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alexOarga committed Dec 13, 2021
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Expand Up @@ -23,11 +23,10 @@ CONTRABASS takes as input an SBML files of genome-scale models, and provides as
**Essential Reactions:** A reaction is considered an essential reaction if its deletion, this is, restricting its flux to zero, causes the objective (e.g. cellular growth) to be zero.


_Figure:_ Chokepoint reactions and dead-end metabolites example:

<h1 align="center">
<img alt="Example" title="Example" src="https://github.com/openCONTRABASS/CONTRABASS/blob/main/docs/source/_static/chokepoints_example.png" width="500">
</h1>
<div align="center">
<p>Figure: Chokepoint reactions and dead-end metabolites example:</p>
<img alt="Example" title="Example" src="https://github.com/openCONTRABASS/CONTRABASS/blob/main/docs/source/_static/chokepoints_example.png" width="600">
</div>

The computation of vulnerabilities can also be exploited programmatically via the [Low Level API](#low-level-api) which is based on [COBRApy](https://github.com/opencobra/cobrapy). You can also [try the Low Level API with Binder](https://mybinder.org/v2/gh/openCONTRABASS/CONTRABASS/HEAD?labpath=docs%2Fsource%2FCORE.ipynb).

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The next flowchart provides a graphical description of the available operations that can be performed with CONTRABASS and their respective commands:

<h1 align="center">
<img alt="flowchart" title="flowchart" src="https://github.com/openCONTRABASS/CONTRABASS/blob/main/docs/source/_static/contrabass_flowchart.png" width="500">
<img alt="flowchart" title="flowchart" src="https://github.com/openCONTRABASS/CONTRABASS/blob/main/docs/source/_static/contrabass_flowchart.png" width="550">
</h1>

More information about the parameters of the tool can be obtained by executing ``contrabass -h``.
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