Cited in
(only showing first 100 items - show all)- Inferring reaction systems from ordinary differential equations
- Systems Biology: The Next Frontier for Bioinformatics
- A systems biology approach to understanding alcoholic liver disease molecular mechanism: the development of static and dynamic models
- A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development
- Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs
- SBML to bond graphs: from conversion to composition
- CLUE
- SemanticSBML
- Dynamic publication media with the COPASI R connector (CoRC)
- Smooth functional tempering for nonlinear differential equation models
- Condor-COPASI
- A computational approach to extinction events in chemical reaction networks with discrete state spaces
- Glycolysis in saccharomyces cerevisiae: algorithmic exploration of robustness and origin of oscillations
- Aeon
- Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis
- Bio-PEPA: A framework for the modelling and analysis of biological systems
- Probabilistic approximations of ODEs based bio-pathway dynamics
- An extension of ERODE to reduce Boolean networks by backward Boolean equivalence
- On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity
- PoCaB: A Software Infrastructure to Explore Algebraic Methods for Bio-chemical Reaction Networks
- The \textsc{SDEval} benchmarking toolkit
- Robust modelling, measurement and analysis of human and animal metabolic systems
- Symbolic versus numerical computation and visualization of parameter regions for multistationarity of biological networks
- Analysis of reaction network systems using tropical geometry
- A case study on the parametric occurrence of multiple steady states
- Algorithmic reduction of biological networks with multiple time scales
- Model-based selection of the robust JAK-STAT activation mechanism
- Modelling biological compartments in bio-PEPA
- A geometric method for model reduction of biochemical networks with polynomial rate functions
- Dynamical properties of discrete reaction networks
- A geometric approach for analyzing parametric biological systems by exploiting block triangular structure
- Generalizing Gillespie's direct method to enable network-free simulations
- Bio-PEPA with Events
- Computational challenges in systems biology
- Bio-PEPA
- PNML
- REDLOG
- PetriNets
- OptiML
- CellML
- PoCaB
- Binomials.m2
- sbtoolbox
- Libxml2
- MetaCyc
- TRANSPATH
- Paramotopy
- Ginsim
- BIOCHAM
- Celldesigner
- ProjectionCAD
- PEPA
- iDynoR
- SESSL
- BioSPI
- KEGG2SBML
- COPASI
- BlenX
- libSBML
- Metatool
- PySB
- SakerGrid
- SBMLsimulator
- SloppyCell
- Ernest
- KEGG
- JSBML
- KEGGtranslator
- CoNtRol
- CLPGUI
- Reactome
- Bio-SPICE
- ERODE
- NFsim
- crnpy
- MTT
- JSim
- MetaFork
- ConvAn
- SuBliMinaL
- SOSlib
- tellurium
- SpaceScanner
- Design space toolbox
- STOCHSIM
- CRN++
- MESSI
- CompuCell3D
- MOCCASIN
- KappaTools
- libRoadRunner
- PyDREAM
- Expression2Kinases
- Spatkin
- TRuML
- SimpleSBML
- cPath
- PyBoolNet
- Dizzy
- SBRML
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