Topic: metabolic-network Goto Github
Some thing interesting about metabolic-network
Some thing interesting about metabolic-network
metabolic-network,Computational synthetic biology: Predicting DNA edits for bioengineering
Organization: 20n
Home Page: http://20n.com
metabolic-network,Enumeration of biosynthetic pathways from metabolic networks
User: aarthi31
metabolic-network,Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002
Organization: angione-lab
metabolic-network,[Not maintained and not updated] Draft metabolic network reconstruction using Rhea database, Uniprot and SPARQL queries.
User: arnaudbelcour
metabolic-network,Pathway Tools multiprocessing wrapper (for PathoLogic).
Organization: aureme
metabolic-network,Python library for hAndling metaData of METabolism.
Organization: aureme
Home Page: https://padmet.readthedocs.io/en/latest/
metabolic-network,R codes for creating metamapp graphs and files
User: barupal
metabolic-network,Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL
Organization: bebop
metabolic-network,Python package and workflow for EFM calculation via (mp)lrs and efmtool
User: beeanka
metabolic-network,Trim, extract, and convert GEMs
User: binfalse
Home Page: https://gemtractor.bio.informatik.uni-rostock.de
metabolic-network,Compute minimal metabolic precursors sets that enable the production of target metabolites
Organization: bioasp
Home Page: bioasp.github.io/precursor
metabolic-network,MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.
User: charlesrocabert
Home Page: https://pypi.org/project/MetEvolSim/
metabolic-network,:world_map: A repository of CNApy projects
Organization: cnapy-org
metabolic-network,Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis
Organization: compbtbs
metabolic-network,Chemical reaction balancing web service
Organization: dbkgroup
metabolic-network,Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
User: earmingol
metabolic-network,SBML to RDF conversion
Organization: emetabohub
metabolic-network,findCP CLI package - find ChokePoint reactions in genome-scale metabolic models
Organization: findcp
Home Page: https://findcpcli.readthedocs.io/en/latest/
metabolic-network,findCP core package - find ChokePoint reactions in genome-scale metabolic models
Organization: findcp
Home Page: https://findcpcore.readthedocs.io/en/latest/
metabolic-network,A python library for metabolic networks sampling and analysis
Organization: geomscale
metabolic-network,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.
Organization: gibbslab
metabolic-network,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.
Organization: gibbslab
metabolic-network,Enzymatic Link Prediction
Organization: hassounlab
metabolic-network,MOOMIN is a tool for analysing differential expression data
User: htpusa
metabolic-network,Search for and find thermodynamic advantages for product synthesis using metabolic single-species community models
Organization: klamt-lab
metabolic-network,Create stoichiometric metabolic network models of single-species or multi-species communities
Organization: klamt-lab
metabolic-network,GPU-accelerated algorithms for flux sampling in CUDA.jl
Organization: lcsb-biocore
metabolic-network,Code for Model-based Design of Bistable Cell Factories for Metabolic Engineering
Organization: lmse
Home Page: https://doi.org/10.1093/bioinformatics/btx769
metabolic-network,A study on multi-omic oscillations in Escherichia coli metabolic networks. Journal paper.
User: lodeguns
Home Page: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2175-5
metabolic-network,A GPU implementation of the sampling algorithm ACHR.
User: marouenbg
metabolic-network,Open source genome-scale metabolic models of human and model animals
Organization: metabolicatlas
Home Page: https://metabolicatlas.org
metabolic-network,MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks
Organization: metanetx
metabolic-network,Kinetic modeling of glucose and acetate metabolisms in E. coli
Organization: metasys-lisbp
Home Page: https://elifesciences.org/articles/63661
metabolic-network,Diversity-based enumeration of optimal context-specific metabolic networks
Organization: metexplore
metabolic-network,The systematic identification of functional metabolic control mechanisms relies mostly on the integration of data but barely considers the connectivity of the metabolic network. However, recent geometric deep learning approaches show promising performances in the prediction of links in network or graph structures. By using a dream-case in silico network of E. coli’s central metabolism including metabolic and regulatory connections, we first generated data suitable for the prediction of regulatory links between metabolites and enzymes. By merging data with a Graph Convolutional Neuronal Network along the structure of the metabolic network we can classify links in the graph as either ‘regulatory’ or ‘non-regulatory’. Here we show, how such a neuronal network can be trained and also be used to fill knowledge gaps to identify functional metabolic control mechanisms.
User: mlempp
metabolic-network,A Universal Modeling Language for Metabolic Flux Analysis
Organization: modsim
metabolic-network,debugging biological networks to reach coherence, completeness and consistency
User: namin
metabolic-network,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.
User: niupuhua1234
metabolic-network,COBRApy is a package for constraint-based modeling of metabolic networks.
Organization: opencobra
Home Page: http://opencobra.github.io/cobrapy/
metabolic-network,A RMosek optimization interface for the Sybil package
User: r2rahul
metabolic-network,An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Organization: resendislab
Home Page: http://resendislab.github.io/corda
metabolic-network,Common biochemical and topological attributes of metabolic genes recurrently dysregulated in tumors.
Organization: sriram-lab
Home Page: https://cancerandmetabolism.biomedcentral.com/articles/10.1186/s40170-020-0211-1
metabolic-network,Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002
User: svijayakumar32
metabolic-network,Genome-scale model of Yarrowia lipolytica.
Organization: sysbiochalmers
Home Page: http://www.nature.com/articles/npjsba20165
metabolic-network,Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
Organization: sysbiomics
Home Page: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-245
metabolic-network,Infer metabolic directions from moment differences of mass-weighted intensity distributions
User: tubanlee
Home Page: https://doi.org/10.5281/zenodo.10616979
metabolic-network,A new computational pipeline that can be used to convert expression (RNA-seq) data into predicted flux potentials that indicate metabolic function
User: walhoutlab
metabolic-network,Agent-based metabolic modelling of microbial communities in time and continuous µ-meter-scale space
User: waschina
Home Page: https://waschina.github.io/Eutropia
metabolic-network,Curation and analysis of metabolic models
Organization: zhanglab
Home Page: https://zhanglab.github.io/psamm/
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