MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models

Bioinformatics. 2011 Mar 1;27(5):734-5. doi: 10.1093/bioinformatics/btq727. Epub 2011 Jan 5.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Confidence Intervals
  • Models, Biological*
  • Models, Statistical*
  • Software*
  • Systems Biology / methods*