Browse simulation projects
Browse simulator tools
Browse the docs
View full simulation details including customizable plots, files, logs, and more.
Project
Download File
Open Modeling and Exchange (OMEX)
iEC1368_DH5a.xml
Systems Biology Markup Language (SBML)
iJO1366.Central-metabolism.escher.json
Escher
iJO1366.Central-metabolism.png
Portable Network Graphics (PNG)
iJO1366.Central-metabolism.vg.json
Vega
iJO1366.Fatty-acid-beta-oxidation.escher.json
iJO1366.Fatty-acid-beta-oxidation.png
iJO1366.Fatty-acid-beta-oxidation.vg.json
iJO1366.Fatty-acid-biosynthesis--saturated-.escher.json
iJO1366.Fatty-acid-biosynthesis--saturated-.png
iJO1366.Fatty-acid-biosynthesis--saturated-.vg.json
iJO1366.Nucleotide-and-histidine-biosynthesis.escher.json
iJO1366.Nucleotide-and-histidine-biosynthesis.png
iJO1366.Nucleotide-and-histidine-biosynthesis.vg.json
iJO1366.Nucleotide-metabolism.escher.json
iJO1366.Nucleotide-metabolism.png
iJO1366.Nucleotide-metabolism.vg.json
LICENSE
TEXT
metadata.rdf
OMEX Metadata
simulation.sedml
Simulation Experiment Description Markup Language (SED-ML)
Outputs
JavaScript Object Notation (JSON) in BioSimulators simulator schema
Zip of HDF5 and PDF files
Log
JavaScript Object Notation (JSON) in BioSimulators log schema
bigg.model:iEC1368_DH5a
Jonathan M. Monk, Anna Koza, Miguel A. Campodonico, Daniel Machado, Jose Miguel Seoane, Bernhard O. Palsson, Markus J. Herrgård & Adam M. Feist. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Systems 3, 3: 238-251.e12 (2016).
BiGG
Steady state
flux balance analysis
SBML
SED-ML
COMBINE/OMEX
COBRApy 0.24.0
621d901cb50991044c7a1c2b
metabolic process
Escherichia coli DH5[alpha] strain DH5alpha contig_90_1, whole genome shotgun sequence
Escherichia coli DH5[alpha]
Systems Biology Research Group at the University of California, San Diego
Jonathan R. Karr
View project essentials in the liteweight Reproducibility Portal.