DA 1.0: parameter estimation of biological pathways using data assimilation approach.

Abstract

Data assimilation (DA) is a computational approach that estimates unknown parameters in a pathway model using time-course information. Particle filtering, the underlying method used, is a well-established statistical method that approximates the joint posterior distributions of parameters by using sequentially generated Monte Carlo samples. In this article, we report the release of Java-based software (DA 1.0) with an intuitive and user-friendly interface to allow users to carry out parameters estimation using DA. DA 1.0 was developed using Java and thus would be executable on any platform installed with JDK 6.0 (not JRE 6.0) or later. DA 1.0 is freely available for academic users and can be launched or downloaded from http://da.csml.org.