ProMoT: modular modeling for systems biology
نویسندگان
چکیده
SUMMARY The modeling tool PROMOT facilitates the efficient and comprehensible setup and editing of modular models coupled with customizable visual representations. Since its last major publication in 2003, PROMOT has gained new functionality in particular support of logical models, efficient editing, visual exploration, model validation and support for SBML. AVAILABILITY PROMOT is an open source project and freely available at http://www.mpi-magdeburg.mpg.de/projects/promot/.
منابع مشابه
Modular Modeling of Cellular Systems with ProMoT/Diva
MOTIVATION Need for software to setup and analyze complex mathematical models for cellular systems in a modular way, that also integrates the experimental environment of the cells. RESULTS A computer framework is described which allows the building of modularly structured models using an abstract, modular and general modeling methodology. With this methodology, reusable modeling entities are ...
متن کاملAn Improved Modular Modeling for Analysis of Closed-Cycle Absorption Cooling Systems
A detailed modular modeling of an absorbent cooling system is presented in this paper. The model including the key components is described in terms of design parameters, inputs, control variables, and outputs. The model is used to simulate the operating conditions for estimating the behavior of individual components and system performance, and to conduct a sensitivity analysis based on the give...
متن کاملAutomatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules
MOTIVATION The modularity of biochemical networks in general, and signaling networks in particular, has been extensively studied over the past few years. It has been proposed to be a useful property to analyze signaling networks: by decomposing the network into subsystems, more manageable units are obtained that are easier to analyze. While many powerful algorithms are available to identify mod...
متن کاملApplication of the Process Modeling Tool Promot to the Modeling of Metabolic Networks
The process modeling tool ProMoT [6, 5] has been developed for the object-oriented and equation-based modeling of chemical processes. This contribution presents the application of ProMoT to a novel application field: the design and implementation of a knowledge base for modeling metabolic networks in living cells. This knowledge base contains predefined modeling entities for the hierarchical ag...
متن کاملProgramming biological models in Python using PySB
Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Bioinformatics
دوره 25 شماره
صفحات -
تاریخ انتشار 2009