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BASIS Software
Gillespie Stochastic Simulator
Download:
gillespie2-0.2.tar.gz
Version 0.2 is modified for libsbml 3.2 compatability and with a new facility for including random distributions with MathML using CSymbol element (see distributions (PDF) for further details).
To decompress and unpack the archive, type:
tar –xvfz gillespie2-0.2.tar.gz
The makefile and source code are in the directory src.
The directory test contains some sbml files to test the simulator.
The file README.txt gives instructions for installing and running
the simulator.
The simulator also includes an optional swig python interface.
Discrete Stochastic Model Test Suite
This test suite contains SBML models which can be used to validate a stochastic simulator.
pysbml (Python SBML Library)
pysbml is a library for console-based modelling in Python. More information about pysbml, and the library itself can be found here.
SBML Web Services
A variety of SBML tools are exposed as BASIS web-services. These tools include model visualization, validation and conversion to an HTML document for displaying SBML within a web-browser. Please look through our Python demo script for more information.
SBML Shorthand
SBML shorthand is a version of SBML that is much easier to read and write by hand than real SBML. Further details about SBML shorthand can be found Darren Wilkinson's web pages.
BASIS SOAP Web Services
BASIS user: BASIS user account registration, modification, etc.
http://basis1.ncl.ac.uk:81//BasisWebServices/BasisUserService?WSDL
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisUserService?WSDL
BASIS model: model upload, modification, share, etc.
http://basis1.ncl.ac.uk:81//BasisWebServices/BasisModelService?WSDL
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisModelService?WSDL
BASIS simulation: Runs simulation, checks job status, retrieves results, etc.
http://basis1.ncl.ac.uk:81//BasisWebServices/BasisSimulationService?WSDL
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisSimulationService?WSDL
BASIS SBML: SBML upload, modification, conversion, etc.
http://basis1.ncl.ac.uk:81//BasisWebServices/BasisSBMLService?WSDL
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisSBMLService?WSDL
BASIS forward simulation: forward simulation with given sbml model and parameters
http://basis1.ncl.ac.uk:81/BasisWebServicesDebug/ForwardSimulationService?wsdl
https://basis1.ncl.ac.uk:8181/BasisWebServicesDebug/ForwardSimulationService?wsdl
BASIS R portal: enables invocation with R script
http://basis1.ncl.ac.uk:81//BasisWebServices/BasisWSRPortalService?WSDL
https://basis1.ncl.ac.uk:8181//BasisWebServices/BasisWSRPortalService?WSDL
BASIS SOAP Web Services R Client Library
NEWS: We have recently submitted an article which provides an overview of BASIS and CaliBayes, and illustrates the architecture and its use in practice: (more infomation...)
Chen, Y., Lawless, C., Gillespie, C.S., Wu, J., Boys, R.J., Wilkinson, D.J. (2009) CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models, in submission.
basisR_0.1-4.tar.gz
basisR_0.1-4.zip
