<ns4:p>JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological pharmacological systems through the testing of model solutions against data. It designed interactive, iterative manipulation code, handling multiple data sets parameter sets, making comparisons among different models running simultaneously or separately. Interactive use supported by large collection graphical user interfaces writing compilation diagnostics, defining...

Abstract We describe a web-based tool, MakeSBML ( https://sys-bio.github.io/makesbml/ ), that provides an installation-free application for creating, editing, and searching the Biomodels repository SBML-based models. is client-based web translates models expressed in human-readable Antimony to System Biology Markup Language (SBML) vice-versa. Since it requires no installation on user’s part. Currently, hosted GitHub page where design makes trivial move other hosts. This model software...

<ns4:p>JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological pharmacological systems through the testing of model solutions against data. It designed interactive, iterative manipulation code, handling multiple data sets parameter sets, making comparisons among different models running simultaneously or separately. Interactive use supported by large collection graphical user interfaces writing compilation diagnostics, defining...

A four-region (capillary plasma, endothelium, interstitial fluid, cell) multipath model was configured to describe the kinetics of blood-tissue exchange for small solutes in lung, accounting regional flow heterogeneity, permeation cell membranes and through interendothelial clefts, intracellular reactions. Serotonin uptake data from Multiple indicator dilution "bolus sweep" experiments Rickaby coworkers (Rickaby DA, Linehan JH, Bronikowski TA, Dawson CA. J Appl Physiol 51: 405-414, 1981; CA,...

<ns4:p>JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological pharmacological systems through the testing of model solutions against data. It designed interactive, iterative manipulation code, handling multiple data sets parameter sets, making comparisons among different models running simultaneously or separately. Interactive use supported by large collection graphical user interfaces writing compilation diagnostics, defining...

Abstract Biology is perhaps the most complex of sciences, given incredible variety chemical species that are interconnected in spatial and temporal pathways daunting to understand. Their interconnections lead emergent properties such as memory, consciousness, recognition self non‐self. To understand how these reactions cellular life characterized by activation, inhibition, regulation, homeostasis, adaptation, computational analyses simulations essential, a fact recognized biological...

Enzyme kinetics is challenging for students to understand and apply. Why? Perhaps it's because we teach it in isolation rarely revisit a class or throughout the biology chemistry curricula. It also requires integrate mathematical, structural, mechanistic understandings, tall order requiring cognitive processing multiple fields. Students generally conservation of mass, length, volume by about age 11, but derivative quantities take longer. Examples include density (m/V, 15) both concentration...

<ns4:p>The Modular Program Constructor (MPC) is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML) (<ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://www.physiome.org/jsim/">http://www.physiome.org/jsim/</ns4:ext-link>) that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models. A major obstacle writing complex for...

<ns4:p>The Modular Program Constructor (MPC) is an open-source Java based utility, built upon JSim's Mathematical Modeling Language (MML) (<ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://www.physiome.org/jsim/">http://www.physiome.org/jsim/</ns4:ext-link>) that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models. A major obstacle writing complex programs for...

<ns4:p>The Modular Program Constructor (MPC) is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML) (<ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://www.physiome.org/jsim/">http://www.physiome.org/jsim/</ns4:ext-link>) that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models. A major obstacle writing complex for...

Modeling cardiac energetics involves all of the elements supply or demand. It is complicated: exchange processes are distributed in space, heterogeneous, requiring parallel units interacting with each other. Multicomponent, multiscale models for analysis data complicated. Using modular aids building and maintenance. A convenient module one which number connecting variables minimized, internal complexity isolated. The differential equation modeling platform JSim designed model‐based using...

We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository SBML-based models. is client-based web translates models expressed in human-readable Antimony to System Biology Markup Language (SBML) vice-versa. Since it requires no installation on user's part. Currently, hosted GitHub page where design makes trivial move other hosts. This model software deployment also...

Biology is perhaps the most complex of sciences, given incredible variety chemical species that are interconnected in spatial and temporal pathways daunting to understand. Their interconnections lead emergent properties such as memory, consciousness, recognition self non-self. To understand how these reactions cellular life characterized by activation, inhibition, regulation, homeostasis, adaptation, computational analyses simulations essential, a fact recognized biological communities. At...

A four‐region (capillary plasma, endothelium, ISF, cell) blood tissue exchange model describes data from serotonin uptake experiments in dog lungs. Data Multiple Indicator Dilution of Rickaby et al. (JAP 51: 405,1981), and Malcorp 57: 720, 1984) were analyzed to distinguish facilitated transport into the endothelial cells (EC) permeation via interendothelial clefts. The permeability‐surface area products, PS, for inter‐EC clefts low, about 0.2 ml/(g*min). transporter kinetic parameters Km =...