NFsim 1.11 – Biochemical Reaction Simulator

NFsim 1.11

:: DESCRIPTION

NFsim (Network Free Stochastic Simuloator) is a free, open-source, biochemical reaction simulator designed to handle systems that have a large or even infinite number of possible molecular interactions or states. NFsim also has advanced and flexible options for simulating coarse-grained representations of complex nonlinear reaction mechanisms.

NFsim is ideal for modeling polymerization, aggregation, and cooperative reactions that cannot be handled with traditional stochastic or ODE simulators. Models are specified in the BioNetGen Langauge, providing a powerful model building environment.

::DEVELOPER

the Emonet lab at Yale University and the Faeder lab at the University of Pittsburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

NFsim

:: MORE INFORMATION

Citation:

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim.
Sneddon MW, Faeder JR, Emonet T.
Nat Methods. 2011 Feb;8(2):177-83. doi: 10.1038/nmeth.1546.

MACiE 3.0 – Exploring the Diversity of Biochemical Reactions

MACiE 3.0

:: DESCRIPTION

MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of fully annotated enzyme reaction mechanisms.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MACiE: exploring the diversity of biochemical reactions.
Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR.
Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9.

IBRENA 1.0 – In silico Biochemical Reaction Network Analysis

IBRENA 1.0

:: DESCRIPTION

IBRENA (Insilico Biochemical REaction Network Analysis) is a software to aid the analysis of complex biological reaction networks. In order to reduce computation time, in some cases, ordinary differential equations (ODEs) are solved using Visual FORTRAN (HP-Compaq V6.6, Palo Alto, CA) with integrated IMSL library (Visual Numerics Inc., Houston, TX). This reduces the computational time required for time-consuming sensitivity analysis.

::DEVELOPER

Sriram Neelamegham 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 IBRENA

:: MORE INFORMATION

Citation

Liu, G. and S. Neelamegham,
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks.
Bioinformatics (2008) 24 (8): 1109-1111.

 

STOCHSIM 1.4 – Stochastic Simulator for Biochemical Reactions

STOCHSIM 1.4

:: DESCRIPTION

STOCHSIM is a stochastic simulator for (bio)chemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. In STOCHSIM simple two-dimensional spatial structures have been implemented, in which nearest-neighbour interactions of molecules can be simulated.

STOCHSIM provides a general purpose biochemical simulator in which individual molecules or molecular complexes are represented as individual software objects. Reactions between molecules occur stochastically, according to probabilities derived from known rate constants. An important feature of the program is its ability to represent multiple post-translational modifications and conformational states of protein molecules.

::DEVELOPER

Bray Group: Computer Models of Bacterial Chemotaxis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Perl/Tk

:: DOWNLOAD

STOCHSIM

:: MORE INFORMATION

Complementary information about the program is available on the website of Nicolas Le Novère .