Tools for kinetic modeling of biochemical networks

Rui Alves, Fernando Antunes, Armindo Salvador
2006 Nature Biotechnology  
The number of software packages for kinetic modeling of biochemical networks continues to grow. Although most packages share a common core of functionality, the specific capabilities and user interfaces of different packages mean that choosing the best package for a given task is not trivial. We compare 12 software packages with respect to their functionality, reliability, efficiency, user-friendliness and compatibility. Although most programs performed reliably in all numerical tasks tested,
more » ... ML compatibility and the set-up of multicompartmentalization are problematic in many packages. For simple models, GEPASI seems the best choice for nonexpert users. For large-scale models, environments such as Jarnac/JDesigner are preferable, because they allow modular implementation of models. Virtual Cell is the most versatile program and provides the simplest and clearest functionality for setting up multicompartmentalization. The rapid popularization of software for kinetic modeling as a tool in biological research makes a comparative review of a representative sample of the available software timely. This outline is intended to guide non-experts in choosing the best kinetic modeling software to meet the requirements of the task at hand. General information about the software packages Using a set of test models (Supplementary Note 1 online), we evaluated both stand-alone simulators and Internet simulation servers ( Table 1) . Whereas stand-alone simulators store models and perform the numerical computations in the user's computer, Internet simulation servers do so centrally, in the remote server. The latter approach allows multiple researchers at distant locations to collaborate in developing and analyzing a model. It also renders the simulations independent of the locally available computational resources, which is relevant for computationintensive stochastic (in the case of BASIS) or reaction-diffusion (in the case of Virtual Cell) models. However, as the turnaround time for results depends on the workload on the servers and Internet congestion, Internet simulation servers are less effective than stand-alone packages for undemanding simulation tasks. File-sharing systems over the web also permit remote sharing of models using stand-alone simulators. However, Internet simulation servers provide better integrated environments for collaborative work, which are more convenient to use and require less computer-science expertise from users. Available stand-alone simulators range from simple user-friendly simulators (for example, Dynetica, GEPASI, PLAS) to relatively complex modeling environments (for example, Jarnac, JSim). The former are well-suited for non-expert modelers, and are very work-effective for most typical modeling tasks. They have intuitive user interfaces, and even those lacking a graphic user interface permit models to be rapidly set up by using a text interface window and a simple syntax. Modeling environments are better suited for large-scale projects, as they offer functionality for modular set-up of kinetic models and for automation of repetitive tasks. However, they require learning a package-specific modeling language.
doi:10.1038/nbt0606-667 pmid:16763599 fatcat:us5czy23mzgplnkhdevyjnqgxu