CaliBayes and BASIS: e-Science applications for Systems Biology
research
Yuhui Chen
Institute for Ageing and Health
Centre for Integrated Systems Biology of Ageing and Nutrition
Newcastle University, UK
BASISBASIS Biology of Ageing e-Science Integration and Simulation System Biology of Ageing e-Science Integration and Simulation System Web-based Systems Biology application that provides high Web-based Systems Biology application that provides high
performance computing power for dynamic biological simulation.performance computing power for dynamic biological simulation. www.basis.ncl.ac.uk
CaliBayesCaliBayes A powerful tool based on advanced Bayesian statistical A powerful tool based on advanced Bayesian statistical
inference technology for inferences about kinetic parameters inference technology for inferences about kinetic parameters within deterministic and stochastic SBML modelswithin deterministic and stochastic SBML models
www.calibayes.ncl.ac.uk
Introduction
FunctionalitiesFunctionalities
System propertiesSystem properties
System architectureSystem architecture
Combined WorkflowCombined Workflow
BASIS & CaliBayes
FunctionalitiesFunctionalities SBML model toolsSBML model tools
BuildBuild
Store Store
Share (private and public user space)Share (private and public user space) Dynamic stochastic simulationDynamic stochastic simulation
Gillespie stochastic simulatorGillespie stochastic simulator SBML Model and simulation data publishingSBML Model and simulation data publishing Web based interfaceWeb based interface
BASIS
System propertiesSystem properties High throughput computing (HTC)High throughput computing (HTC)
Condor HTC frameworkCondor HTC framework
High performance computingHigh performance computingCISBAN computer cluster (96 CPUs)CISBAN computer cluster (96 CPUs)
Parallel computing software frameworkParallel computing software framework
User friendly interfaceUser friendly interfaceWeb based tools with RIA (Rich Internet Application)Web based tools with RIA (Rich Internet Application)
Web service client libraries (R, Java, Python, Taverna, etc) Web service client libraries (R, Java, Python, Taverna, etc)
DependabilityDependabilityDependable system architectureDependable system architecture
SecuritySecurityUser account controlUser account control
InteroperabilityInteroperabilityWS-I compliant web servicesWS-I compliant web services
BASIS
System architectureSystem architecture
BASIS
System architectureSystem architecture
BASIS
System interfaceSystem interface
Web servicesWeb servicesBASIS user: BASIS user account registration, modification, etc. https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisUserService?WSDLBASIS model: model upload, modification, share, etc. https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisModelService?WSDLBASIS simulation: Runs simulation, checks job status, retrieves results, etc. https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisSimulationService?WSDLBASIS SBML: SBML upload, modification, conversion, etc https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisSBMLService?WSDLBASIS R portal: enables invocation with R script https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisWSRPortalService?WSDL
Web based tools on BASIS websiteWeb based tools on BASIS websiteUser account controlModel editingPrivate and public model managementRun simulations
BASIS
AimAim To provide a powerful new tool for the academic community To provide a powerful new tool for the academic community
based on advanced Bayesian statistical inference technology, based on advanced Bayesian statistical inference technology, which enables inferences to be made about kinetic parameters which enables inferences to be made about kinetic parameters within large and complex deterministic and stochastic network within large and complex deterministic and stochastic network models of biochemical pathways and cell signalling systems.models of biochemical pathways and cell signalling systems.
CaliBayes
System propertiesSystem properties HTCHTC
Dedicated HTC software frameworkDedicated HTC software framework HPCHPC
Powerful computer clusterPowerful computer cluster DependabilityDependability
Dependable system architectureDependable system architectureFault toleranceFault tolerance
InteroperabilityInteroperabilityWS-I compliant SOAP web servicesWS-I compliant SOAP web services
User friendlyUser friendlyWeb service client libraries (Java, R, etc)Web service client libraries (Java, R, etc)
Grid computingGrid computingSimulation web services: Fern, Copasi, BASIS, etcSimulation web services: Fern, Copasi, BASIS, etc
Free CaliBayes Java APIFree CaliBayes Java API
CaliBayes
System architectureSystem architecture
CaliBayes
System interfaceSystem interface CaliBayes web services:CaliBayes web services:
https://calibayes2.ncl.ac.uk:8181//CalibayesWS/CalibayesService?WSDLhttps://calibayes2.ncl.ac.uk:8181//CalibayesWS/CalibayesService?WSDL
Cohort simulation web services:Cohort simulation web services: https://calibayes2.ncl.ac.uk:8181//CalibayesWS/SimCohortService?WSDL#https://calibayes2.ncl.ac.uk:8181//CalibayesWS/SimCohortService?WSDL#
CaliBayes
Integrated application
Step 1: Create modelStep 1: Create model
Tools:Tools: BASIS SBML web servicesBASIS SBML web services BASIS web-based BASIS web-based
mod2sbml convertermod2sbml converter basisR (package)basisR (package)
Integrated application
Step 2: prepare for calibrationStep 2: prepare for calibration Prior distributionPrior distribution Experimental dataExperimental data settings, etcsettings, etc
Tools:Tools: calibayesR packagecalibayesR package
Integrated application
Step 3: calibrate the modelStep 3: calibrate the model produce posterior distributionproduce posterior distribution
Tools:Tools: CaliBayes web servicesCaliBayes web services calibayesR packagecalibayesR package
Integrated application
Step 4: Step 4: in silicoin silico experiments with the model experiments with the model
Tools:Tools: BASIS Forward simulation web servicesBASIS Forward simulation web services basisR (package)basisR (package) CaliBayes Cohort simulation web servicesCaliBayes Cohort simulation web services calibayesR (package)calibayesR (package)
Integrated application
FunctionalitiesFunctionalities
DependabilityDependability
Scalability and capacityScalability and capacity
SecuritySecurity
Rich Internet applicationRich Internet application
Future work
BASISBASIS Conor LawlessConor Lawless Carole Proctor Carole Proctor Colin GillespieColin Gillespie Daryl ShanleyDaryl Shanley Darren WilkinsonDarren Wilkinson Richard BoysRichard Boys Tom KirkwoodTom Kirkwood
TEAM
CaliBayesCaliBayes Colin GillespieColin Gillespie Conor LawlessConor Lawless Jake WuJake Wu Darren WilkinsonDarren Wilkinson Richard BoysRichard Boys Tom KirkwoodTom Kirkwood
AcknowledgementAcknowledgement Daniel Swan, Anthony Youd, Michael BeatyDaniel Swan, Anthony Youd, Michael Beaty BBSRCBBSRC
Thanks
