Welcome to Vivarium *E. coli*'s documentation! ============================================== Vivarium *E. coli* project is a port of the |text|_ to the `Vivarium framework `_. .. Comment: We need to use text substitution because ReST does not support nesting italics and hyperlinking .. _text: https://doi.org/10.1128/ecosalplus.ESP-0001-2020 .. |text| replace:: Covert Lab's *E. coli* Whole Cell Model .. image:: ./_static/ecoli_master_topology.png :width: 100% :alt: A graph with blue, database symbol nodes at the top and orange, square nodes on the bottom. The blue nodes are connected by solid edges, while the orange nodes are connected to the blue nodes by broken edges. .. toctree:: :maxdepth: 2 Processes Composites Experiments tutorials docs reference/stores API Reference .. WARNING:: This documentation is very much a work in progress. It likely contains errors and poor formatting. The scope of this project is to migrate the Whole Cell Model's processes, and therefore takes the model's sim_data as its starting point in the simulation pipeline. sim_data is a large configuration object created by the parameter calculator (ParCa). For this reason the ``reconstruction/`` and ``wholecell/utils/`` folders have been duplicated here as they are necessary to unpickle the serialized sim_data object. If a new sim_data object is required to be read, the corresponding wcEcoli folders will have to be synchronized. All state handling (previously handled by Bulk- and UniqueMolecules states/containers/views) and the actual running of the simulation (previously ``wholecell.sim.Simulation``) are now handled entirely by Vivarium's core engine and process interface. The new process classes can be found in ``ecoli/processes/*`` and are linked together using a Vivarium topology that is generated in ``ecoli/experiments/ecoli_master_sim.py``.