Public CaliBayes web-services
Publically accessible web-services are provided for the benefit of users who wish to experiment with the calibration services and occasional users. Heavy users are encouraged to deploy the software infrastructure within their own organisation.
Calibration
Web Service WSDL (v2)
Web Service Methods
submit(String algorithm, String simulatorName, String sbmlModel, String expDataXml, String tuningXml, String distributionXml) Clients invoke this method with relevant parameters to fire off a calibration job. The method returns a string result Named "sessionId" that for checking the status of the job and retrieve the calibration result.
- isReady(String sessionId) This method returns a boolean result indicating if the calibration job has finished.
- getResult(String sessionId) Once the calibration job has been completed, clients can retrieve the calibration result via this method. Note: once the result has been retrieved, it will be removed from the sever and may not be retrieved again.
- discard(String sessionId) This method kills a calibration job regardless its execution status.
Simulator web-services
Universal Interface
Here at Newcastle University, we have deployed several Simulator Web Services for Calibayes jobs. An universal Calibayes-Simulator interface has been defined and shared by these services.
- compile(String sbmlFile) uploads a sbml model into the simulator and obtains a session id.
- setSimMethod(String sessionId, String method) sets simulation method, such as "stochastic", "deterministic", etc. The available simulation methods of a simulator can be obtained by invoking getSimMethods()
setParameters(String sessionId, List<String> paramList) uploads a list of parameters(including species) to the simulator
- appendOut(String sessionId, String speciesId, double time) uploads a (species, timepoint) combination. This method can be invoked repeatedly before running simulate() method, in order to load multiple (speciesm, timepoint) combinations.
simulate(String sessionId, List<Double> values) fires off a simulation with a list of initial parameter values. The order of the values in the list must be in accord with their corresponding ids appeared in the paramList being loaded by invoking setParameters() method. The order of the output values in the returned list corresponds to the order of the (species, timepoint) combinations being loaded into the simulator.
- getMethods() returns a list of available simulation methods.
Currently available simulation engines (v2)
Basis-fern
FERN: stochastic
Basis-Copasi
COPASI: stochastic, deterministic
Disclaimer: The Basis-Copasi web services are developed upon COPASI under the Non-Commercial License. Please consult COPASI's Non−Commercial Purpose License before use. We, the developer and provider of the services, can not hold the liability for users' usages of the above relevant services.
Tutorial
A quick guide to using these services can be found in the CaliBayes tutorial