At its core, ubiquity is a modeling language and a set of scripts meant to facilitate model development and deployment. The focus of this vignette is on the model description language. This is a plain text file, referred to as a **system file**. Each line contains a descriptor (e.g. `<P>`

) which defines an aspect of the model, and comments are made with the hash sign (`#`

). What follows is an overview of the different components of the language that can be used to create a system file.

`<P>`

Each system parameter is specified with a name, value, lower bound, upper bound, units, whether it should be editable in the ShinyApp and the ‘type’ of parameter (grouping in the ShinyApp). The values of eps (machine precision, smallest value that is not zero) and inf (infinity) can be used. For example to specify a parameter koffR with a value of .1 that is positive and a parameter KDR with a value of .04 that is also positive:

```
# name value lb ub units editable type
<P> koffR 0.1 eps inf 1/hr yes Target
<P> KDR 0.04 eps inf nM yes Target
```

Often a model will be developed to incorporate different situations or scenarios. For example, a model may be used to describe both healthy and diseased individuals. When these differences are simply parametric in nature, it can be cumbersome to code a model multiple times (once for each parameterization). This framework provides a mechanism for including multiple parameterizations withing the same system file. Consider the system below where we want to describe antibody disposition. For humans this is described by a two compartment model, but for mice a single compartment is needed.

First we create a set of parameters describing the human scenario. These are the mean parameters taken from the literature [DM]:

```
<P> Weight 70.0 eps inf kg yes System # Organism weight
<P> CL 0.0129 eps inf L/hr yes System # Systemic Clearance
<P> Q 0.0329 eps inf L/hr yes System # Inter-compartmental clearance
<P> Vp 3.1 eps inf L yes System # Vol. central compartment
<P> Vt 2.8 eps inf L yes System # Vol. peripheral compartment
```

When a parameter is created using the `<P>`

descriptor it is part of the `default`

parameter set. This is the short name^{1} for a parameter set. A longer more verbose name can be given as well, and this is what will be seen in the ShinyApp. The human parameter set can be labeled using the `PSET`

descriptor in the following way:

`<PSET:default> mAb in Human`

Where `default`

is the parameter set short name name, and “mAb in Human” is the value shown to the user in the ShinyApp.

Next, to add the parameterization for mice we simply create a new set in the following way:

`<PSET:mouse> mAb in Mouse`

This alone would create a new parameter set with a short name `mouse`

, and is an exact copy of the default parameter set. To identify the parametric differences between the `mouse`

and `human`

we use `PSET`

in the following way:

```
<PSET:mouse:Weight > 0.020 # 20 gram mouse
<PSET:mouse:CL > 7.71e-6
<PSET:mouse:Q> 0.0
<PSET:mouse:Vp > 1.6e-3
<PSET:mouse:Vt > 1 # arbitrary
```

Consider the clearance parameter entry where we want the murine half-life of an antibody [VR]:

`<PSET:mouse:CL> 7.71e-6`

We use the set name (`mouse`

) and the parameter name (`CL`

) and then we overwrite the default with the specified value `7.71e-6`

. The other aspects of the parameter (bounds, edit flag, etc.) will be the same as the default value.

`<As>`

and `<Ad>`

A static secondary parameter refers to parameter does not change during a simulation. These are specified using the `<As>`

descriptor and can be written in terms of system parameters or previously defined static secondary parameters. These can be used in differential equations, defining initial conditions, input scaling and model outputs. This is similar to secondary parameters defined in the `$PK`

block in NONMEM. For example, if you wanted to define the rate of elimination in terms of the system parameters for clearance `CL`

and volume of distribution `Vp`

the following would be used:

`<As> kel = CL/Vp`

A dynamic secondary parameters refers to a parameter that can change during a simulation. This typically means it is defined, using the `<Ad>`

descriptor, in terms of a state or another dynamic secondary parameter. These can be used in differential equations and model outputs. These are similar to the parameters defined in the `$DES`

block in NONMEM. For example if you wanted to use the concentration in the central compartment `Cp`

but it was dependent on the amount in that compartment `Ap`

and the volume of that compartment `Vp`

the following would be used:

`<Ad> Cp = Ap/Vp`

`<VP>`

Variance parameters are specified using the same format as system parameters (`<P>`

) :

```
# name value lower_bound upper_bound units editable grouping
<VP > SLOPE 0.01 eps inf 1/hr yes Variance
```

The difference being that the `<VP>`

descriptor is used and that the grouping is set to `Variance`

. These are used when performing parameter estimation and when simulating with residual variability.

`<IIV:?>?`

& `<IIVCOR:?>?`

Any variable name assigned to inter-individual variability (IIV) or correlation/covariance (IIVCOR) term that makes sense to the user may be used. The following sample codes have variable names (eg: ETACL) that most likely make sense to a population modeler or NONMEM user. To define an IIV term named `ETACL`

with a variance of `0.15`

use the following:

`<IIV:ETACL> 0.15`

The next we need to associate this IIV term with a system parameter. To associate this IIV term with the clearance (system parameter `CL`

) and specify that it has a log normal distribution (`LN`

) we would simply write:

`<IIV:ETACL:LN> CL`

Alternatively a normal (`N`

) distribution can be used.

Next we specify the IIV term `ETAV`

with a variance of `0.1`

. This IIV term also has a log normal distribution and is applied to the parameter `V`

:

```
<IIV:ETAV> 0.10
<IIV:ETAV:LN> V
```

Now we can define the covariance (off-diagonal elements) between `CL`

and `V`

to be `0.01`

by using:

`<IIVCOR:ETAV:ETACL> 0.01`

The order isn’t important and the IIV terms can be reversed

`<IIVSET:?>?`

& `<IIVCORSET:?>?`

By default all parameter sets will have inter individual variability specified using the `<IIV>`

and `<IIVCOR>`

descriptors. To associate a specific set of IIVs to a parameter set use the `<IIVSET>`

and `<IIVCORSET>`

descriptors. These set descriptors operate differently than the parameter set descriptors (`<PSET>`

). The `<PSET>`

just overwrites the default values and inherits the default variance/covariance information. If you alter the IIV information for a parameter set it will *reset* the IIV information for that parameter set. The entire variance covariance matrix will need to be specified for that parameter set.

If the parameter set `MYPSET`

has been defined then the following could be used to define the IIV for the parameters `Q`

and `CL`

:

```
<IIVSET:MYPSET:ETAQ> 0.05
<IIVSET:MYPSET:ETAQ:LN> Q
<IIVSET:MYPSET:ETACL> 0.25
<IIVSET:MYPSET:ETACL:LN> CL
<IIVCORSET:MYPSET:ETAQ:ETACL> 0.01
```

All the other system parameters will have no IIV information for this parameter set.

The differential equations in the system can be defined by simply writing them out. Alternative they can ‘built’ by using the different descriptors provided below. Part of the flexibility of ubiquity lies in the ability to combine these different notations. To construct a model (see section below: Bringing it all together) any combination of the five following methods can be used:

- Differential equations
`<ODE:?>`

- Reaction rates
`=?=>`

- Equilibrium relationships
`<=kforward:kreverse=>`

- Sources and sinks
`<S:?>`

- Movement between compartments
`<C>`

`<ODE:?>`

Portions of differential equations can be specified here where ? is the state or compartment. To define `dA/dT`

as `koffR*C - konR*A*B`

we would write:

`<ODE:A> koffR*C - konR*A*B `

It might be more convenient to specify an ODE across several lines, making things more readable. Just use multiple statements and they will be appended together. This would give the same result as the example above:

```
<ODE:A> koffR*C
<ODE:A> - konR*A*B
```

`=?=>`

It may be more convenient to write out chemical reactions rather than differential equations. This can be done using the general form:

`[CR1]Reactant1 + [CR2]Reactant2 + ... =kf=> [CP1]Product1 + [CP2]Product2 + ...`

Where the stoichiometric coefficients, beginning with `CR`

and `CP`

above, in brackets only need to be specified if they are not one. The reaction order will be assumed to be equal to the stoichiometric coefficient of the reactant. For a more specific example Consider decomposition of hydrogen peroxide into water and oxygen:

\[ H_2O_2 \xrightarrow{k_{deg}} H_2O + \frac{1}{2}O_2 \]

In the system format this would be written in the following manner:

`H2O2 =kdeg=> H2O + [1/2]O2`

And this will be translated in to the following differential equations:

```
<ODE:H2O2> - kdeg*H2O2
<ODE:H2O> kdeg*H2O2
<ODE:O2> 0.5*kdeg*H2O2
```

The rates (e.g. `kdeg`

) need to be defined as either a system or secondary parameter. This is where you can put saturable terms, such as Michaelis-Menten kinetics.

###Equilibrium relationships `<=kforward:kreverse=>`

Forward and reverse reaction rates can be written separately:

```
A + B =konR=> C
C =koffR=> A + B
```

Or these can be written as equilibrium equations:

`A + B <=konR:koffR=> C `

To write this as differential equations, the following would be used:

```
<ODE:A> koffR*C - konR*A*B
<ODE:B> koffR*C - konR*A*B
<ODE:C> -koffR*C + konR*A*B
```

`<S:?>`

This method allows turnover to be described in terms of synthesis and degradation terms. If `A`

is produced at a rate of `ksynA`

(mass quantities), degraded at a rate of `kdegA`

, and modeled in concentration units then the sources are specified on the left hand side of `<S:?>`

and the sinks (elimination) are specified on the left hand side of `<S:?>`

. Multiple sources and sinks can be separated by semicolons. In this example with a compartment volume `V`

`ksynA/V <S:A> kdeg*A`

Which is the same as writing out the differential equation:

`<ODE:A> koffR*C - konR*A*B + ksynA/V - kdeg*A`

`<C>`

When mass moves between two physical spaces with different volumes we need to specify, for each compartment, the species, volume and rate of transport. The `<C>`

descriptor allows us to just identify the compartment information separated by semicolons (order is important)

`Species; Volume; Rate <C> Species; Volume; Rate`

For movement between a central compartment `A`

with a volume `V`

to the tissue space `At`

with a volume `Vt`

at rates `kps`

and `ksp`

respectively this is specified in the following manner:

`A; V; kps <C> At; Vt; ksp`

Which is the equivalent of the following differential equation:

```
<ODE:A> -kps*A + ksp*At*Vt/V
<ODE:At> +kps*A*V/Vt - ksp*At
```

As a final example consider the target-mediated drug disposition system above. This system can be defined with a set of ODES:

```
<ODE:Ct> Cp*kpt*Vp/Vt - Ct*ktp
<ODE:Cp> -Cp*kpt + Ct*ktp*Vt/Vp - kel*Cp + koff*CpTp - kon*Cp*Tp
<ODE:Tp> + ksyn/Vp - kint*Tp + koff*CpTp - kon*Cp*Tp
<ODE:CpTp> - kint*CpTp - koff*CpTp + kon*Cp*Tp
```

Or it could simply be defined in terms of the underlying processes:

```
# tissue distribution
Ct; Vt; ktp <C> Cp; Vp; kpt
# equilibrium
Cp + Tp <=kon:koff=> CpTp
# Turnover
ksyn/Vp <S:Tp> kint*Tp
<S:Cp> kel*Cp
<S:CpTp> kint*CpTp
```

`<I>`

By default all initial conditions are zero. You can specify a non-zero initial condition using the `<I>`

string to set a ‘state’ to a ‘value’

`<I> state = value`

Value can be any combination of numbers, system parameters `<P>`

or static secondary parameters `<As`

. Consider a turnover system where the value of `ksyn`

and `kdeg`

are specified as parameters:

```
<P> ksyn 0.1 eps inf 1/hr yes Target
<P> kdeg 0.04 eps inf nM yes Target
```

We can calculate the initial value for a target as:

`<As> T_IC = ksyn/kdeg`

Then we can specify the initial value of the target as:

`<I> T = T_IC`

Inputs into the model include typical interventions such as bolus dosing or continuous infusions. However inputs here refers to mathematical inputs. Typically covariates may be attributes of the system (such as gender, or a specific genotype), but are treated here as inputs. When defining inputs it is necessary to provide typical/placeholder values. These provide default values for both the ShinyApp interface as well as the scripting level (Matlab and R) where they can be overwritten by the user.

###Bolus dosing `<B:times>`

, `<B:events>`

The `<B:?>`

descriptor is used to define bolus dosing. Dosing information is broken down into a list of `times`

when bolus injections occur and a list of `events`

containing the amount the specified compartment will receive.

Each of these has a `scale`

that is used to convert the bolus dosing information from proscribed units (mg daily) into the units in which the system is coded (nM and hours). So if dosing is done on days 0, 1, 2… but the simulation time is hours, then the scale for the dosing times is 24.

The events contain the magnitude of the bolus at a given time. If you have multiple compartments receiving a bolus, the times must include all times in which a bolus may be applied to the system. If a state does not receive a bolus on a particular time, it’s magnitude at that time is 0.

To illustrate this consider the following dosing schedule:

In this example we want to dose two different drugs into two different states/compartments. Drug 1 (**D1**) will be dosed into `Cp1`

and drug 2 (**D2**) into `Cp2`

. Dosing will be in mg/kg but concentrations are in mg/ml. The dosing time is in days, but the simulation time units are hours. We will be dosing **D1** at **8** & **2** mpk on days **0** & **6**. **D2** will be dosed at **5** mpk on day **9**.

```
# type state values scale units
<B:times>; [0 6 9]; 24; days
<B:events>; Cp1; [8 2 0]; 70/V1; mpk
<B:events>; Cp2; [0 0 5]; 70/V2; mpk
```

Assume `V1`

and `V2`

are the compartmental volumes for **D1** and **D2** in ml, and the subject body weight is 70 kg. This would convert those doses in mpk into mg/ml. Again these are the default doses that can be overwritten both in the ShinyApp and within scripts.

`<R:?>`

Rates of infusion are defined using the `<R:?>`

descriptor. Like bolus values, infusion rates have two components. There is a component that specifies switching times (e.g. switching from 10 mg/hr to 0). And each switching time has a corresponding rate of infusion. This infusion rate will be held constant until the next time. Also like the bolus specification there is a **scale** associated with both infusion `times`

and the `levels`

that converts the proscriptive units into the units of the simulation. Consider the following example:

```
# name time/levels values scale units
<R:myrate>; times; [0 30]; 1/60; min
<R:myrate>; levels; [1 0]; 60; mg/min
```

These two entries create the infusion rate called `myrate`

. This can be used in any of your system specifications (e.g., `<ODE:Cp> myrate/Vp`

). The first row specifies the times when the rate is changed (`0`

and `30`

minutes). If the system is coded in terms of hours, then the scale of `1/60`

must be used. The levels indicate a rate of `1`

mg/min that is switched off at `30`

minutes. This has to be converted to mg/hr using the scale of `60`

. You can add as many paired rate entries as you need to describe as many infusion interventions as necessary.

`<CV:?>`

, `<CVSET:?:?>`

###Simple covariates For simulation purposes covariates (normally found in a dataset) need to be defined. Covariates can be either constant or change with time. The times values *must be the same scale as the system*. The following defines the value for the covariate `RACE`

:

```
<CV:RACE>; times; [0]; hours
<CV:RACE>; values; [1]; ethnicity
```

Covariates can also change with time. In this case consider the subject weight (`WGT`

). It begins at `70`

and measurements are made at several time points.

```
<CV:WGT>; times; [ 0 1680 3360 5040 10080]; hours
<CV:WGT>; values; [70 65 60 58 56]; kg
```

Next we can alter how the simulations will interpret these values by setting the type of covariate. By default the weight will be linearly interpolated (`type = linear`

), however we can hold the weight constant until the next measurement is encountered (last value carried forward) by declaring the type as `step`

`<CVTYPE:WGT> step`

Now if the model was parameterized for male and female subjects we can define two parameter sets (as described above) to account for this:

```
<PSET:default> Male
<PSET:female> Female
```

And the values for the covariate can be changed for the set ‘female’:

```
<CVSET:female:WGT>; times; [ 0 1680 3360 10080]
<CVSET:female:WGT>; values; [60 55 52 50]
```

Detailed time course profiles can be created as well. For example, to create a covariate profile that is zero from time 0-1 and at time 1 it jumps to 8 and decreases at a rate of 1 per unit time until time 5 where it stays at the value 4 until time 12. It might have a profile like the following:

```
# name time/values values units
<CV:mycov> ; times; [0 .999 1 5 12]; hours
<CV:mycov> ; values; [0 0 8 4 4 ]; --
<CVTYPE:mycov> linear
```

Outputs are defined here in terms of states, parameters, secondary parameters, input rates, and covariates listed above. The format used is:

`<O> name = expression`

For example:

```
<O> A_obs = A
<O> Coverage = A/(KD + A)
<O> QC_CLtot = Cp*CL/Vp + Cp*Vmax/(Km+Cp)
```

Outputs that begin with `QC`

, like `QC_CLtot`

above, will not be displayed in the ShinyApp. This is intended to make them available at the scripting level for quality control (QC) purposes.

Most of the standard operators behave as expected (`+`

, `-`

, `*`

, & `/`

) because most languages use these consistently. There are however certain operators and functions that differ between languages. For example, consider the power function (\(a^b\)). In FORTRAN this would be `a**b`

, in Matlab it is `a^b`

, and in C it is `pow(a,b)`

. Given the objectives here (write once and create multiple formats), this can be quite challenging. The solution used here is to convert language specific functions and operators into generic functions. So the power operator would be:

`SIMINT_POWER[a][b]`

This would then be converted to the appropriate output format depending on the output target. The following generic functions can be used:

Operator/Function | Example | Format |
---|---|---|

power | \(a^b\) | `SIMINT_POWER[a][b]` |

exponential | \(e^a\) | `SIMINT_EXP[a]` |

log base 10 | \(\log(a)\) | `SIMINT_LOG10[a]` |

log base e | \(\ln(a)\) | `SIMINT_LOGN[a]` |

less than | \(a < b\) | `SIMINT_LT[a][b]` |

less than or equal | \(a \le b\) | `SIMINT_LE[a][b]` |

greater than | \(a > b\) | `SIMINT_GT[a][b]` |

greater than or equal | \(a \ge b\) | `SIMINT_GE[a][b]` |

equal | \(a == b\) | `SIMINT_EQ[a][b]` |

and | \(a \& b\) | `SIMINT_AND[a][b]` |

For some systems you will want to access the simulation time. To do this you can use the internal variable `SIMINT_TIME`

.

The free amount of a drug `Cfree`

which is binding to a receptor with an affinity of `KD`

given total values `Ctot`

and `Rtot`

the following can be calculated using the following equation:

\[ C_{free}=\frac{1}{2} \left[ (C_{tot}-R_{tot}-K_D) + \sqrt{(C_{tot}-R_{tot}-K_D)^2 + 4K_DC_{tot}} \right] \]

This can be tedious, especially using the generic functions above. To make this easier you can use the following generic function:

`<Ad> Cfree = SIMINT_QEQ[Ctot][Rtot][KD]`

To get `Rfree`

, just switch the first two arguments:

`<Ad> Rfree = SIMINT_QEQ[Rtot][Ctot][KD]`

Each system has default units in which it is constructed, and should be indicated in the comments of the model. It can be useful (for generating figures for example) to show simulations in different time scales. Now this can be achieved by multiplying the time outputs by the correct scaling factor. However this requires the end user to (1) remember the original timescale and (2) correctly scale that value.

Now while this is not particularly challenging from a mathematical perspective, it introduces a chance for error. It is possible, instead, to specify time scale information using the `<TS:?>`

descriptor. If the system is coded in hours, the following will define timescales for the default (hours), days, weeks and months:

```
<TS:hours> 1.0
<TS:days> 1.0/24.0
<TS:weeks> 1.0/24.0/7.0
<TS:months> 1.0/24.0/7.0/4.0
```

These are used both in the **ShinyApp** and at the command line in **Matlab** and **R**

Consider the following systems:

**PBPK:** Most of the organs in these systems are mathematically identical, with only variations in the parameters. However coding each of these organs or modifying an existing system (say to incorporate the presences of a target in each organ) can become tedious.

**Anti-drug antibody generation:** If we consider ADAs generated in response to therapeutic proteins, the response will consist of a distribution of ADAs in terms of their concentration and a separate distribution in terms of their affinity. Modeling this maturation process and the interactions between the ADAs, the therapeutic protein, and drug targets becomes unmanageable quickly.

The question is: How can we make difficult problems easy and intractable problems possible? The solution implemented here allows the system to be defined in terms of **mathematical sets**

`<SET:?>?`

Consider the interactions occurring in an assay designed to detect drug (`D`

) present in serum. In this assay a biotinylated target (`TB`

) is used to pull down the drug and a labeled target (`TL`

) is the signaling molecule used. The assay will provide a signal when a complex containing both `TB`

and `TL`

are present (`TB:D:TL`

or `TL:D:TB`

). Samples can contain soluble target as well (`TS`

) which can interfere with the assay. To model this assay, the following interactions should be considered:

Several options are available to construct this system. The ODEs could simply be typed out for every possible combination. It’s also possible to use the equilibrium `<=kon:koff=>`

for all the interactions as well. However, there is another option that will handle the enumeration more easily. First we define the two mathematical sets `TSi`

and `TSk`

:

```
<SET:TSi> TL; TB; TS
<SET:TSk> TL; TB; TS
```

With these defined we can then use the curly brace notation (`{ }`

) with any of the descriptors used to construct a system. For example, the initial conditions for each of the target states are defined as parameters (`T0_TL`

, `T0_TS`

, `T0_TB`

) in the model. These have to be identified as initial conditions using the `<I>`

notation, and can be done with a single statement: This line:

`<I> {TSi} = T0_{TSi} `

Expands to:

```
<I> TL = T0_TL
<I> TB = T0_TB
<I> TS = T0_TS
```

Similar to the initial condition, the equilibrium between the monomeric drug and the different targets can be defined using a single statement:

`D + {TSi} <=kon:koff=> D_{TSi}`

That uses only one of the sets (`TSi`

) and will be expanded for each element in that set. To account for the formation of complexes that contain a drug molecule and two different target molecules, the following statement is used:

`D_{TSi} + {TSk} <=kon:koff=> {TSk}_D_{TSi}`

This statement contains two different sets (`TSi`

and `TSk`

). When multiple sets are encountered, every possible combination is evaluated

`<IF:?:?>`

To specify a conditional assignment use the statement:

`<IF:name:COND> boolean; value`

Here `name`

is the name of the secondary parameter be defined and `COND`

indicates that we have a Boolean condition that needs to be satisfied. The condition (`boolean`

) can be and, or, greater than, etc. relationships. The parameter will be assigned to have the value when this Boolean relationship is true. These conditions can be a function of different elements of the system depending on whether or not name refers to a static or dynamic secondary parameter:

`<As>`

function of system parameters, previously defined static secondary parameters and covariates that do not change for a given subject.`<Ad>`

function of system parameters, static secondary parameters, states, previously defined dynamic secondary parameters and covariates.

It is important to include a default `ELSE`

condition:

`<IF:name:ELSE> value`

To see an example use the following command (use `?system_new`

to see a list of the available system file examples):

`system_new(system_file="pwc", file_name="system-pwc.txt")`

In this example we specify fast (`kelf`

) and slow (`kels`

) rates of elimination. We want to have the fast rate be active when the drug concentration is above `Cth`

and the time is below `Tf`

. The system parameters would look like:

```
<P> kelf 1.0 eps inf 1/time yes System
<P> kels 0.01 eps inf 1/time yes System
<P> Cth 10 eps inf conc yes System
<P> Tf 10 eps inf time yes System
```

Now we need to define the rate of elimination such that the constraints above are followed. First we define `kel`

as a dynamic secondary parameter with a value of 0.0. Then we define the different conditions and relevant values:

```
<Ad > kel = 0.0
<IF:kel:COND> SIMINT_AND[SIMINT_LT[SIMINT_TIME][Tf]][ SIMINT_GT[Cp][Cth]]; kelf
<IF:kel:ELSE> kels
```

By default, the build script will construct odes, parameter sets, etc. automatically. This means that the order of states/compartments are going to be arbitrary. Sometimes it is necessary to specify the order of your states or outputs. For example when using NONMEM the order in the control stream must correlate with the values in the dataset. To specify that a state `Cp`

should be compartment `3`

, the following should be used:

`<INDEX:STATE:Cp> 3`

The general notation for an output or state `name`

assigned to a `number`

is:

```
<INDEX:STATE:name> number
<INDEX:OUTPUT:name> number
```

Several options can be specified using the `<OPT:?`

delimiter. If you’ve defined the `days`

timescale using `<TS:?>?`

this can be used as the timescale for plotting in the ShinyApp by using:

`<OPT:TS> days`

To define the default output times for the ShinyApp and simulation scripts use the following:

`<OPT:output_times> SIMINT_SEQ[0][100][1]`

parameter set short names must start with a letter and containing only letters, numbers, and _↩