Recent Studies in kinetic modeling of Genome-scale:
Constructing kinetic models of metabolism at genome-scales: A review (Link)
Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions (Link)
Here
we have listed some softwares for kinetic modeling and analysis.
| Kinetic Modeling Softwares | ||
| Name | Description | Reference |
| JWS
(Homepage) |
It is an Online Systems Biology tool for simulation of kinetic models from a curated model database. However it is possible to access the metabolic Models through the web page. | PMID:
15072998 |
| COPASI
(Homepage) |
It is a software application for simulation and analysis of biochemical networks and their dynamics. It is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. | PMID:
17032683 |
| Jarnac
(Homepage) |
It is a language for describing and manipulating cellular system models and can be used to describe metabolic, signal transduction and gene networks, or in fact any physical system which can be described in terms of a network and associated flows. It is a simulator of reaction networks and provides many computational services, includes time course simulation (ODE or stochastic), steady state analysis, basic structural properties of networks, dynamic properties like the Jacobian, elasticities, sensitivities, eigenvalues etc. It also supports a scripting language that allows experienced users to directly interact with the computational engine. | Sauro, Herbert M., and D. A. Fell. "Jarnac: a system for interactive metabolic analysis." Animating the Cellular Map: Proceedings of the 9th International Meeting on BioThermoKinetics. Stellenbosch University Press, 2000 |
| SBW
(Homepage) |
the Systems Biology Workbench (SBW) is an open source framework connecting heterogeneous software applications. It is made up of two kinds of components: 1) The applications that a user would use (Modules). 2) The software framework that allows developers to cross programming language boundaries and connect application modules to form new applications. | Frank T. Bergmann, Herbert M. Sauro. Computational systems biology: modularity and composition: SBW - a modular framework for systems biology., Proceedings of the 37th conference on Winter simulation, Pages: 1637 - 1645, December 2006 |
| JSim
(Homepage) |
It is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. Its primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. Models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. Its model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. It also imports and exports model archive formats SBML and CellML. | PMID:
24555116 |
| MathSBML
(Homepage) |
It is an open-source package for working with SBML models in Mathematica. It provides facilities for reading SBML models, converting them to systems of ordinary differential equations for simulation and plotting in Mathematica, and translating the models to other formats. | PMID:
15087311 |
| SBToolbox
(Homepage) |
The Systems Biology Toolbox for MATLAB offers systems biologists an open and user extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological systems. | PMID:
16317076 |
| VCell
(Homepage) |
The Virtual Cell is a computational environment designed for cell biologists, to facilitate the construction of models and the generation of predictive simulations from them. It is a unique computational environment for modeling and simulation of cell biology. It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The creation of biological or mathematical models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. | PMID:
14573350 |
| BioNetGen
(Homepage) |
It is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. | PMID:
15217809 |
| Cellerator/xCellerator
(Homepage) |
It is a Mathematica package designed to aide biological modeling via the automated conversion of chemical reactions into ODEs and their subsequent solution via numerical integration. | PMID:
12651737 |
| JigCell
(Homepage) |
It is a joint effort by members of the Departments of Biological Sciences and Computer Science at Virginia Tech. Its goal is to advance the state of the art for modeling in Systems Biology. | PMID:
15273159 |
| PottersWheel
(Homepage) |
This is a very comprehensive parameter-fitting tool that works well with the SBToolBox but can also be used alone. In the area of generating non-linear confidence limits on parameter fits and analyzing the resulting fit, it is better than the capabilities of COPASI. The experimental data input formats are also very flexible. The tool provides a number of optimization algorithms, including Genetic and simulated annealing approaches. For a Matlab user interested in doing parameter fitting properly, this tool is a serious contender, especially as the built-in optimization methods in Matlab itself are not sufficiently robust for fitting biochemical models. A further advantage of this tool is that is comes with copious documentation. PottersWheel combined with the SBToolbox2 is a powerful mix. | PMID:
18614583 |
| R Packages
(Homepage) |
There is limited support for dynamic modeling in R, but this is changing. Given the growing interest in using R in biological research, it would not be surprising if further work is done in this area. Currently, the two tools that are of interest include the SBMLR package by Tomas Radivoyevitch and a more modern version by Michael Lawrence, called RSBML. Modeling is in all cases limited to simple time-course simulations. Both packages use the ODEPACK library for integrating the ODEs, which arguably is superior to CVODE from SUNDIALS. | Not Available |
| SBML-PET-MPI
(Homepage) |
It is a parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models. The tool allows the user to perform parameter estimation, parameter uncertainty and identifiability analysis by collectively fitting multiple experimental data sets. It can run on Windows, Linux and Mac OS systems. | PMID:
16926221 |
| SloppyCell
(Homepage) |
It is a software environment for simulation and analysis of biomolecular networks. It includes deterministic and stochastic dynamical simulations, sensitivity analysis without finite-difference derviatives, optimization methods to fit parameters to experimental data, simulation of multiple related networks sharing common parameters, and stochastic Bayesian analysis of parameter space to estimate error bars associated with optimal fits. | Christopher R. Myers, Ryan N. Gutenkunst, James P. Sethna "Python unleashed on systems biology" Computing in Science and Engineering 9:34 (2007); arXiv:0704.3259 |
| E-Cell
(Homepage) |
The E-Cell Project develops general technologies and theoretical supports for computational biology with the grand aim to make precise whole cell simulation at the molecular level possible. | PMID:
10068694 |
| SOSlib
(Homepage) |
It is a programming library and a command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). It is written in C and distributed under the terms of the GNU Lesser General Public License. The package employs libSBML's AST (Abstract Syntax Tree) for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. CVODES, the sensitivity-enabled ODE solver in the SUNDIALS package is used for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems. | Not Available |
| Tav4SB
(Homepage) |
The Taverna services for Systems Biology (Tav4SB) project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Its operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. Its operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. | PMID:
22480273 |
| KiMoSys
(Homepage) |
It is a web application for quantitative KInetic MOdels of biological SYStems. It is a freely accessible web site that combines tasks for experimental data-store, search and share, and tools in order to build ODE-based kinetic models into a single platform. | PMID:
25115331 |
| SBMLsqueezer
(Homepage) |
It generates kinetic equations for biochemical networks according to context of each reaction. When used as a plug-in for CellDesigner it uses the information from the SBGN representation of all network components. In the stand-alone mode, SBMLsqueezer evaluates the Systems Biology Ontology (SBO) annotations to extract this information. An online version of SBMLsqueezer is available that runs without instally any software on the local machine. The rate laws that can be produced by SBMLsqueezer include several types of generalized mass action. | Paper_Link |