#
metabolic-network
Here are 53 public repositories matching this topic...
Computational synthetic biology: Predicting DNA edits for bioengineering
data-mining
deep-learning
synthetic-biology
biochemistry
fermentation
metabolic-network
bioengineering
computational-synthetic-biology
acetaminophen
reaction-operators
metabolic-engineering
enzyme-function
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Updated
Mar 27, 2017 - Java
debugging biological networks to reach coherence, completeness and consistency
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Updated
Jul 19, 2021 - Common Lisp
Curation and analysis of metabolic models
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Updated
May 12, 2021 - Python
Visualizing and Analyzing Metabolic Networks with Reaction Pattern Recognition
reaction
network
sequencing
motif
reactions
pattern-recognition
proteomics
metabolism
metabolomics
omics
metabolic-network
contextualization
metabolic-data
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Updated
Aug 12, 2021 - JavaScript
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
flux
bioinformatics
genome
modeling
systems-biology
biochemistry
metabolism
reconstruction
cobra
cobrapy
metabolic-models
metabolic-network
metabolic-reconstruction
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Updated
Oct 24, 2018 - Python
2
vissarion
commented
May 28, 2021
dingo currently has a limited number of examples of use, mainly in tests.
Create an example directory and add analysis for networks from public datasets e.g. http://bigg.ucsd.edu
Other use cases using FVA, FBA or sampling for metabolic models are welcome to be added there too.
1
Open source genome-scale metabolic models of human and model animals
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Updated
Sep 1, 2021 - Vue
MOOMIN is a tool for analysing differential expression data
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Updated
Jun 29, 2020 - MATLAB
A Universal Modeling Language for Metabolic Flux Analysis
modeling-language
specification-language
metabolic-models
metabolic-network
metabolic-engineering
metabolic-flux-analysis
13c-mfa
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Updated
Jun 22, 2021 - C++
R codes for creating metamapp graphs and files
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Updated
Sep 1, 2021 - JavaScript
Genome-scale model of Yarrowia lipolytica.
systems-biology
stoichiometric-reactions
metabolic-models
metabolic-network
metabolic-reconstruction
constraint-based-modeling
metabolic-engineering
omics-data-integration
yarrowia-lipolytica
genome-scale-models
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Updated
Jul 30, 2021 - MATLAB
Diversity-based enumeration of optimal context-specific metabolic networks
optimization
metabolism
metabolic-network
metabolic-reconstruction
constraint-based-modeling
metabolic-engineering
cobra-toolbox
omics-data-integration
metabolic-pathways
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Updated
Jul 2, 2021 - MATLAB
TRIMER is a package for building integrated metabolic–regulatory models base on Bayesian network. TRIMER can be used for knockout phenotype prediction and knock flux prediction.
bayesian-network
metabolic-network
flux-balance-analysis
genome-scale-models
metabolic-regulatory-model
knock-out-phenotype-prediction
knock-out-flux-prediction
transcriptional-regulations
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Updated
Jun 2, 2021 - MATLAB
Enzymatic Link Prediction
machine-learning
bioinformatics
metabolic-network
metabolic-reconstruction
metabolic-engineering
enzyme-function
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Updated
Aug 19, 2020 - Python
An R package to find the gaps in metabolic networks, and fill it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also include the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database.
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Updated
Dec 5, 2020 - R
Chemical reaction balancing web service
python
bioinformatics
microservice
chemistry
cheminformatics
systems-biology
web-service
metabolic-models
metabolic-network
metabolic-reconstruction
metabolic-engineering
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Updated
Sep 13, 2017 - Python
A GPU implementation of the sampling algorithm ACHR.
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Updated
Apr 7, 2020 - Cuda
An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.
bioinformatics
gene-expression
metabolism
metabolic-models
metabolic-network
fba-fluxes
flux-balance-analysis
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Updated
May 2, 2017 - R
A Python package to simulate the long-term evolution of metabolic levels.
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Updated
Mar 16, 2021 - Python
Trim, extract, and convert GEMs
csv
enzyme
extract
gml
trim
dot
phenotype
filtering
graphml
sbml
metabolic-network
genome-scale-models
subnetwork
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Updated
Jun 8, 2021 - Python
A new computational pipeline that can be used to convert expression (RNA-seq) data into predicted flux potentials that indicate metabolic function
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Updated
May 3, 2021 - MATLAB
Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002
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Updated
May 8, 2021 - Python
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
metabolic-network
flux-balance-analysis
metabolic-model
reconstructed-metabolic-network
aspergillus-oryzae
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Updated
Mar 29, 2019 - MATLAB
A study on multi-omic oscillations in Escherichia coli metabolic networks. Journal paper.
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Updated
Nov 22, 2018 - R
Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
python
bioinformatics
modeling
systems-biology
computational-biology
biochemistry
modeling-tool
cobra
cobrapy
metabolic-models
metabolic-network
metabolic-reconstruction
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Updated
Mar 13, 2020 - Jupyter Notebook
MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks
reconciliation
chemoinformatics
metabolic-models
metabolic-network
metabolic-reconstruction
biochemical-reactions
metabolites
metabolic-pathways
metabolite-identification
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Updated
Mar 8, 2018
findCP core package - find ChokePoint reactions in genome-scale metabolic models
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Updated
Aug 18, 2021 - HTML
Python package and workflow for EFM calculation via (mp)lrs and efmtool
python
flux
bioinformatics
systems-biology
computational-biology
biochemistry
metabolism
cobrapy
metabolic-models
sbml
metabolic-network
sbml-model
mplrs
efmtool
lexicographic-reverse-search
elementary-flux-modes
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Updated
Jun 25, 2021 - Python
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Hello maintainers of the amazing package,
I recently updated cobrapy and am experienced unexpected behavior with cobra.test.create_test_model("salmonella")
Two things are unusual:
`Model does not contain SBML fbc package information.
SBML package