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copasi

Proxy REST Service for Copasi

Complex Pathway Simulator (COPASI) is a software application for simulation and analysis of biochemical networks and their dynamics developed by the Mendes Lab at VBI and Kummer Lab at EML Research. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI also carries out several analyses of the network and the dynamics, such as steady state stability, parameter sensitivity, elementary flux modes, Lyapunov exponents. Any feature of a model can be optimized using a variety of diverse non-linear optimization algorithms. Parameter values can be estimated from data using a very customizable framework.

We here provide a REST service for this COPASI software as a proxy to the COPASI Web User Interface.

Users of this service should also consult the original documentations of COPASI, and cite the following article.

  • Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., and Kummer, U. (2006). COPASI — a COmplex PAthway SImulator. Bioinformatics 22, 3067-74.

Overview

Base URL
Syntax
http://rest.g-language.org/copasi/[analysis]/[ID]/[option]=[value]/
List of available methods

File upload

POST your model in SBML or CopasiML format to this URL, and an ID is returned. Using the given ID, you can view the uploaded model in SBML format (if CopasiML is uploaded, it is readily converted to SBML) can be seen at the following URL:

Simulation

syntax
http://rest.g-language.org/copasi/simulate/[ID]/
options
  • Logging start time: start (default: 0)
  • Step size: stepsize (default: 0.01)
  • Step number: steps (default: 10)
example

Metabolic Control Analysis

syntax
http://rest.g-language.org/copasi/mca/[ID]/
options
  • Modulation Factor: modulation (default: 1e-9)
example

Sensitivity

syntax
http://rest.g-language.org/copasi/sensitivity/[ID]/
options
  • Delta factor: delta (default: 0.001)
  • Delta minimum: minimum (default: 1e-12)
example

Steady State Analysis

syntax
http://rest.g-language.org/copasi/steadystate/[ID]/
options
  • None.
example
copasi.txt · Last modified: 2014/01/18 07:44 (external edit)