Use the form below to create a COMBINE/OMEX archive for simulating a model. This archive will contain your model and a SED-ML file generated from the form below. You can then use runBioSimulations to execute your archive, or you can download the archive.

  1. Upload a model or enter a URL where a model is located.
  2. Select the format of the model (e.g., BNGL, SBML).
  3. Select the type of simulation that you'd like to execute (e.g., steady-state, time course).
  4. Configure the parameters of your simulation (e.g., start time, end time).
  5. Select the algorithm that you'd like to use to execute your simulation (e.g., CVODE, SSA).
  6. Configure the parameters of the selected algorithm (e.g., error tolerance, seed).
  7. Describe the namespaces needed to specify changes to your model and observables of your simulation.
  8. Describe any attributes of your model that you'd like to change (e.g., initial conditions).
  9. Describe the simulation observables that you'd like to record (e.g., concentrations of species, fluxes of reactions).

For models encoded in SBML, SBML-fbc, and SBML-qual, the namespaces, changes, and observables sections will be pre-populated from your model. Going forward, we aim to extend this to additional model formats.

Model *
Select a local file or enter a URL for file in a model format such as BNGL or SBML.
Select a method for providing a model file Upload a local file Enter a URL for a file Select a model file Enter a URL for a model file Select the format of the model {{ format.name }}

Select a model file in a format such as the BioNetGen Language (BNGL ) or the Systems Biology Markup Language (SBML ). Model files can either be uploaded from your local computer or loaded from a publicly-accessible URL.

Numerous BNGL models are available from RuleHub . Numerous SBML models are available from BiGG , BioModels , the Cell Collective , and JWS Online .

Uploaded files are limited to 64 MB. Files up to 1 GB can be submitted via URLs.

Please select a method for upload a model file. Please select a model file. Currently, model file uploads are limited to 256 MB. Larger models must be submitted through URLs. Please enter a valid URL. Please select a model format.
Modeling and simulation methods *
Select a type of model framework, a type of simulation, and an algorithm for executing the simulation.
Select a modeling framework {{ framework.name }} Select a type of simulation {{ simulationType.name }} Select a simulation algorithm {{ simulationAlgorithm.name }}
Select a modeling framework, a type of simulation, and an algorithm for executing the simulation. Please select a modeling framework. Please select a type of simulation. Please select a simulation algorithm.
Simulation *
Configure a simulation.
Enter the step size Enter a step size. The step size must be a positive float.
Enter the initial time Enter the end time Enter the time to start recording the rsults Enter the number of steps to record Time step
Enter the initial time of the simulation, the time when the simulation should terminate, the first time when output should be recorded, and the number of steps that should be recorded between the output start and termination times. This combination of inputs specifies a time step. The initial time must be a float. The output end time must be a float. The output start time must be a float. The number of steps must be a non-negative integer. The output start time must be at least the initial time. The output end time must be at least the output start time.
Simulation algorithm parameters
Configure parameters of the selected algorithm.
Configure the parameters of the selected algorithm
Name
More info
Supporting simulators
Type
Default
Recommended range
New value
{{ param.value.name }}
{{ param.value.simulatorsStr }}
{{ param.value.type }}
{{ param.value.formattedValue }}
{{ param.value.formattedRecommendedRangeJoined }}
Enter new values to override the default values of one or more parameters. The value of one of or more parameters is invalid.
Model namespaces
Describe the namespaces of the parameters and variables of your model.
Enter the prefix and URI for each namespace needed to reference the parameters and variables of your model.
Prefix
URI *
Describe the namespaces needed to reference the parameters and variables of your model (e.g., sbml: http://www.sbml.org/sbml/level2/version4 for SBML L2V4). One or more properties of one or more namespaces is invalid. The prefixes of the namespaces must be unique.
Model changes
Describe changes that should be applied to the attributes of your model, such as to its initial conditions or kinetic parameters.
Enter the target for each change and the value it should be set to.
Id *
Name
Target *
Default
New value

Describe the changes that should be applied to the attributes of your model (e.g., set the value of target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='k1']/@value to the new value 2.1). For XML-based model languages such as SBML, targets should be XPaths to XML attributes.

The ids and names data will not be exported to SED-ML because these attributes are not supported by SED-ML L1V3. Once simulation tools update to SED-ML L1V4, we will export this information to SED-ML.

The default value of each attribute is provided as a reference. This information will not be encoded into the generated SED-ML document.

One or more properties of one or more changes invalid. The ids of the changes must be unique.
Observables *
Describe the variables that should be recorded from your simulation.
Enter the id, name, and symbol/target of each variable that should be recoded *
Id *
Name
Type *
Address *
{{ variableType.name }}
Describe the variables (e.g., time symbol urn:sedml:symbol:time, species target /sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='atp']) that should be recorded from your simulation and enter an unique id and, optionally, a descriptive name for each variable. For XML-based model languages such as SBML, targets should be XPaths to XML attributes. One or more properties of one or more variables is invalid. The ids of the variables must be unique.
Recommended simulation tools
Tools that likely have the capabilities to execute your simulation.
Based on the information about, below are simulation tools which likely can execute your simulation:
Name
Algorithm compatability
Algorithm parameter compatability
More info
{{ compatibleSimulator.simulator.name }}
{{ compatibleSimulator.maxPolicy.level }}. {{ compatibleSimulator.maxPolicy.name }}
{{ compatibleSimulator.parametersCompatibility ? 'Yes' : 'No' }}

Not all simulation tools have the capabilities to execute all possible simulations because most simulation tools do not support every aspect of modeling standards such as SBML and SED-ML. We are working to encourage developers to more fully support these standards and to catalog which features each tool supports so that we are better able to recommend simulation tools going forward.

No single simulation tool supports the selected combination of parameters. Please clear the value of one or more parameters.