Software and resources

Software and resources#

In this page we will keep a list of the software approaches we are aware of for the various metabolic modeling tasks. Apparently, this list can never be complete, but it can be improved with your contribution! So, feel free to make a PR adding something or contact us to do that for you.

Reconstruction, gap-flling, validation#

DEMETER

Further constraints#

Thermodynamics#

Tool	Description	Architecture	Repo	DOI
pyTFA*	implementations of the original thermodynamics-based Flux Analysis (TFA) paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, which enables straightforward integration of metabolite concentration measurements.	stand-alone	GitHub	OA
OptMDFpathway**	integration of thermodynamic information in metabolic models to assess the feasibility of flux distributions by thermodynamic driving forces. Extends the framework of Max-min Driving Force (MDF) for thermodynamic pathway analysis. Identifies both the optimal MDF for a desired phenotypic behavior and the respective pathway that supports the optimal driving force.	stand-alone	GitHub	OA

matTFA is the MATLAB version of pyTFA ** part of the CNApy library

Enzymes#

Tool	Description	Architecture	Repo	DOI
AutoPACMEN	Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method.	stand-alone	GitHub	OA
ETGEMs	Construction of enzymatic and thermodynamic constrained GEMs in a single Pyomo* modelling framework.	scripts	GitHub	OA

*Python-based, open-source optimization modeling language

Transporter annotations#

Tool	Description	Architecture	Repo	DOI
SPOT*	machine learning model that can successfully predict specific substrates for arbitrary transport protein	stand-alone	GitHub	OA
TranSyT	Identifies transport systems and the compounds carried across membranes, based on the annotations of the Transporter Classification Database (TCDB). Generates the respective transport reactions while providing the respective Gene-Protein-Reaction associations.	web-sevice	GitHub	OA

They showed that the majority of TCDB entries are of low UniProt-based annotation scores.

Databases#

Tool	Description	Link	DOI
equilibrator	estimated thermodynamic constants	link	OA
SABIO-RK	curated information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions.	link	OA

has also an API library equilibrator-api ReadTheDocs | GitLab

and a cache one equilibrator-cache: A database application for caching data used by eQuilibrator and related projects. Stored data includes compound names, structures, protonation state information, reaction and enzyme info, and cross-references to other databases. All compounds stored in equilibrator-cache are cross-referenced using InChIKey. GitLab

Topological approaches#

QFCA
FluxModeCalculator

Efficient Elementary flux mode (EFM) calculation

paper | GitHub (part of the MCS repo)

Dynamic approaches#

dfba GitLab repo Documentation paper A recent approach for dynamic FBA that considers the solution non-uniqueness.

-COMETS

-BacArena

Community modelling#

mergem
PyCoMo

Data integration#

FASTCROMICS
TRFBA

tellurium:

https://tellurium.analogmachine.org

A Python Environment for Reproducible Dynamical Modeling of Biological Networks

Other resources and tools of interest#

Tool	Description	Architecture	Repo	DOI
gRodon2	predicts maximal growth rates using genomic data	R-package	GitHub	OA