Prediction, Analysis and Simulation of Metabolic Reaction Networks

PASMet is a web-based platform for predicting, modelling and analysing metabolic systems. It is a non-commercial and user-friendly tool for assisting non-experts in mathematical modelling, computing or programming to work on computational biology.

See available tools


Prediction 1

Prediction of metabolic pathway

This function processes time-series data of metabolite concentrations and utilises them to predict a probable metabolic pathway using Granger causality test.

Prediction 2

Prediction of metabolic pathway and regulation

This function uses time-series of metabolic concentrations to predict a probable metabolic pathway with regulations using BST-loglem method which combines statistical techniques and mathematical modelling.


Construction of mathematical model

This function utilises time-series data of metabolite concentrations to construct a simple mathematical model. The model parameters are estimated using Levenberg-Marquardt algorithm coupled with ODE solver.


Simulation of metabolic behaviour

This function offeres the selection of methods to solve ordinary differential equations to observe dynamic behaviours of metabolite conccentrations using a mathematical model.


Analysis of metabolic system

This function analyses metabolic systems using a mathematical model. It provides sensitivity analysis, logarithmic gains, and bottleneck ranking indicator to compare perturbation effects and check model stability.



  • A tutorial on how to use PASMet is available here.




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Every comment helps us to improve PASMet.
Please feel free to contact us for queries, discussions and suggestions.

PASMet Development Team
Metabolic Systems Research Team
RIKEN Center for Sustainable Resource Science
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan

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