MIRACH: efficient model checker for quantitative biological pathway models
- 1NUS Graduate School for Integrative Sciences and Engineering, Singapore 117597, 2School of Computing, National University of Singapore, Computing Drive, Singapore 117417 and 3Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- * To whom correspondence should be addressed.
- Received December 2, 2010.
- Revision received December 2, 2010.
- Accepted December 27, 2010.
Abstract
Summary: Model checking is playing an increasingly important role in systems biology as larger and more complex biological pathways are being modeled. In this article we report the release of an efficient model checker MIRACH 1.0, which supports any model written in popular formats such as CSML and SBML. MIRACH is integrated with a Petri-net-based simulation engine, enabling efficient online (on-the-fly) checking. In our experiment, by using Levchenko et al. model, we reveal that timesaving gains by using MIRACH easily surpass 400% compared with its offline-based counterpart.
Availability and implementation: MIRACH 1.0 was developed using Java and thus executable on any platform installed with JDK 6.0 (not JRE 6.0) or later. MIRACH 1.0, along with its source codes, documentation and examples are available at http://sourceforge.net/projects/mirach/ under the LGPLv3 license.
Contact: masao{at}ims.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
- © The Author 2011. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
