SimBiology

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In SimBiology, there is a limited set of units one case use. Amount, or concentration. This is often inconvenient, as (for example) I might want to use timers (units of time), or surrogates for concentration (like MFI for nanomoles/milliliter). Too, many sbml models use units that aren't in the set of acceptable ones. One can use user-defined units, but these generally link with defined units and this means that one could have unit conversions that have no bearing on reality. What is the recommended work-around for this? What progress has been made with respect to allowing species units that are neither amounts nor concentrations? Thanks!

I based my model construction on this PBPK model: PBPK by Armin Sepp. While this is a very convenient script for building a PBPK two-pore model, it's very incovenient for my application to have the species Units defined in molarity. Is there a convenient way to organically switch this model from molarity to grams (or any weight unit)? Fast way to convert a model from molarity to grams Hi @Elisa, I would recommend to leave the model as is and add observables that convert the states of interest to units of grams using the associated molecular weight. Best regards, Jérémy simbiology pbpk units

Is there a way on simbiology Model Builder to set the unit of all species at the same time? For example, something like an option: Set all Species units to micromole. ?

I wonder why SimBiology does not detect any issues in the following model. A cell, Cell, is producing signaling molecule, Sig, with following reaction: Reaction 1: Cell -> Cell + Sig: kprod * Cell Reaction 2: Sig -> null: kel*Sig Units are as follows Cell [molecule] Sig [mole / milliliter] kprod [gram / (molecule * day)] kel [1/day] The ODE seems to be correct: d(Sig)/dt = 1/Comp1*((kprod*Cell) - ((kel*Sig)*Comp1)) BUT there should be an error as the units don't match. Any comments would be very appreciated! See below the screenshort of the model and settings plus sbproj. EDIT: adding molecular mass into the production rate: kprod / MM * Cell solves the unit Issue of course, but I would expect that such inconsistency would be detected by the software. PS: MM [g/mol]

I would like to use "mL/kg" for compartment unit and "mg/kg" for species unit in SimBiology model. After I add "milliliter/kilogram" in library and enter it in CapacityUnits for compartment, I get a following warning message. ERROR: Configuration Warning Invalid CapacityUnits. Valid unit types are length, area, and volume. kA03q000001HnlWCAS 000147611

SimBiology において、compartment を 100mL/kg や、species を 1 mg/kg などの単位で設定することができるか、教えてください。​ ライブラリに milliliter/kilogram を登録した後、compartment の CapacityUnits にこの単位を設定すると、以下の警告メッセージが表示されます。   Configuration Warning Invalid CapacityUnits. Valid unit types are length, area, and volume. kA03q000001HnlWCAS 000147611

Hi, I am tyring to build a model using reversible mass action kinetics (Matlab R2016a, Win 8.1 x64). My species units are all in molarity and I calculate the forward reaction rate units should 1/(mol/l)*second and reverse reaction units as 1/second. However, Simbiology repeatedly fails dimensional analysis when trying to run a simulation reporting that 'Quantities of different dimensions cannot be added or subtracted'. My reactions are all quite straight forward: [A]*[B] < - > [AB] so I don't understand why this is causing such problems. Also tried the units from the <https://uk.mathworks.com/help/simbio/ug/defining-reaction-rates-with-mass-action-kinetics.html manual> but still the same error. Does anybody know how to resolve this? I have even tried randomly changing units to all possible combinations in the drop down menus and no units of concentration or mass pass dimensional analysis. Thanks for any help.