Units

BioModME supports basic units for species and parameters in a model. The unit definition system is created from the R package “measurements” (https://cran.r-project.org/web/packages/measurements/measurements.pdf). This package supports several commonly used units. The user can define the units how they want and the application will convert them to a base unit in the backend for processing.

Unit Conversion

To convert units, go to the units section of the data table for the variable. For example, we will look at a parameter table example. The third column in the table is units. By clicking the units square, we can change the unit type.

The program will only allow you to convert to accepted units for that type. Meaning, for example, V_cell has the units of litter, so it can only be changed to another unit of volume (such as mL). For a list of all units and their values, see the unit definition section. If you attempt to convert to a unit that is not allowed, a warning will appear.

Converting Compound Units

Often parameter values will have multiple unit definitions. From the parameter table example above, the parameter “k_r1” has a unit definition of mol/(l*min). This has units of count, volume, and time. To convert this, the user needs to ensure they repeat the whole expression changing the appropriate unit in the proper place. For example,

\[(mol/(l*min))\]

is an appropriate expression. However,

\[umol/(min*L)\]

will return an error. As well as not putting the mathematical notion back in its correct place (the division, multiplication, and parenthesis) or having any of the units not be the correct conversion type (i.e. using volume units when you should be using temp).

Unit Definitions

Below are the unit definitions used in this application. The left-hand side is the term that can be put into the application (parenthesis terms are alternat acceptable names) while the right side is the definition of the unit abbreviation.

Count

fmol:

femto-mol

pmol:

pico-mol

nmol:

nano-mol

umol:

micro-mol

mmol:

milli-mol

mol:

mol

Flow

ml_per_sec:

milliliter per second

ml_per_min:

milliliter per min

ml_per_hr:

milliliter per hour

l_per_sec (LPS):

liter per second

l_per_min (LPM):

liter per min

l_per_hr (LPH):

liter per hour

Temperature

C:

Celsius

F:

Fahrenheit

K:

Kelvin

R:

Rankine

Time

nsec:

nano-second

usec:

micro-second

msec:

milli-second

sec:

second

min:

minute

hr:

hour

day:

day

wk:

week

mon:

month

yr:

year

dec:

decade

cen:

century

Volume

ul (uL):

micro-Liter

ml (mL):

milli-Liter

dl (dL):

deci-Liter

l (L):

Liter

us_tsp:

US teaspoon

us_tbsp:

US tablespoon

us_oz:

US ounce

us_cup:

US cup

us_pint:

US pint

us_quart:

US quart

us_gal:

US gallon

cm3:

centimeter cubed

dm3:

decimeter cubed

m3:

meter cubed

km3:

kilometer cubed

in3:

inch cubed

ft3:

feet cubed