Easy Metabolic Simulations with PASMet

December 26, 2016

A new tool to assist mathematical analysis in the life sciences

RIKEN CSRS researchers have developed a web tool for reproducing the metabolic behaviors of intracellular chemical reactions on a computer, calling it PASMet (Prediction, Analysis and Simulation of Metabolic Reaction Networks).

The thousands of chemical compounds in a cell undergo a large number of chemical reactions as part of a “metabolite reaction network.” Computer analysis is used to understand the metabolic dynamics and systems of these networks, but such analysis requires specialized knowledge of mathematics and programming, which has largely restricted such work to scientists such as information scientists.

PASMet has been designed as an entry-level web tool for mathematical analysis of metabolism. Researchers simply upload the time-series data for metabolite amounts obtained from biological experiments to PASMet, which runs a simulation to predict unknown metabolic networks or build mathematical models. One example would be a simulation of the changes in the amounts of metabolic products resulting from a gene modification.

In addition to providing a basic understanding of metabolic networks, PASMet is expected to simplify applied research such as artificial metabolism design. PASMet also has the potential to contribute to identification of metabolic pathways for drug discovery through increased understanding of metabolic changes related to human diseases.


Original article
Nucleic Acids Research doi:10.1093/nar/gkw415
K. Sriyudthsak, R. F. Mejia, M. Arita, M. Y. Hirai,
"PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems".

Masami Hirai; Team Leader
Kansuporn Sriyudthsak; Research Scientist
Metabolic Systems Research Team