ecell

REST Service for E-Cell 3

E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components driven by multiple algorithms with different timescales to coexist in a model. E-Cell 3 is mainly developed by the Institute for Advanced Biosciences, Keio University. E-Cell 3 supports models in the SBML standard as well as E-Cell Model description language EML.

We here provide a REST service for this E-Cell software through Bio::ECell module.

• E-Cell Project home: http://www.e-cell.org/
• Bio::ECell: http://search.cpan.org/search?query=Bio%3A%3AEcell&mode=all

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

• http://www.e-cell.org/ecell/software/e_cell-3-documentation
• A Multi-algorithm, Multi-timescale Method for Cell Simulation, Kouichi Takahashi, Kazunari Kaizu, Bin Hu, and Masaru Tomita, Bioinformatics, 20: 538-546, 2004.

Overview

Base URL

• http://rest.g-language.org/ecell/

Syntax

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

File upload

• http://rest.g-language.org/ecell/

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

• http://rest.g-language.org/ecell/data/[ID]/[ID].eml

Simulation

syntax

http://rest.g-language.org/ecell/run/[ID]/

Another ID is returned to view the results at the following URL:

• http://rest.g-language.org/ecell/data/[Session ID]/

This folder contains models in the original format submitted to the service, model in EML format, and the time-series in ECD format as well as graphs in PNG format.

options

• Step size: step (default: 0.001)
• Duration: duration (default: 10)

example

• http://rest.g-language.org/ecell/run/672F5C/step=0.001/duration=10