Package: contrabass
CONTRABASS - Constraint-based model vulnerabilities analysisCONTRABASSis a tool for the detection of vulnerabilities in metabolic models. The main purpose of the tool is to compute chokepoint and essential reactions by taking into account both the topology and the dynamic information of the model. In addition to the detection of vulnerabilities, CONTRABASS can compute essential genes, compute and remove dead-end metabolites, compute different sets of growth-dependent reactions, and update the flux bounds of the reactions according to the results of Flux Variability Analysis.CONTRABASS takes as input the SBML file of a metabolic model, and provides as output a spreadsheet file and an html file reporting the obtained results. CONTRABASS accounts for the following sets of reactions and metabolites:Chokepoint reactions:A reaction is a chokepoint if it is the unique consumer or the only producer of a given metabolite.Essential Reactions:A reaction is essential if its deletion, or equivalently, restricting its flux to zero, causes a significant decrease in the objective function (e.g. cellular growth).Dead-End Metabolites (DEM):A metabolite is a dead-end metabolite if it is not produced or not consumed by any reaction.Essential reactions for optimal growth:A reaction is essential for optimal growth if its deletion, or equivalently, restricting its flux to zero, causes a decrease in the objective function.Dead reactions:A reaction is dead is its upper flux bound and its lower flux bound are equal to zero.Blocked reactions:A reaction is blocked if its flux is necessarily zero at any possible steady state of the model.Reversible reactions:A reaction is reversible if its upper flux bound is strictly positive and its lower flux bound is strictly negative.Non-reversible reactions:A reaction is non-reversible if it is not dead and not reversible.Essential genes:A gene is essential if the objetive function (e.g. cellular growth) is zero when it is knocked down.Figure: In the network, reactionsReac_2,Reac_5,Reac_6,Reac_7andReac_8are chokepoint reactions.MetabolitesLysineandGlutamateare dead-end metabolites.The computation of vulnerabilities can also be exploited programmatically via theLow Level APIwhich is based onCOBRApy. You can alsotry the Low Level API with Binder.Table of ContentsLicenseOnline WebInstallQuickstartDocumentationTool commandsLow Level APIMaintainersContributingLicenseCONTRABASS is released underGPLv3 license.Online WebCONTRABASS can also be executed through theCONTRABASS Online Web App (http://contrabass.unizar.es).InstallCONTRABASScan be installed viapippackage manager:$pipinstallcontrabassQuickstartGenerate report on vulnerabilities on input modelMODEL.xml$contrabassreportcritical-reactionsMODEL.xmlGenerate report on growth-dependent reactions on input modelMODEL.xml$contrabassreportgrowth-dependent-reactionsMODEL.xmlDocumentationDocumentation is available atreadthedocsand can also bedownloaded.
The previous links include examples and descriptions of the operations that can be performed with the tool.Tool commandsThe next flowchart provides a graphical description of the available operations that can be performed with CONTRABASS and their respective commands:More information about the parameters of the tool can be obtained by executingcontrabass -h.
For a detailed description of the operations see thedocumentation.$contrabassUsage:contrabass[OPTIONS]COMMAND[ARGS]...Computevulnerabilitiesonconstraint-basedmodelsOptions:-h,--helpShowthismessageandexit.-V,--versionShowtheversionandexit.Commands:new-modelExportrefinedconstraint-basedmodel.reportComputevulnerabilitiesonconstraint-basedmodels.Low Level APIThe computation of vulnerabilities can also be exploited via the COBRApy based low level API. For further information see theLow Level API documentation.
You can alsotry it with Binder.Example of network refinement and chokepoint computation:fromcontrabass.coreimportCobraMetabolicModelmodel=CobraMetabolicModel("aureus.xml")# update flux bounds with FVAmodel.fva(update_flux=True)# compute chokepointsmodel.find_chokepoints()# get chokepointsmodel.chokepoints()Maintainers@alexOargaContributingFeel free to dive in!Open an issueor submit PRs.Standard Readme follows theContributor CovenantCode of Conduct.GNU GENERAL PUBLIC LICENSE
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Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.END OF TERMS AND CONDITIONS

        How to Apply These Terms to Your New ProgramsIf you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.To do so, attach the following notices to the program.  It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year>  <name of author>

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.Also add information on how to contact you by electronic and paper mail.If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:<program>  Copyright (C) <year>  <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.The hypothetical commandsshow w' andshow c' should show the appropriate
parts of the General Public License.  Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, seehttps://www.gnu.org/licenses/.The GNU General Public License does not permit incorporating your program
into proprietary programs.  If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library.  If this is what you want to do, use the GNU Lesser General
Public License instead of this License.  But first, please readhttps://www.gnu.org/licenses/why-not-lgpl.html.