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)
BIOMD0000000484_url.sedml
Simulation Experiment Description Markup Language (SED-ML)
BIOMD0000000484_url.xml
Systems Biology Markup Language (SBML)
BIOMD0000000484-biopax2.owl
Resource Description Framework XML (RDF-XML)
BIOMD0000000484-biopax3.owl
BIOMD0000000484-matlab.m
MATLAB
BIOMD0000000484-octave.m
BIOMD0000000484.m
BIOMD0000000484.ode
BIOMD0000000484.pdf
Portable Document Format (PDF)
BIOMD0000000484.png
Portable Network Graphics (PNG)
BIOMD0000000484.sci
Scilab
BIOMD0000000484.svg
Scalable Vector Graphics (SVG)
BIOMD0000000484.vcml
Virtual Cell Markup Language (VCML)
curation_image.png
curation_notes.txt
TEXT
metadata.rdf
OMEX Metadata
Outputs
JavaScript Object Notation (JSON) in BioSimulators simulator schema
Zip of HDF5 and PDF files
Log
JavaScript Object Notation (JSON) in BioSimulators log schema
Bernie J. Daigle, Min K. Roh, Dan T. Gillespie & Linda R. Petzold. Automated estimation of rare event probabilities in biochemical systems. The Journal of Chemical Physics 134, 4 (2011).
Min K. Roh, Dan T. Gillespie & Linda R. Petzold. State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm. The Journal of Chemical Physics 133, 17 (2010).
Youfang Cao & Jie Liang. Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method. The Journal of Chemical Physics 139, 2 (2013).
Uniform time course
CVODE
SBML
SED-ML
COMBINE/OMEX
AMICI 0.11.25
647a4b4377b6669655060f0c
BioModels
View project essentials in the liteweight Reproducibility Portal.