MATLAB vs Python

RAVEN ships as a MATLAB toolbox and as the Python package raven-toolbox. The two have large overlap, but differ in important ways:

• The MATLAB version works completely independently — including independently of the COBRA Toolbox — although ravenCobraWrapper can translate between the RAVEN and COBRA model formats.
• raven-toolbox is built on top of cobrapy.
• As a result, some functions are MATLAB-only: they are not ported because cobrapy already provides the equivalent. In that case, look for the function in the cobrapy API.

The table below pairs the functions that exist in both implementations (MATLAB camelCase ↔ Python snake_case); click a name to jump to its full reference. Functions that exist in only one implementation appear in that language's API reference tree but not here.

21 paired functions.

RAVEN (MATLAB)	raven-toolbox (Python)	Summary
applyCondition	apply_condition	Apply a deterministic condition to a model.
checkTasks	check_tasks	Perform a set of simulations as defined in a task file.
expandModel	expand_model	Expand reactions that use several gene associations.
exportForGit	export_for_git	Export a model for a Git-maintained model repository.
FSEOF	fseof	Flux Scanning based on Enforced Objective Flux.
getElementalBalance	get_elemental_balance	Check whether the reactions of a model are balanced.
getKEGGModelForOrganism	get_kegg_model_for_organism	Reconstruct a model from KEGG protein homology.
getModelFromHomology	get_model_from_homology	Build a draft model for model_for by transferring reactions from templates.
mergeCompartments	merge_compartments	Merge all compartments in a model.
mergeModels	merge_models	Merge models into one model structure.
parseHPA	parse_hpa	Parse a database dump of the Human Protein Atlas (HPA).
parseHPArna	parse_hpa_rna	Parse a dump of Human Protein Atlas (HPA) RNA-Seq data.
parseTaskList	parse_task_list	Parse a task list file.
predictLocalization	predict_localization	Place a caller-specified set of reactions in compartments via MILP.
randomSampling	random_sampling	Sample the flux solution space (entry point for all samplers).
readYAMLmodel	read_yaml_model	Read a model structure from a YAML file.
removeGenes	remove_genes	Delete a set of genes from a model.
reporterMetabolites	reporter_metabolites	Identify metabolites around which transcriptional changes occur.
setGAM	set_gam	Set the growth-associated maintenance (GAM) coefficient.
sortIdentifiers	sort_identifiers	Sort model identifiers alphabetically.
writeYAMLmodel	write_yaml_model	Write a model to a yaml file matching cobrapy's structure.