Reverse Dependencies of cobra

The following projects have a declared dependency on cobra:

• autopacmen-Paulocracy — The AutoPACMEN package
• biosimulator-processes — no summary
• biosimulators-cobrapy — BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.
• biosimulators-masspy — BioSimulators-compliant command-line interface to the MASSpy simulation program.
• BOFdat — Package to generate biomass objective function stoichiometric coefficients from experimental data
• ChiMera-GSMR — ChiMera: An easy-to-use pipeline for Genome-based Metabolic Network reconstruction, evaluation, and visualization.
• ChiMera-ModelBuilder — ChiMera: An easy-to-use pipeline for Genome-based Metabolic Network reconstruction, evaluation, and visualization.
• cobra-utils — TBD
• Cobra2D — A package for building time- and space-resolved metabolic models.
• cobrakbase — KBase interface for COBRApy
• cobramod — Python package for pathway-centric modification and extension of genome-scale metabolic networks
• cobrapy-bigg-client — BiGG API - programmatic access to the BiGG Models database
• cometspy — The Python interface to COMETS
• commmodelpy — The commmodelpy package
• contrabass — Constraint-based model vulnerabilities analysis
• corda — Genome-scale model construction with CORDA
• csm4cobra — Tools and methods for context-specific metabolic modeling
• csmemo — A Library implementing constraint-based methods for context-specific metabolic modeling
• dexom-python — DEXOM implementation in python using cobrapy
• DielModels — DielModels:
• driven — driven - data-driven constraint-based analysis
• ECMpy2.0 — Automated construction of enzyme constraint models using ECMpy workflow.
• efmlrs — Extracts EFMs from result file of mplrs and decompresses EFMs from efmtool and mplrs results that have been compressed with EFMlrs
• enkie — ENKIE - The ENzyme KInetics Estimator
• equilibrator-api — Calculation of standard thermodynamic potentials of biochemical reactions
• Escher — Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Metabolic Pathways
• Escher-legacy — Escher-legacy: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Metabolic Pathways
• fastsl — FastSL-py is an efficient algorithm to identify synthetic lethal gene/reaction sets in genome-scale metabolic models.
• fbc-curation — FBC reference files for SBML model curation.
• findCPcore — findCP core package
• geckopy — Methods for using the GECKO model with cobrapy
• gemcat — A toolbox for gene expression-based prediction of metabolic alterations
• GEMEditor — A graphical editor for the reconstruction, annotation and testing of genome-scale models
• gempipe — no summary
• gemsembler — A tool for assembling and comparing several types of Genome-Scale Metabolic Models.
• gsmodutils — Utilities for the management and testing of genome scale models in a cross platform, open manner.
• iambcodes — Functions for data analysis support at the iAMB in RWTH Aachen.
• imatpy — "Python implementation of the Integrative Metabolic Analysis Tool (iMAT) algorithm for context specific metabolic modeling."
• incawrapper — General Repository for Omics Data Handling tools
• kb-analysis — H1 human embryonic stem cells (hESCs) Data Analysis
• masspy — MASSpy is a package for dynamic modeling of biological processes.
• mcescher — Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Metabolic Pathways
• medusa-cobra — Ensemble modeling using constraint-based reconstruction and analysis (COBRA)
• memote — the genome-scale metabolic model test suite
• metabolitics3d — metabolitics3d
• metalo — Metabolic analysis of Logical models extracted from maps
• mewpy — MEWpy - Metabolic Engineering in Python
• micom — Microbial community modeling based on cobrapy.
• miom — Mixed Integer Optimization for Metabolism
• mmodes — Metabolic Models based Ordinary Differential Equations Simulation
• ModelSEEDpy — Python package for building and analyzing models using ModelSEED
• moped — Stoichiometric metabolic modelling
• mptool — Enumeration and sampling of minimal pathways in metabolic (sub)networks.
• mqc — MQC is a Genome-scale metabolic network model quality control tool
• multitfa — Multivariate thermodynamics-based metabolic flux analysis in Python.
• optimModels — optimModels - strain optimization
• optslope — OptSlope - A tool for metabolic engineering, based on the OptSlope algorithm
• padmet — Padmet package for metabolic network
• PAModelpy — Python framework for building and analysing protein allocation models
• pgp-reconstruction — Pathway-Guided Pruning Reconstruction of constraint-based metabolic models
• pipeGEM — Processing and integrating data with genome-scale metabolic models (GEM)
• PolyRound — A python package for rounding polytopes.
• pycomo — PyCoMo is a software package for generating and analysing compartmentalized community metabolic models
• pyfastcore — A python-based implementation for the context-specific metabolic model extraction methods from Vlassis et al. 2014
• pymCADRE — The pymCADRE tool is an advanced re-implementation of the metabolic Context-specificity Assessed by Deterministic Reaction Evaluation (mCADRE) algorithm in Python. It constructs tissue-specific metabolic models by leveraging gene expression data and literature-based evidence, along with network topology information.
• pymgpipe — Community level microbiome metabolic modeling in Python
• pytfa — pyTFA, Thermodynamics-based Flux Analysis in Python
• q2-micom — QIIME 2 plugin for metabolic modeling of microbial communities.
• reconstructor — COBRApy Compatible Genome Scale Metabolic Network Reconstruction Tool: Reconstructor
• refineGEMs — refineGEMs: a python package intended to help with the curation of genome-scale metabolic models (GEMS)
• rpextractsink — 'retropath2 sink generator'
• sambaflux — Sampling Biomarker Analysis using flux sampling
• sambapy — A small example package
• sammi — A wrapper for running the Semi-Automated Metabolic Map Illustrator (SAMMI) using Python
• scarcc — no summary
• scCellFie — A tool for studying metabolic tasks from single-cell and spatial transcriptomics
• scobra — Supplementary package for COBRApy
• silvio — silvio is an environment for Simulation of Virtual Organisms. silvio contains several linked microbial models.
• spamdfba — no summary
• ssbio-edbr — Tools to enable structural systems biology, forked from SBRG/ssbio
• straindesign — Computational strain design package for the COBRApy framework
• TASMANIAN-DEVIL — TASMANIAN DEVIL: a software package for classifying gene activity from omics data sets, simplifying metabolic networks, and visualizing the estimated phenotypic fluxes of nutrients