wc_lang documentation

This package defines wc_lang, a data-driven language for concisely describing WC models.

Whole-cell (WC) models are comprehensive computational models of all of the biochemical activity inside individaul cells [Karr et al., 2015; Macklin et al., 2014]. WC models have great potential to enable bioengineers to rationally design microorganisms for industrial and medical applications and to enable physicians to personalize medical therapy [Carrera and Covert, 2015]. Please see WholeCell.org for more information about WC modeling, including perspectives, reviews, and tutorials.

References

  • Carrera J & Covert MW. (2015). Why Build Whole-Cell Models? Trends in Cell Biology, 25(12), 719-722. DOI: 10.1016/j.tcb.2015.09.004

  • Karr JR, Takahashi K & Funahashi A. (2015). The principles of whole-cell modeling. Current Opinion in Microbiology, 27, 18-24. DOI: 10.1016/j.mib.2015.06.004

  • Macklin DN, Ruggero NA & Covert MW. (2014). The future of whole-cell modeling. Current Opinion in Biotechnology, 28, 111-115. DOI: 10.1016/j.copbio.2014.01.012

Contents

Installation

Prerequisites

  • Python

  • Pip

Latest release from PyPI

Run the following command to install the latest version from PyPI:

wc_lang

Latest revision from GitHub

Run the following command to install the latest version from GitHub:

pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils
pip install git+https://github.com/KarrLab/obj_tables.git#egg=obj_tables
pip install git+https://github.com/KarrLab/wc_lang.git#egg=wc_lang

Overview of wc_lang

Units

Quantity

Attributes

Dimensions

Units

Units class

Time

wc_lang.core.Model.time_units

time

s

wc_lang.core.TimeUnit

Compartment density

wc_lang.core.Compartment.density
wc_lang.core.Compartment.density_units

mass / volume

g l^-1

wc_lang.core.DensityUnit

Compartment volume

wc_lang.core.Compartment.volume
wc_lang.core.Compartment.volume_units

volume

l^-1

wc_lang.core.VolumeUnit

Distribution of initial
concentration of a
species at the beginning
of the cell cycle
wc_lang.core.Concentration.distribution
wc_lang.core.Concentration.mean
wc_lang.core.Concentration.std
wc_lang.core.Concentration.units
molecule,
molecule volume-1
molecule,
M

wc_lang.core.ConcentrationUnit

Species count

wc_lang.core.Species.units

molecule

molecule

wc_lang.core.MoleculeCountUnit

Observable count

wc_lang.core.ObservableExpression.expression
wc_lang.core.Observable.units

molecule

molecule

wc_lang.core.MoleculeCountUnit

Observable coefficient

wc_lang.core.ObservableExpression.expression

dimensionless

none

wc_lang.core.ObservableCoefficientUnit

Reaction participant

wc_lang.core.SpeciesCoefficient.coefficient

dimensionless

none

wc_lang.core.ReactionParticipantUnit

Reaction rate

wc_lang.core.RateLawExpression.expression
wc_lang.core.RateLaw.units
wc_lang.core.DfbaObjective.reaction_rate_units
wc_lang.core.DfbaObjReaction.units

time-1

s-1,

wc_lang.core.ReactionRateUnit

Reaction flux bounds

wc_lang.core.Reaction.flux_min
wc_lang.core.Reaction.flux_max
wc_lang.core.Reaction.flux_bound_units

volume-1 time-1

M s^-1

wc_lang.core.ReactionFluxUnit

dFBA objective

wc_lang.core.DfbaObjectiveExpresssion.expression
wc_lang.core.DfbaObjective.units

time-1

s^-1

wc_lang.core.DfbaObjectiveUnit

dFBA objective coefficient

wc_lang.core.DfbaObjectiveExpresssion.expression
wc_lang.core.DfbaObjective.coefficient_units

time

s

wc_lang.core.DfbaObjectiveCoefficientUnit

dFBA objective species

wc_lang.core.DfbaObjSpecies.value
wc_lang.core.DfbaObjSpecies.units
volume^-1 time^-1,
gDCW^-1 time^-1
M s^-1
mol gDCW^-1 s^-1

wc_lang.core.DfbaObjSpeciesUnit

Function

wc_lang.core.FunctionExpression.expression
wc_lang.core.Function.units

various

various

Parameter

wc_lang.core.Parameter.value
wc_lang.core.Parameter.units

various

various

Stop condition

wc_lang.core.StopCondition.expression
wc_lang.core.StopCondition.units

dimensionless

none

wc_lang.core.StopConditionUnit

Tutorial

About

License

The software is released under the MIT license

The MIT License (MIT)

Copyright (c) 2016 Karr Lab

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, USA.

Acknowledgements

This work was supported by a National Science Foundation INSPIRE award [grant number 1649014].

Questions and comments

Please contact the Karr Lab with any questions or comments.

References