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 |
|
time |
s |
|
Compartment density |
wc_lang.core.Compartment.density wc_lang.core.Compartment.density_units |
mass / volume |
g l^-1 |
|
Compartment volume |
wc_lang.core.Compartment.volume wc_lang.core.Compartment.volume_units |
volume |
l^-1 |
|
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
|
|
Species count |
|
molecule |
molecule |
|
Observable count |
wc_lang.core.ObservableExpression.expression wc_lang.core.Observable.units |
molecule |
molecule |
|
Observable coefficient |
|
dimensionless |
none |
|
Reaction participant |
|
dimensionless |
none |
|
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, |
|
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 |
|
dFBA objective |
wc_lang.core.DfbaObjectiveExpresssion.expression wc_lang.core.DfbaObjective.units |
time-1 |
s^-1 |
|
dFBA objective coefficient |
wc_lang.core.DfbaObjectiveExpresssion.expression wc_lang.core.DfbaObjective.coefficient_units |
time |
s |
|
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
|
|
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 |
|
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].