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July 16, 2008, at 05:59 PM by SB -
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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.

March 22, 2008, at 11:31 AM by SB -
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  • Review and Comparison of Systems Biology Simulation Tools for Translational Research
March 22, 2008, at 11:27 AM by SB -
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  • A review of Systems Biology Simulation Tools
  • A review of resources for Systems Biology
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Other reviews and lists of Modeling and simulation resources

  • A selection of databases and tools for modelling signalling networks
  • A list of simulation tools
March 20, 2008, at 04:59 PM by SB -
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Here is an introductory course to computer modelling for synthetic and systemics biology at the Imperial College, London]

March 20, 2008, at 04:57 PM by SB -
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Tutorial on Cell Designer

March 20, 2008, at 03:40 PM by SB -
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BIOCHAM

 

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).

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

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BIOCHAM

 

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).

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

Link to the Biocham webpage

MGS

March 20, 2008, at 03:18 PM by SB -
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Biocham

to:

BIOCHAM

 

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).

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

Link to the Biocham webpage

March 19, 2008, at 03:56 PM by SB -
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  • [[http://sbw.kgi.edu/sbwWiki/doku.php?id=sysbio:sbw]| 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
to:
  • 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
March 19, 2008, at 03:23 PM by SB -
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Outils de production

to:

Production tools

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

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Très complet et mise en relation possible avec SBW

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Very complete, can be linked with SBW

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lien vers la page web

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Link to the Copasi Webpage

March 19, 2008, at 03:19 PM by SB -
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    (:toc:)
March 19, 2008, at 03:18 PM by SB -
March 19, 2008, at 03:18 PM by SB -
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A évaluer... et comparer avec http://sbw.kgi.edu/sbwWiki/sysbio/jdesigner?

Lien vers la page web

to:

A évaluer... et comparer avec JDesigner

Lien vers la page web

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  • http://sbw.kgi.edu/sbwWiki/doku.php?id=sysbio:sbw?: 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
  • http://sbw.kgi.edu/sbwWiki/sysbio/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.
to:
  • [[http://sbw.kgi.edu/sbwWiki/doku.php?id=sysbio:sbw]| 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.
March 19, 2008, at 03:16 PM by SB -
March 19, 2008, at 03:16 PM by SB -
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Ressources Informatiques

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(:title Ressources Informatiques:)

Outils de production

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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

March 13, 2008, at 03:02 PM by SB -
March 13, 2008, at 02:48 PM by SB -
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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

March 13, 2008, at 02:33 PM by SB -
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A évaluer...

Lien vers la page web

to:

A évaluer... et comparer avec http://sbw.kgi.edu/sbwWiki/sysbio/jdesigner?

Lien vers la page web

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:

  • http://sbw.kgi.edu/sbwWiki/doku.php?id=sysbio:sbw?: 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
  • http://sbw.kgi.edu/sbwWiki/sysbio/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

Très complet et mise en relation possible avec 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. 

lien vers la page web

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

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

Biocham

MGS

March 13, 2008, at 02:01 PM by SB -
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Ressources Informatiques

CellDesignerTM

A modeling tool of biochemical networks

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.

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.

A évaluer...

Lien vers la page web


Page last modified on July 16, 2008, at 05:59 PM