NAME

Bio::ECell - Perl interface for E-Cell Simulation Environment.

SYNOPSIS

    use Bio::ECell;

    my $ecell = Bio::ECell::new();

    $ecell->loadModel("simple.eml");
    $ecell->message("Message from Perl!");

    my $logger = $ecell->createLoggerStub('Variable:/:S:Value');
    $logger->create();

    print $ecell->getCurrentTime(), "\n";
    $ecell->run(100);
    print $ecell->getCurrentTime(), "\n";

    my $data = Bio::ECell->ECDDataFile($logger );
    $data->setDataName( $logger->getName() );
    $data->save('S.ecd');

DESCRIPTION

Bio::ECell is a Perl interface for the E-Cell Simulation Environment version 3 (http://www.e-cell.org/), a generic cell simulation software for molecular cell biology researches that allow object-oriented modeling and simulation, multi-algorithm/time-scale simulation, and scripting through Python. This module allows scripting of sessions with Perl.

For the details of the E-Cell API, users should refer to the chapter about scripting a simulation session of E-Cell3 Users Manual, available at the above-mentioned web-site.

new

The constructor is just a wrapper around the instance given by

    ecell.Session(ecell.emc.Simulator())

in Python.

Basically functions required for scripting can be called from this instance.

ECDDataFile

ECDDataFile constructor can be called as follows:

    $ecell = Bio::ECell::new();
    $logger = $ecell->createLoggerStub('Path-name-for-logger');
    $logger->create();
    $data = Bio::ECell->ECDDataFile( $logger );

Here usage is slightly different from the Python interface, passing the logger instance instead of the DATA tuple. Internally the system calls logger.getData() to pass onto ECDDataFile.

SEE ALSO

For complete descriptions of E-Cell API, see http://www.e-cell.org/software/documentation/ecell3-users-manual_0606.pdf

AUTHOR

Kazuharu Arakawa, <gaou@sfc.keio.ac.jp>

COPYRIGHT AND LICENSE

Copyright (C) 2007 by Kazuharu Arakawa

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.5 or, at your option, any later version of Perl 5 you may have available.