "reach": - --complex '$Method.complex' - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Galaxy/tools/ebcsgen/macros.xml b/Galaxy/tools/ebcsgen/macros.xml deleted file mode 100644 index 4f2b643..0000000 --- a/Galaxy/tools/ebcsgen/macros.xml +++ /dev/null @@ -1,17 +0,0 @@ - - 2.1.0 - - - - - - - - diff --git a/Galaxy/tools/ebcsgen/test-data/parametrised.bcsl.ts 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- "t": 14 - } - ] -} \ No newline at end of file diff --git a/Galaxy/tools/ebcsgen/test-data/pctl_model_checking.bcsl.ts b/Galaxy/tools/ebcsgen/test-data/pctl_model_checking.bcsl.ts deleted file mode 100644 index 2887b17..0000000 --- a/Galaxy/tools/ebcsgen/test-data/pctl_model_checking.bcsl.ts +++ /dev/null @@ -1,75 +0,0 @@ -{ - "nodes": { - "1": "(inf, inf, inf)", - "2": "(1, 2, 0)", - "3": "(0, 1, 0)", - "4": "(0, 2, 0)", - "5": "(2, 1, 0)", - "6": "(2, 2, 0)", - "7": "(1, 1, 0)" - }, - "edges": [ - { - "s": 7, - "t": 3, - "p": 0.8 - }, - { - "s": 3, - "t": 4, - "p": 1.0 - }, - { - "s": 5, - "t": 7, - "p": 0.9855072463768116 - }, - { - "s": 1, - "t": 1, - "p": 1 - }, - { - "s": 2, - "t": 1, - "p": 0.2 - }, - { - "s": 5, - "t": 6, - "p": 0.014492753623188406 - }, - { - "s": 6, - "t": 1, - "p": 0.014492753623188406 - }, - { - "s": 6, - "t": 2, - "p": 0.9855072463768116 - }, - { - "s": 4, - "t": 1, - "p": 1.0 - }, - { - "s": 2, - "t": 4, - "p": 0.8 - }, - { - "s": 7, - "t": 2, - "p": 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-73/320,33/128,81/160,167/320,AllViolated -73/320,33/128,167/320,43/80,AllViolated -33/128,23/80,167/320,43/80,AllViolated -203/640,111/320,81/160,167/320,AllSat -203/640,111/320,167/320,43/80,AllSat -203/640,111/320,43/80,177/320,AllSat -203/640,111/320,177/320,91/160,AllSat -203/640,111/320,91/160,187/320,AllSat -203/640,111/320,187/320,3/5,AllSat -51/640,121/1280,1/10,69/640,AllViolated -51/640,121/1280,69/640,37/320,AllViolated -121/1280,7/64,69/640,37/320,AllViolated -159/1280,89/640,1/10,69/640,AllSat -159/1280,89/640,69/640,37/320,AllSat -159/1280,89/640,37/320,79/640,AllSat -7/64,159/1280,21/160,89/640,AllViolated -7/64,159/1280,89/640,47/320,AllViolated -7/64,159/1280,47/320,99/640,AllViolated -7/64,159/1280,99/640,13/80,AllViolated -159/1280,89/640,99/640,13/80,AllViolated -197/1280,27/160,47/320,99/640,AllSat -197/1280,27/160,99/640,13/80,AllSat -197/1280,27/160,13/80,109/640,AllSat -89/640,197/1280,57/320,119/640,AllViolated -89/640,197/1280,119/640,31/160,AllViolated -89/640,197/1280,31/160,129/640,AllViolated -89/640,197/1280,129/640,67/320,AllViolated -197/1280,27/160,129/640,67/320,AllViolated -47/256,127/640,31/160,129/640,AllSat -47/256,127/640,129/640,67/320,AllSat -47/256,127/640,67/320,139/640,AllSat -27/160,47/256,9/40,149/640,AllViolated -27/160,47/256,149/640,77/320,AllViolated -27/160,47/256,77/320,159/640,AllViolated -27/160,47/256,159/640,41/160,AllViolated -127/640,273/1280,77/320,159/640,AllSat -273/1280,73/320,77/320,159/640,AllSat -273/1280,73/320,159/640,41/160,AllSat -273/1280,73/320,41/160,169/640,AllSat -273/1280,73/320,169/640,87/320,AllSat -273/1280,73/320,87/320,179/640,AllSat -127/640,273/1280,23/80,189/640,AllViolated -127/640,273/1280,189/640,97/320,AllViolated -127/640,273/1280,97/320,199/640,AllViolated -127/640,273/1280,199/640,51/160,AllViolated -127/640,273/1280,51/160,209/640,AllViolated -127/640,273/1280,209/640,107/320,AllViolated -273/1280,73/320,209/640,107/320,AllViolated -311/1280,33/128,51/160,209/640,AllSat -311/1280,33/128,209/640,107/320,AllSat -311/1280,33/128,107/320,219/640,AllSat -311/1280,33/128,219/640,7/20,AllSat -311/1280,33/128,7/20,229/640,AllSat -73/320,311/1280,117/320,239/640,AllViolated -73/320,311/1280,239/640,61/160,AllViolated -73/320,311/1280,61/160,249/640,AllViolated -73/320,311/1280,249/640,127/320,AllViolated -73/320,311/1280,127/320,259/640,AllViolated -73/320,311/1280,259/640,33/80,AllViolated -33/128,349/1280,127/320,259/640,AllSat -349/1280,23/80,127/320,259/640,AllSat -349/1280,23/80,259/640,33/80,AllSat -349/1280,23/80,33/80,269/640,AllSat -349/1280,23/80,269/640,137/320,AllSat -349/1280,23/80,137/320,279/640,AllSat -349/1280,23/80,279/640,71/160,AllSat -349/1280,23/80,71/160,289/640,AllSat -33/128,349/1280,299/640,19/40,AllViolated -33/128,349/1280,19/40,309/640,AllViolated -33/128,349/1280,309/640,157/320,AllViolated -33/128,349/1280,157/320,319/640,AllViolated -33/128,349/1280,319/640,81/160,AllViolated -33/128,349/1280,81/160,329/640,AllViolated -33/128,349/1280,329/640,167/320,AllViolated -23/80,387/1280,81/160,329/640,AllSat -387/1280,203/640,81/160,329/640,AllSat -387/1280,203/640,329/640,167/320,AllSat -387/1280,203/640,167/320,339/640,AllSat -387/1280,203/640,339/640,43/80,AllSat -387/1280,203/640,43/80,349/640,AllSat -387/1280,203/640,349/640,177/320,AllSat -387/1280,203/640,177/320,359/640,AllSat -387/1280,203/640,359/640,91/160,AllSat -387/1280,203/640,91/160,369/640,AllSat -387/1280,203/640,369/640,187/320,AllSat -23/80,387/1280,379/640,3/5,AllViolated -121/1280,261/2560,1/10,133/1280,AllViolated -121/1280,261/2560,133/1280,69/640,AllViolated -7/64,299/2560,1/10,133/1280,AllSat -299/2560,159/1280,1/10,133/1280,AllSat -299/2560,159/1280,133/1280,69/640,AllSat -299/2560,159/1280,69/640,143/1280,AllSat -7/64,299/2560,153/1280,79/640,AllViolated -7/64,299/2560,79/640,163/1280,AllViolated -7/64,299/2560,163/1280,21/160,AllViolated -299/2560,159/1280,163/1280,21/160,AllViolated -337/2560,89/640,79/640,163/1280,AllSat -337/2560,89/640,163/1280,21/160,AllSat -337/2560,89/640,21/160,173/1280,AllSat -159/1280,337/2560,89/640,183/1280,AllViolated -159/1280,337/2560,183/1280,47/320,AllViolated -159/1280,337/2560,47/320,193/1280,AllViolated -159/1280,337/2560,193/1280,99/640,AllViolated -337/2560,89/640,193/1280,99/640,AllViolated -75/512,197/1280,47/320,193/1280,AllSat -75/512,197/1280,193/1280,99/640,AllSat -75/512,197/1280,99/640,203/1280,AllSat -89/640,75/512,13/80,213/1280,AllViolated -89/640,75/512,213/1280,109/640,AllViolated -89/640,75/512,109/640,223/1280,AllViolated -89/640,75/512,223/1280,57/320,AllViolated -75/512,197/1280,223/1280,57/320,AllViolated -413/2560,27/160,109/640,223/1280,AllSat -413/2560,27/160,223/1280,57/320,AllSat -413/2560,27/160,57/320,233/1280,AllSat -197/1280,413/2560,119/640,243/1280,AllViolated -197/1280,413/2560,243/1280,31/160,AllViolated -197/1280,413/2560,31/160,253/1280,AllViolated -197/1280,413/2560,253/1280,129/640,AllViolated -413/2560,27/160,253/1280,129/640,AllViolated -451/2560,47/256,31/160,253/1280,AllSat -451/2560,47/256,253/1280,129/640,AllSat -451/2560,47/256,129/640,263/1280,AllSat -451/2560,47/256,263/1280,67/320,AllSat -27/160,451/2560,273/1280,139/640,AllViolated -27/160,451/2560,139/640,283/1280,AllViolated -27/160,451/2560,283/1280,9/40,AllViolated -47/256,489/2560,139/640,283/1280,AllSat -489/2560,127/640,139/640,283/1280,AllSat -489/2560,127/640,283/1280,9/40,AllSat -489/2560,127/640,9/40,293/1280,AllSat -489/2560,127/640,293/1280,149/640,AllSat -489/2560,127/640,149/640,303/1280,AllSat -47/256,489/2560,77/320,313/1280,AllViolated -47/256,489/2560,313/1280,159/640,AllViolated -47/256,489/2560,159/640,323/1280,AllViolated -47/256,489/2560,323/1280,41/160,AllViolated -127/640,527/2560,159/640,323/1280,AllSat -527/2560,273/1280,159/640,323/1280,AllSat -527/2560,273/1280,323/1280,41/160,AllSat -527/2560,273/1280,41/160,333/1280,AllSat -527/2560,273/1280,333/1280,169/640,AllSat -527/2560,273/1280,169/640,343/1280,AllSat -127/640,527/2560,87/320,353/1280,AllViolated -127/640,527/2560,353/1280,179/640,AllViolated -127/640,527/2560,179/640,363/1280,AllViolated -127/640,527/2560,363/1280,23/80,AllViolated -273/1280,113/512,179/640,363/1280,AllSat -113/512,73/320,179/640,363/1280,AllSat -113/512,73/320,363/1280,23/80,AllSat -113/512,73/320,23/80,373/1280,AllSat -113/512,73/320,373/1280,189/640,AllSat -113/512,73/320,189/640,383/1280,AllSat -113/512,73/320,383/1280,97/320,AllSat -273/1280,113/512,393/1280,199/640,AllViolated -273/1280,113/512,199/640,403/1280,AllViolated -273/1280,113/512,403/1280,51/160,AllViolated -273/1280,113/512,51/160,413/1280,AllViolated -273/1280,113/512,413/1280,209/640,AllViolated -603/2560,311/1280,51/160,413/1280,AllSat -603/2560,311/1280,413/1280,209/640,AllSat -603/2560,311/1280,209/640,423/1280,AllSat -603/2560,311/1280,423/1280,107/320,AllSat -603/2560,311/1280,107/320,433/1280,AllSat -73/320,603/2560,443/1280,7/20,AllViolated -73/320,603/2560,7/20,453/1280,AllViolated -73/320,603/2560,453/1280,229/640,AllViolated -73/320,603/2560,229/640,463/1280,AllViolated -73/320,603/2560,463/1280,117/320,AllViolated -311/1280,641/2560,229/640,463/1280,AllSat -641/2560,33/128,229/640,463/1280,AllSat -641/2560,33/128,463/1280,117/320,AllSat -641/2560,33/128,117/320,473/1280,AllSat -641/2560,33/128,473/1280,239/640,AllSat -641/2560,33/128,239/640,483/1280,AllSat -641/2560,33/128,483/1280,61/160,AllSat -311/1280,641/2560,493/1280,249/640,AllViolated -311/1280,641/2560,249/640,503/1280,AllViolated -311/1280,641/2560,503/1280,127/320,AllViolated -311/1280,641/2560,127/320,513/1280,AllViolated -311/1280,641/2560,513/1280,259/640,AllViolated -311/1280,641/2560,259/640,523/1280,AllViolated -311/1280,641/2560,523/1280,33/80,AllViolated -641/2560,33/128,523/1280,33/80,AllViolated -679/2560,349/1280,259/640,523/1280,AllSat -679/2560,349/1280,523/1280,33/80,AllSat -679/2560,349/1280,33/80,533/1280,AllSat -679/2560,349/1280,533/1280,269/640,AllSat -679/2560,349/1280,269/640,543/1280,AllSat -679/2560,349/1280,543/1280,137/320,AllSat -679/2560,349/1280,137/320,553/1280,AllSat -33/128,679/2560,279/640,563/1280,AllViolated -33/128,679/2560,563/1280,71/160,AllViolated -33/128,679/2560,71/160,573/1280,AllViolated -33/128,679/2560,573/1280,289/640,AllViolated -33/128,679/2560,289/640,583/1280,AllViolated -33/128,679/2560,583/1280,147/320,AllViolated -349/1280,717/2560,289/640,583/1280,AllSat -717/2560,23/80,289/640,583/1280,AllSat -717/2560,23/80,583/1280,147/320,AllSat -33/128,679/2560,147/320,593/1280,AllViolated -33/128,679/2560,593/1280,299/640,AllViolated -679/2560,349/1280,593/1280,299/640,AllViolated -717/2560,23/80,147/320,593/1280,AllSat -717/2560,23/80,593/1280,299/640,AllSat -717/2560,23/80,299/640,603/1280,AllSat -717/2560,23/80,603/1280,19/40,AllSat -717/2560,23/80,19/40,613/1280,AllSat -717/2560,23/80,613/1280,309/640,AllSat -717/2560,23/80,309/640,623/1280,AllSat -349/1280,717/2560,157/320,633/1280,AllViolated -349/1280,717/2560,633/1280,319/640,AllViolated -349/1280,717/2560,319/640,643/1280,AllViolated -349/1280,717/2560,643/1280,81/160,AllViolated -349/1280,717/2560,81/160,653/1280,AllViolated -349/1280,717/2560,653/1280,329/640,AllViolated -349/1280,717/2560,329/640,663/1280,AllViolated -349/1280,717/2560,663/1280,167/320,AllViolated -23/80,151/512,329/640,663/1280,AllSat -151/512,387/1280,329/640,663/1280,AllSat -151/512,387/1280,663/1280,167/320,AllSat -151/512,387/1280,167/320,673/1280,AllSat -151/512,387/1280,673/1280,339/640,AllSat -151/512,387/1280,339/640,683/1280,AllSat -151/512,387/1280,683/1280,43/80,AllSat -151/512,387/1280,43/80,693/1280,AllSat -151/512,387/1280,693/1280,349/640,AllSat -151/512,387/1280,349/640,703/1280,AllSat -23/80,151/512,177/320,713/1280,AllViolated -23/80,151/512,713/1280,359/640,AllViolated -23/80,151/512,359/640,723/1280,AllViolated -23/80,151/512,723/1280,91/160,AllViolated -23/80,151/512,91/160,733/1280,AllViolated -23/80,151/512,733/1280,369/640,AllViolated -23/80,151/512,369/640,743/1280,AllViolated -23/80,151/512,743/1280,187/320,AllViolated -23/80,151/512,187/320,753/1280,AllViolated -23/80,151/512,753/1280,379/640,AllViolated -793/2560,203/640,187/320,753/1280,AllSat -387/1280,793/2560,753/1280,379/640,ExistsSat -793/2560,203/640,753/1280,379/640,ExistsSat -387/1280,793/2560,379/640,763/1280,ExistsSat -793/2560,203/640,379/640,763/1280,ExistsSat -387/1280,793/2560,763/1280,3/5,ExistsSat -793/2560,203/640,763/1280,3/5,ExistsSat -261/2560,541/5120,1/10,261/2560,Unknown -541/5120,7/64,1/10,261/2560,Unknown -261/2560,541/5120,261/2560,133/1280,Unknown -541/5120,7/64,261/2560,133/1280,Unknown -261/2560,541/5120,133/1280,271/2560,Unknown -541/5120,7/64,133/1280,271/2560,Unknown -261/2560,541/5120,271/2560,69/640,Unknown -541/5120,7/64,271/2560,69/640,Unknown -7/64,579/5120,133/1280,271/2560,Unknown -579/5120,299/2560,133/1280,271/2560,Unknown -7/64,579/5120,271/2560,69/640,Unknown -579/5120,299/2560,271/2560,69/640,Unknown -7/64,579/5120,69/640,281/2560,Unknown -579/5120,299/2560,69/640,281/2560,Unknown -7/64,579/5120,281/2560,143/1280,Unknown -579/5120,299/2560,281/2560,143/1280,Unknown -7/64,579/5120,143/1280,291/2560,Unknown -579/5120,299/2560,143/1280,291/2560,Unknown -7/64,579/5120,291/2560,37/320,Unknown -579/5120,299/2560,291/2560,37/320,Unknown -299/2560,617/5120,143/1280,291/2560,Unknown -617/5120,159/1280,143/1280,291/2560,Unknown -299/2560,617/5120,291/2560,37/320,Unknown -617/5120,159/1280,291/2560,37/320,Unknown -7/64,579/5120,37/320,301/2560,Unknown -579/5120,299/2560,37/320,301/2560,Unknown -7/64,579/5120,301/2560,153/1280,Unknown -579/5120,299/2560,301/2560,153/1280,Unknown -299/2560,617/5120,37/320,301/2560,Unknown -617/5120,159/1280,37/320,301/2560,Unknown -299/2560,617/5120,301/2560,153/1280,Unknown -617/5120,159/1280,301/2560,153/1280,Unknown -299/2560,617/5120,153/1280,311/2560,Unknown -617/5120,159/1280,153/1280,311/2560,Unknown -299/2560,617/5120,311/2560,79/640,Unknown -617/5120,159/1280,311/2560,79/640,Unknown -299/2560,617/5120,79/640,321/2560,Unknown -617/5120,159/1280,79/640,321/2560,Unknown -299/2560,617/5120,321/2560,163/1280,Unknown -617/5120,159/1280,321/2560,163/1280,Unknown -159/1280,131/1024,79/640,321/2560,Unknown -131/1024,337/2560,79/640,321/2560,Unknown -159/1280,131/1024,321/2560,163/1280,Unknown -131/1024,337/2560,321/2560,163/1280,Unknown -159/1280,131/1024,163/1280,331/2560,Unknown -131/1024,337/2560,163/1280,331/2560,Unknown -159/1280,131/1024,331/2560,21/160,Unknown -131/1024,337/2560,331/2560,21/160,Unknown -159/1280,131/1024,21/160,341/2560,Unknown -131/1024,337/2560,21/160,341/2560,Unknown -159/1280,131/1024,341/2560,173/1280,Unknown -131/1024,337/2560,341/2560,173/1280,Unknown -159/1280,131/1024,173/1280,351/2560,Unknown -131/1024,337/2560,173/1280,351/2560,Unknown -159/1280,131/1024,351/2560,89/640,Unknown -131/1024,337/2560,351/2560,89/640,Unknown -337/2560,693/5120,173/1280,351/2560,Unknown -693/5120,89/640,173/1280,351/2560,Unknown -337/2560,693/5120,351/2560,89/640,Unknown -693/5120,89/640,351/2560,89/640,Unknown -337/2560,693/5120,89/640,361/2560,Unknown -693/5120,89/640,89/640,361/2560,Unknown -337/2560,693/5120,361/2560,183/1280,Unknown -693/5120,89/640,361/2560,183/1280,Unknown -337/2560,693/5120,183/1280,371/2560,Unknown -693/5120,89/640,183/1280,371/2560,Unknown -337/2560,693/5120,371/2560,47/320,Unknown -693/5120,89/640,371/2560,47/320,Unknown -337/2560,693/5120,47/320,381/2560,Unknown -693/5120,89/640,47/320,381/2560,Unknown -337/2560,693/5120,381/2560,193/1280,Unknown -693/5120,89/640,381/2560,193/1280,Unknown -89/640,731/5120,47/320,381/2560,Unknown -731/5120,75/512,47/320,381/2560,Unknown -89/640,731/5120,381/2560,193/1280,Unknown -731/5120,75/512,381/2560,193/1280,Unknown -89/640,731/5120,193/1280,391/2560,Unknown -731/5120,75/512,193/1280,391/2560,Unknown 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-1339/5120,679/2560,137/320,1101/2560,Unknown -33/128,1339/5120,1101/2560,553/1280,Unknown -1339/5120,679/2560,1101/2560,553/1280,Unknown -33/128,1339/5120,553/1280,1111/2560,Unknown -1339/5120,679/2560,553/1280,1111/2560,Unknown -33/128,1339/5120,1111/2560,279/640,Unknown -1339/5120,679/2560,1111/2560,279/640,Unknown -679/2560,1377/5120,553/1280,1111/2560,Unknown -1377/5120,349/1280,553/1280,1111/2560,Unknown -679/2560,1377/5120,1111/2560,279/640,Unknown -1377/5120,349/1280,1111/2560,279/640,Unknown -679/2560,1377/5120,279/640,1121/2560,Unknown -1377/5120,349/1280,279/640,1121/2560,Unknown -679/2560,1377/5120,1121/2560,563/1280,Unknown -1377/5120,349/1280,1121/2560,563/1280,Unknown -679/2560,1377/5120,563/1280,1131/2560,Unknown -1377/5120,349/1280,563/1280,1131/2560,Unknown -679/2560,1377/5120,1131/2560,71/160,Unknown -1377/5120,349/1280,1131/2560,71/160,Unknown -679/2560,1377/5120,71/160,1141/2560,Unknown -1377/5120,349/1280,71/160,1141/2560,Unknown -679/2560,1377/5120,1141/2560,573/1280,Unknown -1377/5120,349/1280,1141/2560,573/1280,Unknown -679/2560,1377/5120,573/1280,1151/2560,Unknown -1377/5120,349/1280,573/1280,1151/2560,Unknown -679/2560,1377/5120,1151/2560,289/640,Unknown -1377/5120,349/1280,1151/2560,289/640,Unknown -679/2560,1377/5120,289/640,1161/2560,Unknown -1377/5120,349/1280,289/640,1161/2560,Unknown -679/2560,1377/5120,1161/2560,583/1280,Unknown -1377/5120,349/1280,1161/2560,583/1280,Unknown -679/2560,1377/5120,583/1280,1171/2560,Unknown -1377/5120,349/1280,583/1280,1171/2560,Unknown -679/2560,1377/5120,1171/2560,147/320,Unknown -1377/5120,349/1280,1171/2560,147/320,Unknown -349/1280,283/1024,583/1280,1171/2560,Unknown -283/1024,717/2560,583/1280,1171/2560,Unknown -349/1280,283/1024,1171/2560,147/320,Unknown -283/1024,717/2560,1171/2560,147/320,Unknown -679/2560,1377/5120,147/320,1181/2560,Unknown -1377/5120,349/1280,147/320,1181/2560,Unknown -679/2560,1377/5120,1181/2560,593/1280,Unknown -1377/5120,349/1280,1181/2560,593/1280,Unknown -349/1280,283/1024,147/320,1181/2560,Unknown -283/1024,717/2560,147/320,1181/2560,Unknown -349/1280,283/1024,1181/2560,593/1280,Unknown -283/1024,717/2560,1181/2560,593/1280,Unknown -349/1280,283/1024,593/1280,1191/2560,Unknown -283/1024,717/2560,593/1280,1191/2560,Unknown -349/1280,283/1024,1191/2560,299/640,Unknown -283/1024,717/2560,1191/2560,299/640,Unknown -349/1280,283/1024,299/640,1201/2560,Unknown -283/1024,717/2560,299/640,1201/2560,Unknown -349/1280,283/1024,1201/2560,603/1280,Unknown -283/1024,717/2560,1201/2560,603/1280,Unknown -349/1280,283/1024,603/1280,1211/2560,Unknown -283/1024,717/2560,603/1280,1211/2560,Unknown -349/1280,283/1024,1211/2560,19/40,Unknown -283/1024,717/2560,1211/2560,19/40,Unknown -349/1280,283/1024,19/40,1221/2560,Unknown -283/1024,717/2560,19/40,1221/2560,Unknown -349/1280,283/1024,1221/2560,613/1280,Unknown -283/1024,717/2560,1221/2560,613/1280,Unknown -349/1280,283/1024,613/1280,1231/2560,Unknown -283/1024,717/2560,613/1280,1231/2560,Unknown -349/1280,283/1024,1231/2560,309/640,Unknown -283/1024,717/2560,1231/2560,309/640,Unknown -349/1280,283/1024,309/640,1241/2560,Unknown -283/1024,717/2560,309/640,1241/2560,Unknown -349/1280,283/1024,1241/2560,623/1280,Unknown -283/1024,717/2560,1241/2560,623/1280,Unknown -349/1280,283/1024,623/1280,1251/2560,Unknown -283/1024,717/2560,623/1280,1251/2560,Unknown -349/1280,283/1024,1251/2560,157/320,Unknown -283/1024,717/2560,1251/2560,157/320,Unknown -717/2560,1453/5120,623/1280,1251/2560,Unknown -1453/5120,23/80,623/1280,1251/2560,Unknown -717/2560,1453/5120,1251/2560,157/320,Unknown -1453/5120,23/80,1251/2560,157/320,Unknown -717/2560,1453/5120,157/320,1261/2560,Unknown -1453/5120,23/80,157/320,1261/2560,Unknown -717/2560,1453/5120,1261/2560,633/1280,Unknown -1453/5120,23/80,1261/2560,633/1280,Unknown -717/2560,1453/5120,633/1280,1271/2560,Unknown -1453/5120,23/80,633/1280,1271/2560,Unknown -717/2560,1453/5120,1271/2560,319/640,Unknown -1453/5120,23/80,1271/2560,319/640,Unknown -717/2560,1453/5120,319/640,1281/2560,Unknown -1453/5120,23/80,319/640,1281/2560,Unknown -717/2560,1453/5120,1281/2560,643/1280,Unknown -1453/5120,23/80,1281/2560,643/1280,Unknown -717/2560,1453/5120,643/1280,1291/2560,Unknown -1453/5120,23/80,643/1280,1291/2560,Unknown -717/2560,1453/5120,1291/2560,81/160,Unknown -1453/5120,23/80,1291/2560,81/160,Unknown -717/2560,1453/5120,81/160,1301/2560,Unknown -1453/5120,23/80,81/160,1301/2560,Unknown -717/2560,1453/5120,1301/2560,653/1280,Unknown -1453/5120,23/80,1301/2560,653/1280,Unknown -717/2560,1453/5120,653/1280,1311/2560,Unknown -1453/5120,23/80,653/1280,1311/2560,Unknown -717/2560,1453/5120,1311/2560,329/640,Unknown -1453/5120,23/80,1311/2560,329/640,Unknown -717/2560,1453/5120,329/640,1321/2560,Unknown -1453/5120,23/80,329/640,1321/2560,Unknown -717/2560,1453/5120,1321/2560,663/1280,Unknown -1453/5120,23/80,1321/2560,663/1280,Unknown -717/2560,1453/5120,663/1280,1331/2560,Unknown -1453/5120,23/80,663/1280,1331/2560,Unknown -717/2560,1453/5120,1331/2560,167/320,Unknown -1453/5120,23/80,1331/2560,167/320,Unknown -23/80,1491/5120,663/1280,1331/2560,Unknown -1491/5120,151/512,663/1280,1331/2560,Unknown -23/80,1491/5120,1331/2560,167/320,Unknown -1491/5120,151/512,1331/2560,167/320,Unknown -23/80,1491/5120,167/320,1341/2560,Unknown -1491/5120,151/512,167/320,1341/2560,Unknown -23/80,1491/5120,1341/2560,673/1280,Unknown -1491/5120,151/512,1341/2560,673/1280,Unknown -23/80,1491/5120,673/1280,1351/2560,Unknown -1491/5120,151/512,673/1280,1351/2560,Unknown -23/80,1491/5120,1351/2560,339/640,Unknown -1491/5120,151/512,1351/2560,339/640,Unknown -23/80,1491/5120,339/640,1361/2560,Unknown -1491/5120,151/512,339/640,1361/2560,Unknown -23/80,1491/5120,1361/2560,683/1280,Unknown -1491/5120,151/512,1361/2560,683/1280,Unknown -23/80,1491/5120,683/1280,1371/2560,Unknown -1491/5120,151/512,683/1280,1371/2560,Unknown -23/80,1491/5120,1371/2560,43/80,Unknown -1491/5120,151/512,1371/2560,43/80,Unknown -23/80,1491/5120,43/80,1381/2560,Unknown -1491/5120,151/512,43/80,1381/2560,Unknown -23/80,1491/5120,1381/2560,693/1280,Unknown -1491/5120,151/512,1381/2560,693/1280,Unknown -23/80,1491/5120,693/1280,1391/2560,Unknown -1491/5120,151/512,693/1280,1391/2560,Unknown -23/80,1491/5120,1391/2560,349/640,Unknown -1491/5120,151/512,1391/2560,349/640,Unknown -23/80,1491/5120,349/640,1401/2560,Unknown -1491/5120,151/512,349/640,1401/2560,Unknown -23/80,1491/5120,1401/2560,703/1280,Unknown -1491/5120,151/512,1401/2560,703/1280,Unknown -23/80,1491/5120,703/1280,1411/2560,Unknown -1491/5120,151/512,703/1280,1411/2560,Unknown -23/80,1491/5120,1411/2560,177/320,Unknown -1491/5120,151/512,1411/2560,177/320,Unknown -151/512,1529/5120,703/1280,1411/2560,Unknown -1529/5120,387/1280,703/1280,1411/2560,Unknown -151/512,1529/5120,1411/2560,177/320,Unknown -1529/5120,387/1280,1411/2560,177/320,Unknown -151/512,1529/5120,177/320,1421/2560,Unknown -1529/5120,387/1280,177/320,1421/2560,Unknown -151/512,1529/5120,1421/2560,713/1280,Unknown -1529/5120,387/1280,1421/2560,713/1280,Unknown -151/512,1529/5120,713/1280,1431/2560,Unknown -1529/5120,387/1280,713/1280,1431/2560,Unknown -151/512,1529/5120,1431/2560,359/640,Unknown -1529/5120,387/1280,1431/2560,359/640,Unknown -151/512,1529/5120,359/640,1441/2560,Unknown -1529/5120,387/1280,359/640,1441/2560,Unknown -151/512,1529/5120,1441/2560,723/1280,Unknown -1529/5120,387/1280,1441/2560,723/1280,Unknown -151/512,1529/5120,723/1280,1451/2560,Unknown -1529/5120,387/1280,723/1280,1451/2560,Unknown -151/512,1529/5120,1451/2560,91/160,Unknown -1529/5120,387/1280,1451/2560,91/160,Unknown -151/512,1529/5120,91/160,1461/2560,Unknown -1529/5120,387/1280,91/160,1461/2560,Unknown -151/512,1529/5120,1461/2560,733/1280,Unknown -1529/5120,387/1280,1461/2560,733/1280,Unknown -151/512,1529/5120,733/1280,1471/2560,Unknown -1529/5120,387/1280,733/1280,1471/2560,Unknown -151/512,1529/5120,1471/2560,369/640,Unknown -1529/5120,387/1280,1471/2560,369/640,Unknown -151/512,1529/5120,369/640,1481/2560,Unknown -1529/5120,387/1280,369/640,1481/2560,Unknown -151/512,1529/5120,1481/2560,743/1280,Unknown -1529/5120,387/1280,1481/2560,743/1280,Unknown -151/512,1529/5120,743/1280,1491/2560,Unknown -1529/5120,387/1280,743/1280,1491/2560,Unknown -151/512,1529/5120,1491/2560,187/320,Unknown -1529/5120,387/1280,1491/2560,187/320,Unknown -151/512,1529/5120,187/320,1501/2560,Unknown -1529/5120,387/1280,187/320,1501/2560,Unknown -151/512,1529/5120,1501/2560,753/1280,Unknown -1529/5120,387/1280,1501/2560,753/1280,Unknown -151/512,1529/5120,753/1280,1511/2560,Unknown -1529/5120,387/1280,753/1280,1511/2560,Unknown -151/512,1529/5120,1511/2560,379/640,Unknown -1529/5120,387/1280,1511/2560,379/640,Unknown -387/1280,1567/5120,187/320,1501/2560,Unknown -1567/5120,793/2560,187/320,1501/2560,Unknown -387/1280,1567/5120,1501/2560,753/1280,Unknown -1567/5120,793/2560,1501/2560,753/1280,Unknown diff --git a/Galaxy/tools/ebcsgen/test-data/reduced.bcsl.model b/Galaxy/tools/ebcsgen/test-data/reduced.bcsl.model deleted file mode 100644 index bfaa940..0000000 --- a/Galaxy/tools/ebcsgen/test-data/reduced.bcsl.model +++ /dev/null @@ -1,7 +0,0 @@ -#! rules -P()::cell => P()::out @ 1.0 - -#! inits -1 P()::cell - -#! definitions diff --git a/Galaxy/tools/ebcsgen/test-data/redundant.bcsl.model b/Galaxy/tools/ebcsgen/test-data/redundant.bcsl.model deleted file mode 100644 index a90384a..0000000 --- a/Galaxy/tools/ebcsgen/test-data/redundant.bcsl.model +++ /dev/null @@ -1,8 +0,0 @@ -#! rules -r1_S ~ P(S{i})::cell => P(S{a})::cell -r1_T ~ P(T{i})::cell => P(T{a})::cell -r2 ~ P()::cell => P()::out -r1_X ~ P(T{i})::cell => P(T{a})::cell - -#! inits -1 P(S{i},T{i})::cell \ No newline at end of file diff --git a/Galaxy/tools/ebcsgen/test-data/repressilator.bcsl.model b/Galaxy/tools/ebcsgen/test-data/repressilator.bcsl.model deleted file mode 100644 index f4df1f9..0000000 --- a/Galaxy/tools/ebcsgen/test-data/repressilator.bcsl.model +++ /dev/null @@ -1,15 +0,0 @@ -#! rules -X()::rep => @ k1*[X()::rep] -Y()::rep => @ k2*[Y()::rep] -Z()::rep => @ k1*[Z()::rep] - => X()::rep @ 5**4/(5**4+[Z()::rep]**4) - => Y()::rep @ 5**4/(5**4+[X()::rep]**4) - => Z()::rep @ 5**4/(5**4+[Y()::rep]**4) - -#! inits -1 X()::rep -1 Y()::rep - -#! definitions -k1 = 0.05 -k2 = 0.12 diff --git a/Galaxy/tools/ebcsgen/test-data/simple.bcsl.model b/Galaxy/tools/ebcsgen/test-data/simple.bcsl.model deleted file mode 100644 index b05d773..0000000 --- a/Galaxy/tools/ebcsgen/test-data/simple.bcsl.model +++ /dev/null @@ -1,7 +0,0 @@ -#! rules -r1_S ~ P(S{i})::cell => P(S{a})::cell -r1_T ~ P(T{i})::cell => P(T{a})::cell -r2 ~ P()::cell => P()::out - -#! inits -1 P(S{i},T{i})::cell \ No newline at end of file diff --git a/Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts b/Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts deleted file mode 100644 index 2c1b6f8..0000000 --- a/Galaxy/tools/ebcsgen/test-data/simple.bcsl.ts +++ /dev/null @@ -1,98 +0,0 @@ -{ - "nodes": { - "1": "(0, 0, 0, 0, 0, 1, 0, 0)", - "2": "(0, 0, 1, 0, 0, 0, 0, 0)", - "3": "(1, 0, 0, 0, 0, 0, 0, 0)", - "4": "(0, 0, 0, 1, 0, 0, 0, 0)", - "5": "(0, 0, 0, 0, 0, 0, 1, 0)", - "6": "(0, 0, 0, 0, 0, 0, 0, 1)", - "7": "(0, 0, 0, 0, 1, 0, 0, 0)", - "8": "(0, 1, 0, 0, 0, 0, 0, 0)" - }, - "edges": [ - { - "s": 8, - "t": 8, - "p": 1, - "label": "\u03b5" - }, - { - "s": 3, - "t": 8, - "p": 1.0, - "label": "r2" - }, - { - "s": 5, - "t": 6, - "p": 0.3333333333333333, - "label": "r2" - }, - { - "s": 6, - "t": 6, - "p": 1, - "label": "\u03b5" - }, - { - "s": 2, - "t": 3, - "p": 0.5, - "label": "r1_T" - }, - { - "s": 7, - "t": 1, - "p": 0.5, - "label": "r2" - }, - { - "s": 5, - "t": 2, - "p": 0.3333333333333333, - "label": "r1_S" - }, - { - "s": 7, - "t": 3, - "p": 0.5, - "label": "r1_S" - }, - { - "s": 4, - "t": 4, - "p": 1, - "label": "\u03b5" - }, - { - "s": 1, - "t": 1, - "p": 1, - "label": "\u03b5" - }, - { - "s": 5, - "t": 7, - "p": 0.3333333333333333, - "label": "r1_T" - }, - { - "s": 2, - "t": 4, - "p": 0.5, - "label": "r2" - } - ], - "ordering": [ - "P(S{a},T{a})::cell", - "P(S{a},T{a})::out", - "P(S{a},T{i})::cell", - "P(S{a},T{i})::out", - "P(S{i},T{a})::cell", - "P(S{i},T{a})::out", - "P(S{i},T{i})::cell", - "P(S{i},T{i})::out" - ], - "initial": 5, - "bound": 1 -} \ No newline at end of file diff --git a/Galaxy/tools/ebcsgen/test-data/simulation_determ.csv b/Galaxy/tools/ebcsgen/test-data/simulation_determ.csv deleted file mode 100644 index 2fcdb74..0000000 --- a/Galaxy/tools/ebcsgen/test-data/simulation_determ.csv +++ /dev/null @@ -1,1002 +0,0 @@ -times,X()::rep,Y()::rep,Z()::rep -0.0,1.660577881102624e-24,1.660577881102624e-24,0.0 -0.1,0.09975040973417111,0.0994023743454972,0.09975040978871946 -0.2,0.19900321952224012,0.19761896848213056,0.19900322194212805 -0.30000000000000004,0.29776044327163925,0.29466344696781566,0.2977604695417275 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-99.60000000000001,3.4521732785060646,6.952497334776885,6.490563276628219 -99.7,3.461002415678205,6.950485623255075,6.479252567391758 -99.80000000000001,3.469921672936583,6.948343092814243,6.468018137967923 -99.9,3.4789303599793704,6.9460691328601945,6.45686088366796 -100.0,3.4880277673576505,6.943663138605678,6.445781705157098 From 5eca9c2403887be54b727d88d0a5f4038a45f56f Mon Sep 17 00:00:00 2001 From: Markta Opichalov Date: Mon, 9 Dec 2024 07:19:15 +0100 Subject: [PATCH 3/3] moved the top-level API functions to directory in the root of this repository --- Galaxy/tools/ebcsgen/.shed.yml | 57 ------------------- .../ebcsgen_ctl_model_checking.py | 0 .../ebcsgen => api}/ebcsgen_generate_ts.py | 0 .../ebcsgen_pctl_model_checking.py | 0 .../ebcsgen_pctl_parameter_synthesis.py | 0 .../ebcsgen => api}/ebcsgen_sbml_export.py | 0 .../tools/ebcsgen => api}/ebcsgen_simulate.py | 0 .../ebcsgen_static_analysis.py | 0 8 files changed, 57 deletions(-) delete mode 100644 Galaxy/tools/ebcsgen/.shed.yml rename {Galaxy/tools/ebcsgen => api}/ebcsgen_ctl_model_checking.py (100%) rename {Galaxy/tools/ebcsgen => api}/ebcsgen_generate_ts.py (100%) rename {Galaxy/tools/ebcsgen => api}/ebcsgen_pctl_model_checking.py (100%) rename {Galaxy/tools/ebcsgen => api}/ebcsgen_pctl_parameter_synthesis.py (100%) rename {Galaxy/tools/ebcsgen => api}/ebcsgen_sbml_export.py (100%) rename {Galaxy/tools/ebcsgen => api}/ebcsgen_simulate.py (100%) rename {Galaxy/tools/ebcsgen => api}/ebcsgen_static_analysis.py (100%) diff --git a/Galaxy/tools/ebcsgen/.shed.yml b/Galaxy/tools/ebcsgen/.shed.yml deleted file mode 100644 index 60166cf..0000000 --- a/Galaxy/tools/ebcsgen/.shed.yml +++ /dev/null @@ -1,57 +0,0 @@ -owner: sybila -remote_repository_url: "https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen" -homepage_url: "https://github.com/sybila/eBCSgen" -categories: - - Systems Biology -repositories: - ebcsgen_generate_transition_system: - description: "Generate transition system of the given BCSL model." - include: - - ebcsgen_generate_ts.xml - - ebcsgen_generate_ts.py - - test-data/simple.bcsl.model - - macros.xml - ebcsgen_pctl_model_checking: - description: "Explicit PCTL model checking of given transition system." - include: - - ebcsgen_pctl_model_checking.xml - - ebcsgen_pctl_model_checking.py - - test-data/pctl_model_checking.bcsl.ts - - macros.xml - ebcsgen_simulation: - description: "Simulation of the given BCSL model." - include: - - ebcsgen_simulate.xml - - ebcsgen_simulate.py - - test-data/repressilator.bcsl.model - - test-data/simulation_determ.csv - - macros.xml - ebcsgen_ctl_model_checking: - description: "Explicit CTL model checking of given transition system." - include: - - ebcsgen_ctl_model_checking.xml - - ebcsgen_ctl_model_checking.py - - test-data/simple.bcsl.ts - - macros.xml - ebcsgen_pctl_parameter_synthesis: - description: "PCTL parameter synthesis of given parametric transition system." - include: - - ebcsgen_pctl_parameter_synthesis.xml - - ebcsgen_pctl_parameter_synthesis.py - - test-data/parametrised.bcsl.ts - - macros.xml - ebcsgen_sbml_export: - description: "Export given BCSL model to SBML with usage of SBML-multi package." - include: - - ebcsgen_sbml_export.xml - - ebcsgen_sbml_export.py - - test-data/simple.bcsl.model - - macros.xml - ebcsgen_static_analysis: - description: "Run static analysis techniques on given BCSL model." - include: - - ebcsgen_static_analysis.xml - - ebcsgen_static_analysis.py - - test-data/redundant.bcsl.model - - test-data/reduced.bcsl.model - - macros.xml diff --git a/Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.py b/api/ebcsgen_ctl_model_checking.py similarity index 100% rename from Galaxy/tools/ebcsgen/ebcsgen_ctl_model_checking.py rename to api/ebcsgen_ctl_model_checking.py diff --git a/Galaxy/tools/ebcsgen/ebcsgen_generate_ts.py b/api/ebcsgen_generate_ts.py similarity index 100% rename from Galaxy/tools/ebcsgen/ebcsgen_generate_ts.py rename to api/ebcsgen_generate_ts.py diff --git a/Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.py b/api/ebcsgen_pctl_model_checking.py similarity index 100% rename from Galaxy/tools/ebcsgen/ebcsgen_pctl_model_checking.py rename to api/ebcsgen_pctl_model_checking.py diff --git a/Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.py b/api/ebcsgen_pctl_parameter_synthesis.py similarity index 100% rename from Galaxy/tools/ebcsgen/ebcsgen_pctl_parameter_synthesis.py rename to api/ebcsgen_pctl_parameter_synthesis.py diff --git a/Galaxy/tools/ebcsgen/ebcsgen_sbml_export.py b/api/ebcsgen_sbml_export.py similarity index 100% rename from Galaxy/tools/ebcsgen/ebcsgen_sbml_export.py rename to api/ebcsgen_sbml_export.py diff --git a/Galaxy/tools/ebcsgen/ebcsgen_simulate.py b/api/ebcsgen_simulate.py similarity index 100% rename from Galaxy/tools/ebcsgen/ebcsgen_simulate.py rename to api/ebcsgen_simulate.py diff --git a/Galaxy/tools/ebcsgen/ebcsgen_static_analysis.py b/api/ebcsgen_static_analysis.py similarity index 100% rename from Galaxy/tools/ebcsgen/ebcsgen_static_analysis.py rename to api/ebcsgen_static_analysis.py