Koschorreck Markus, Gilles Ernst Dieter
Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr, 1, 39106 Magdeburg, Germany.
BMC Syst Biol. 2008 Oct 31;2:91. doi: 10.1186/1752-0509-2-91.
Combinatorial complexity is a challenging problem for the modeling of cellular signal transduction since the association of a few proteins can give rise to an enormous amount of feasible protein complexes. The layer-based approach is an approximative, but accurate method for the mathematical modeling of signaling systems with inherent combinatorial complexity. The number of variables in the simulation equations is highly reduced and the resulting dynamic models show a pronounced modularity. Layer-based modeling allows for the modeling of systems not accessible previously.
ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models, according to the layer-based approach. The model is defined using a simple but powerful rule-based syntax that supports the concepts of modularity and macrostates. ALC performs consistency checks on the model definition and provides the model output in different formats (C MEX, MATLAB, Mathematica and SBML) as ready-to-run simulation files. ALC also provides additional documentation files that simplify the publication or presentation of the models. The tool can be used offline or via a form on the ALC website.
ALC allows for a simple rule-based generation of layer-based reduced models. The model files are given in different formats as ready-to-run simulation files.
组合复杂性对于细胞信号转导建模而言是一个具有挑战性的问题，因为少数蛋白质的关联可能产生大量可行的蛋白质复合物。基于层的方法是一种用于对具有内在组合复杂性的信号系统进行数学建模的近似但准确的方法。模拟方程中的变量数量大幅减少，所得动态模型呈现出显著的模块化。基于层的建模允许对以前无法建模的系统进行建模。
ALC（自动层构建）是一个计算机程序，它根据基于层的方法极大地简化了简化模块化模型的构建。该模型使用简单但强大的基于规则的语法进行定义，这种语法支持模块化和宏观状态的概念。ALC对模型定义进行一致性检查，并以不同格式（C MEX、MATLAB、Mathematica和SBML）提供模型输出作为可直接运行的模拟文件。ALC还提供额外的文档文件，简化了模型的发表或展示。该工具既可以离线使用，也可以通过ALC网站上的表单使用。
ALC允许基于简单规则生成基于层的简化模型。模型文件以不同格式作为可直接运行的模拟文件给出。
