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Here is an introductory course to computer modelling for synthetic and systemics biology at the Imperial College, London]

Production tools

Software useful for work in systems biology and synthetic biology. Rather modelling and simulation tools.

BIOCHAM

 Attach:biocham.jpg

BIOCHAM is a programming environment for modeling biochemical systems, making simulations and querying the model in temporal logic. It uses a simple rule-based language for modeling biochemical systems, that can then be efficiently simulated (either boolean or numerical). Biocham can be used in a terminal environment and is fully scriptable. It has also an elegant graphical interface simple to use. Compared to other software for biochemical modelling it's originality is the existence of a powerful query language based on temporal logic, (CTL or LTL with arithmetic constraints over reals) that enables sophisticated queries on the temporal properties of the model. Example of query: can my model oscillate in a reasonable range of parameters with a period larger than a given value, lower than another limit and amplitude ton less than this other value? Other sophisticated feature enable the system to correct and complete a model, either by changing rules or by estimating parameters.

BIOCHAM is compatible with many standard formats for the model specification (xppaux, scilab, smbl).

Attach:biocham2.jpg The beta of the new version includes also stochastic simulation and hopefully will soon be available.

Link to the Biocham webpage

MGS

MGS is a very broad programming language (DSL) devoted to the simulation of biological processes. It's special features are:

  • to be declarative and functional contrary to the usual languages which are procedural. That is, the user writes down rules of behavior for the system that can occur at any time. It is not necessary to specify a defined succession of steps in the program. Only the properties must be described.
  • includes the possibility to describe o complex spatial structures
  • generically includes many type of possible interactions between the elements, parallel evolution, stochastic interactions (via Gillespie Algorithm)
  • Enables the simulation and representation of spatial dynamics.

MGS as a general programming language can be used for a wide range of applications it can be especially useful in particular for modelling and representing graphically spatiotemporal biological processes such as differentiation and morphogenesis.

Link to the MGS webpage

Dizzy

Attach:Dizzy.jpg

Excellent programme de simulation déterministe et stochastique. Dizzy est un simulateur basé sur sur syntaxe assez proche de Biocham où le systèmes de réactions biochimiques est décrit textuellement suivant les descriptions usuelles de réactions chimiques (du style A=B->C) . Il implémente plusieurs algorithmes de calcul déterministes et plusieurs variantes de simulations Monté Carlo (Gillespie et simplifications). Le même modèle peut directement être simulé de manière déterministe et stochastique. Il est possible de commander les simulation en batch pour automatiser des traitements. Parmi les particularités rares: possibilités de simuler des systèmes à retard, des simulations stochastiques réactions incluant des approximations quasi-statiques de type Michaelis-Menten.

Lien vers la page de Dizzy

CellDesignerTM

A modeling tool of biochemical networks Attach:cellDesigner.jpg

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Intuitive user-interface helps you to draw a diagram in rich graphical representation with your own design.

Attach:graph1.jpg

Une interface graphique pour tracer des réseaux de régulation et des réseaux métabolique, pour éviter d'écrire des équations... En sortie un représentation du modèle dynamique de réseau en dans le standard SMBL qui peut être repris par plusieurs autres logiciels de simulation. Inclus aussi le lien avec un solgiciel intégré de simulation numérique des équations différentielles.

Attach:graph2.jpg

A évaluer... et comparer avec JDesigner

Août 2008: CellDesigner 4.0 released!

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system, and are stored using the Systems Biology Markup Language (SBML).

CellDesigner 4.0 is now adopting the SBGN (systems biology graphical notation) process diagram Level 1 early proposal. Find out more on new features of CellDesigner Ver.4.0

Lien vers la page web

Tutorial on Cell Designer

Systems Biology Workbench (SBW)

An opensource software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms-to communicate and use each others’ capabilities. There are over 75 different packages for simulating cellular networks.

Basic modules:

  • Jarnac: A fast simulator of reaction networks. This is one of the main modules in SBW, it provides may 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. Jarnac is only recommended for very experienced users. If you want a nice easy tool to do simulations then use JDesigner which comes with SBW
  • JDesigner: This is a friendly GUI front end to an SBW compatible simulator. It allows users to ‘draw’ networks on screen and simulate them. JDesigner uses Jarnac as it’s current simulation backend. Attention: JDesigner is a Win32 application.

Copasi Complex Pathway Simulator

Very complete, can be linked with SBW

  • Model:
    * Chemical reaction network.
    * Arbitrary kinetic functions.
    * ODEs for compartments, species, and global quantities.
    * Assignments for compartments, species, and global quantities.
    * Initial assignments for compartments, species, and global quantities. 
  • Analysis:
    * Stochastic and deterministic time course simulation
    * Steady state analysis (including stability).
    * Metabolic control analysis/sensitivity analysis.
    * Elementary mode analysis .
    * Mass conservation analysis.
    * Calculation of Lyapunov exponents.
    * Parameter scans.
    * Optimization of arbitrary objective functions.
    * Parameter estimation using data from time course and/or steady state experiments simultaneously. 
  • Graphical User Interface (CopasiUI)
    * Sliders for interactive parameter changes. 

Link to the Copasi Webpage

JDesigner

Attach:Jdesigner.png

Un autre environnement de simulation de circuits génétiques incluant une interface graphique pour dessiner les circuits (pour ceux qui n'aiment pas écrire les équations différentielles). Non encore testé, par contre le tutoriel est très intéressant sur la modélisation biochimiques, éventuellement utilisable aussi avec d'autres programmes pour les exemples. Fonctionne seulement sur Windows.

Biochemical Modelling with JDesigner tutorial?

Lien vers la page principale de JDesigner

BioNetS

An easy to use and blazingly fast stochastic ODE solver, using Gillespie, chemical Langevin, and any hybrid of the two. Linux,MacOSX, Windows

Works as a http://biospice.sourceforge.net/? Agent.

Ling to the webpage

SgnSim

Programme de simulation stochastique très complet. Fonctionne seulement sur Windows.

Particularités: avec Dizzy un des rares simulateurs stochastiques permettant d'inclure des retards dans les simulations stochastiques. Possibilité aussi d'inclure des cinétiques avec des probabilités stochastiques suivant des fonctions arbitraires, permettant par exemple des approximations quasi-statiques.

Vers la page de téléchargement de sgnsim

Référence sur sgnsim discutant aussi de manière générale des simulations stochastiques de circuits de régulation génétique: Andre S. Ribeiro; Jason Lloyd-Price, (2007) SGN Sim, a Stochastic Genetic Networks Simulator, Bioinformatics, 23(6):777-779. doi:10.1093/bioinformatics/btm004

BioSpice

Bio-SPICE, an open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells. In addition, our goal is to develop and serve a user community committed to using, extending, and exploiting these tools to further our knowledge of biological processes.

Link to the webpage

SmartCell

SmartCell to provide an idea of the evolution of a network in one cell. Based on sotchastic algorithm, SmartCell need multiple runs to have mean results. To help the user, SmartCell is distributed with a graphic user interface, that allow the creation of model with a user friendly interface, and also the analyze and traitment of results after the runs.

Link to the webpage Article comparing spatial stochastic simulation software

Systems Biology Research Tool (SBRT)

Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput) experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results

The Systems Biology Research Tool is a free, easy-to-use, open-source, integrated software platformto facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion

The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability), to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

Link to the presenting paper

Link to the SBRT page

For Graph analysis, a very different software from the simulation programs presented in the rest of this page. By Andreas Wagner, a researcher who had very relevant contributions in System Biology.

Tools in beta state or in development

Many project are under development to provide new tools for modelling and synthetic circuits engineering. We report here some projects in an early phase maybe not mature yest for use in production.

GenoCAD

An interesting development for a computer tool for designing synthetic genetic sequences syntaxically correct for genetic activites using data from a standardised library.

There currently is a gap between the few academic groups who have the capability of running small scale proof-of-concept projects in synthetic biology and the people who could identify and benefit from biomedical and industrial applications of this technology. They are creating the infrastructure making it possible for non-specialist to design large-scale genetic systems that could be used in basic biological research or product development programs. GenoCAD aims at adapting the workflow developed by the electronics industry, to automate the design and fabrication of electronic circuits, to the design and assembly of Very Large Scale Integrated genetic systems. The group at the VirginiaTech isdeveloping the molecular tools, algorithms, and software applications that will make the computer assisted design and fabrication of genetic systems a reality within a 5 year time frame. In addition, starting as early as 2008, we will be able to provide services to scientists not affiliated directly with the GenoCAD project.

link to genoCAD

Article on GenoCAD development

Other reviews and lists of Modeling and simulation resources

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Page last modified on July 04, 2009, at 11:36 AM