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.

• COPASI Project home: http://www.copasi.org/tiki-index.php
• COPASI Web User Interface: http://turing.mib.man.ac.uk:8080/CopasiWeb/CopasiWebUI/

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

• http://rest.g-language.org/copasi/
• http://useG.jp/copasi/ (this URL forwards to the above)

Syntax

http://rest.g-language.org/copasi/[analysis]/[ID]/[option]=[value]/

List of available methods

• http://rest.g-language.org/copasi/ (analysis methods)

File upload

• http://rest.g-language.org/copasi/ 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:
• http://rest.g-language.org/copasi/[ID]/[ID].xml

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

• http://rest.g-language.org/copasi/simulate/5A0ECD/start=0/steps=20/

Metabolic Control Analysis

syntax

http://rest.g-language.org/copasi/mca/[ID]/

options

• Modulation Factor: modulation (default: 1e-9)

example

• http://rest.g-language.org/copasi/mca/5A0ECD/modulation=1e-8/

Sensitivity

syntax

http://rest.g-language.org/copasi/sensitivity/[ID]/

options

• Delta factor: delta (default: 0.001)
• Delta minimum: minimum (default: 1e-12)

example

• http://rest.g-language.org/copasi/sensitivity/5A0ECD/delta=0.005/

Steady State Analysis

syntax

http://rest.g-language.org/copasi/steadystate/[ID]/

options

• None.

example

• http://rest.g-language.org/copasi/sensitivity/5A0ECD/