{ "cells": [ { "cell_type": "markdown", "id": "04ae6f8f", "metadata": {}, "source": [ "# Configuration\n", "\n", "MICOM is a full-fledged package for metabolic modeling including a variety of algorithms to build and simulate microbial community models but also to manage metabolic model databases, growth media and taxonomic information. Naturally, there are always small parameters or different approaches that can be used for each step. In newer versions of MICOM those are managed by a global configuration that get attached to each Batch. By default a configuration with sensible defaults is used, but you may change those at any time.\n", "\n", "The configuration is divided into categories for each major step in the analysis to make it clear which settings will affect which step. A full documentation of all settings follows here, but we also encourage you to read through the [methods](/logic) section to understand what they mean.\n", "\n", "## Configuration settings\n", "\n", "### Global\n", "\n", "Settings that are used in many places.\n", "\n", "| name | type | description |\n", "|---------------------|-------|------------------------------------------------------------------|\n", "| tolerance | float | The solver tolerance. Flux values and growth rates are only accurate to this value. |\n", "| solver | str | The solver to use. |\n", "| threads | int | The number of threads/CPUs to use for calculations. |\n", "| progress | bool | Whether to show progress bars. |\n", "\n", "### 🔨 Build\n", "\n", "Those settings control the building of community models.\n", "\n", "| name | type | description |\n", "|---------------------|-------|------------------------------------------------------------------|\n", "| cutoff | float | The relative abundance cutoff for taxa. Taxa below that are excluded. |\n", "| force_rebuild | bool | Whether to rebuild models if an existing community model is found. |\n", "\n", "### 📊 Simulation\n", "\n", "Settings that affect growth simulations.\n", "\n", "| name | type | description |\n", "|---------------------|-------|------------------------------------------------------------------|\n", "| strategy | str | The strategy/algorithm to use for growth simulation. |\n", "| flux_method | str | The method to use for estimating likely flux distributions. |\n", "| host_method | str | The method to use for including host models. |\n", "| host_growth | float | The maintenance flux/rate for the host models. |\n", "| host_relative | bool | Whether to interpret `host_growth` as percentage of the maximum. |\n", "\n", "### 🔗 Flux Coupling\n", "\n", "Settings that affect flux coupling. This will control how enzyme usage is connected to the growth rate. Enabling this\n", "will ensure that dead (non-growing) organisms can not perform metabolic reactions with high fluxes. \n", "\n", "| name | type | description |\n", "|---------------------|-------|------------------------------------------------------------------|\n", "| enabled | bool | Whether to enable flux coupling. |\n", "| strategy | str | The strategy/algorithm to use for flux coupling. |\n", "| include_exchanges | bool | Whether to include exchange reaction in flux coupling. |\n", "| constraint | float | The used coupling constraint. |\n", "| lower | float | Excess flux allowed (uncoupled flux bound) |\n", "\n", "### 📁 Databases\n", "\n", "Those settings denote the locations of additional databases required by MICOM.\n", "\n", "| name | type | description |\n", "|---------------------|-------|------------------------------------------------------------------|\n", "| microbial | path/url | The model database for individual taxa. |\n", "| host | dict | A dictional of id->path for the host models. |\n", "| download_location | path | Where to store downloaded databases. |\n", "\n", "### 🍲 Media\n", "\n", "Those settings control the handling of growth media / environmental conditions\n", "\n", "| name | type | description |\n", "|---------------------|-------|------------------------------------------------------------------|\n", "| weights | str | The weights/scaling used for fluxes when obtaining minimal media. |\n", "| max_import | float | The maximum added import flux for individual components. |\n" ] }, { "cell_type": "markdown", "id": "076ead57", "metadata": {}, "source": [ "## Handling configurations\n", "\n", "Configurations are only used by the MICOM Batch API and are thus a part of it. They are handled by the `Configuration` class. When you create a new configuration it will be filled with the default values which should work for most cases." ] }, { "cell_type": "code", "execution_count": 1, "id": "d131dcd0", "metadata": {}, "outputs": [ { "data": { "text/html": [ "Configuration\n", "