title: PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems.
abstract: PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematical modelling. PASMet offers a series of user-functions to handle the time-series data of metabolite concentrations. The functions are organised into four steps: (i) Prediction of a probable metabolic pathway and its regulation; (ii) Construction of mathematical models; (iii) Simulation of metabolic behaviours; and (iv) Analysis of metabolic system characteristics. Each function contains various statistical and mathematical methods that can be used independently. Users who may not have enough knowledge of computing or programming can easily and quickly analyse their local data without software downloads, updates or installations. Users only need to upload their files in comma-separated values (CSV) format or enter their model equations directly into the website. Once the time-series data or mathematical equations are uploaded, PASMet automatically performs computation on server-side. Then, users can interactively view their results and directly download them to their local computers. PASMet is freely available with no login requirement at http://pasmet.riken.jp/ from major web browsers on Windows, Mac and Linux operating systems.
authors.affiliation: RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Kansuporn
authors.initials: K
authors.lastname: Sriyudthsak
authors.affiliation: RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Ramon Francisco
authors.initials: RF
authors.lastname: Mejia
authors.affiliation: RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Arita
authors.affiliation: RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan masami.hirai@riken.jp.
authors.forename: Masami Yokota
authors.initials: MY
authors.lastname: Hirai
mesh_terms: D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D016247:Information Storage and Retrieval; D020407:Internet; D013294:Lactococcus lactis / Q000235:genetics / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D015233:Models, Statistical; D012984:Software