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Updated: Jun 26, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Wagner diagram for modeling O2pathway-calculation and graphical display by the Helsinki O2Pathway Tool
Antti-Pekka E Rissanen1,2, Tom Mikkola1,3, Dominique D Gagnon1,2,4,5
1Helsinki Sports and Exercise Medicine Clinic, Foundation for Sports and Exercise Medicine (HULA), Helsinki, Finland.
None:
Objective.Maximal O2uptake (V˙O2max) reflects the individual's maximal rate of O2transport and utilization through the integrated whole-body pathway composed of the lungs, heart, blood, circulation, and metabolically active tissues. As such,V˙O2maxis strongly associated with physical capacity as well as overall health and thus acts as one predictor of physical performance and as a vital sign in determination of status and progress of numerous clinical conditions. Quantifying the contribution of single parts of the multistep O2pathway toV˙O2maxprovides mechanistic insights into exercise (in)tolerance and into therapy-, training-, or disuse-induced adaptations at individual or group levels. We developed a desktop application (Helsinki O2Pathway Tool-HO2PT) to model numerical and graphical display of the O2pathway based on the 'Wagner diagram' originally formulated by Peter D. Wagner and his colleagues.Approach.The HO2PT was developed and programmed in Python to integrate the Fick principle and Fick's law of diffusion into a computational system to import, calculate, graphically display, and export variables of the Wagner diagram.Main results.The HO2PT models O2pathway both numerically and graphically according to the Wagner diagram and pertains to conditions under which the mitochondrial oxidative capacity of metabolically active tissues exceeds the capacity of the O2transport system to deliver O2to the mitochondria. The tool is based on the Python open source code and libraries and freely and publicly available online for Windows, macOS, and Linux operating systems.Significance.The HO2PT offers a novel functional and demonstrative platform for those interested in examiningV˙O2maxand its determinants by using the Wagner diagram. It will improve access to and usability of Wagner's and his colleagues' integrated physiological model and thereby benefit users across the wide spectrum of contexts such as scientific research, education, exercise testing, sports coaching, and clinical medicine.
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