Download CaliBayes and BASIS

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
Introduction
BASIS
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Biology of Ageing e-Science Integration and Simulation System
Web-based Systems Biology application that provides high
performance computing power for dynamic biological simulation.
www.basis.ncl.ac.uk
CaliBayes
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A powerful tool based on advanced Bayesian statistical
inference technology for inferences about kinetic parameters
within deterministic and stochastic SBML models
www.calibayes.ncl.ac.uk
BASIS & CaliBayes
Functionalities
System properties
System architecture
Combined Workflow
BASIS
Functionalities
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SBML model tools
Build
Store
Share (private and public user space)
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Dynamic stochastic simulation
Gillespie stochastic simulator
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SBML Model and simulation data publishing
Web based interface
BASIS
System properties
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High throughput computing (HTC)
Condor HTC framework
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High performance computing
CISBAN computer cluster (96 CPUs)
Parallel computing software framework
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User friendly interface
Web based tools with RIA (Rich Internet Application)
Web service client libraries (R, Java, Python, Taverna, etc)
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Dependability
Dependable system architecture
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Security
User account control
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Interoperability
WS-I compliant web services
BASIS
System architecture
BASIS
System architecture
BASIS
System interface
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Web services
BASIS user: BASIS user account registration, modification, etc.
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisUserService?WSDL
BASIS model: model upload, modification, share, etc.
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisModelService?WSDL
BASIS simulation: Runs simulation, checks job status, retrieves results, etc.
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisSimulationService?WSDL
BASIS SBML: SBML upload, modification, conversion, etc
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisSBMLService?WSDL
BASIS R portal: enables invocation with R script
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisWSRPortalService?WSDL
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Web based tools on BASIS website
User account control
Model editing
Private and public model management
Run simulations
CaliBayes
Aim
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To provide a powerful new tool for the academic community
based on advanced Bayesian statistical inference technology,
which enables inferences to be made about kinetic parameters
within large and complex deterministic and stochastic network
models of biochemical pathways and cell signalling systems.
CaliBayes
System properties
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HTC
Dedicated HTC software framework
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HPC
Powerful computer cluster
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Dependability
Dependable system architecture
Fault tolerance
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Interoperability
WS-I compliant SOAP web services
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User friendly
Web service client libraries (Java, R, etc)
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Grid computing
Simulation web services: Fern, Copasi, BASIS, etc
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Free CaliBayes Java API
CaliBayes
System architecture
CaliBayes
System interface
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CaliBayes web services:
https://calibayes2.ncl.ac.uk:8181//CalibayesWS/CalibayesService?WSDL
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Cohort simulation web services:
https://calibayes2.ncl.ac.uk:8181//CalibayesWS/SimCohortService?WSDL#
Integrated application
Integrated application
Step 1: Create model
Tools:
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BASIS SBML web services
BASIS web-based
mod2sbml converter
basisR (package)
Integrated application
Step 2: prepare for calibration
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Prior distribution
Experimental data
settings, etc
Tools:
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calibayesR package
Integrated application
Step 3: calibrate the model
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produce posterior distribution
Tools:
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CaliBayes web services
calibayesR package
Integrated application
Step 4: in silico experiments with the model
Tools:
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BASIS Forward simulation web services
basisR (package)
CaliBayes Cohort simulation web services
calibayesR (package)
Future work
Functionalities
Dependability
Scalability and capacity
Security
Rich Internet application
TEAM
BASIS
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Conor Lawless
Carole Proctor
Colin Gillespie
Daryl Shanley
Darren Wilkinson
Richard Boys
Tom Kirkwood
CaliBayes
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Colin Gillespie
Conor Lawless
Jake Wu
Darren Wilkinson
Richard Boys
Tom Kirkwood
Acknowledgement
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Daniel Swan, Anthony Youd, Michael Beaty
BBSRC
Thanks