simbTUM 3.0a – Simulation of Stochastic processes and ODE models in Biology

simbTUM 3.0a

:: DESCRIPTION

simbTUM allows to define ODE-models or stochastic compartemental models of biological processes, to simulate, to fit data and to do some statistics (fitting and statistics for deterministic models only).

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 simbTUM

:: MORE INFORMATION

FPG – Forward Population Genetic Simulation program

FPG

:: DESCRIPTION

FPG (for Forward Population Genetic simulation) simulates a population of constant size that is undergoing various evolutionary processes, including:  mutation, recombination,  natural selection, and migration.   The meaning of “forward” in this context is simply that time, within the simulation, moves forward just as it does in the real world.  This is in contrast to coalescent population genetic simulation in which time, as represented within the simulation, proceeds back into the past.  Coalescent simulations have many advantages, but they are unwieldy if they incorporate natural selection on multiple sites.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 FPG

:: MORE INFORMATION

CafeMol 3.2.1 – Biomolecular Modeling and Simulation Software

CafeMol 3.2.1

:: DESCRIPTION

CafeMol is a general-purpose coarse-grained(CG) biomolecular modeling and simulation software.It can simulate proteins,nucleic acids,lipids and their mixture with various CG models.

::DEVELOPER

Takada Lab ,Kyoto University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortran90/95
  •  C compiler

:: DOWNLOAD

 CafeMol

:: MORE INFORMATION

Citation

Hiroo Kenzaki, Nobuyasu Koga, Naoto Hori, Ryo Kanada, Wenfei Li, Kei-ichi Okazaki, Xin-Qiu Yao, and Shoji Takada ,
CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work,
Journal of Chemical Theory and Computation , 7: 1979-1989, 2011

Protein Investigator 3.0.2 – Simulation of Protein Folding

Protein Investigator 3.0.2

:: DESCRIPTION

Protein Investigator gives students an opportunity to interactively explore protein structure and function in a simplified system. This is a highly-simplified model of protein folding. It is not intended to predict the correct structures of any proteins; it is designed to illustrate the major principles involved in that process.

::DEVELOPER

Brian White

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Protein Investigator

:: MORE INFORMATION

BD_BOX 1.2 – Brownian Dynamics Simulation

BD_BOX 1.2

:: DESCRIPTION

BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BD_BOX

:: MORE INFORMATION

Citation

Maciej Długosz, Paweł Zieliński Joanna Trylska,
Brownian dynamics simulations on CPU and GPU with BD_BOX,
J. Comput. Chem., 32:2734–2744, 2011

HEC 2.0.1 – Haploid Simulation of Bacterial Communities

HEC 2.0.1

:: DESCRIPTION

HEC (Haploid Evolutionary Constructor)  is the tool for simulation of bacterial (more exactly prokaryotic) communities. It is based on the original modeling approach investigated in the Laboratory of molecular-genetic systems at the Institute of Cytology and Genetics (Novosibirsk, Russia).

::DEVELOPER

HEC Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 HEC

:: MORE INFORMATION

Citation:

Simulation of coevolution in community by using the “Evolutionary Constructor” program.
Lashin SA, Suslov VV, Kolchanov NA, Matushkin YG.
In Silico Biol. 2007;7(3):261-75.

FASIMU 2.3.4 – Flux-balance Analysis based SIMUlations

FASIMU 2.3.4

:: DESCRIPTION

FASIMU (Flux-balance Analysis based SIMUlations)is a command line oriented software implementing the most frequently applied FBA(Flux-balance Analysis) algorithms. Moreover, it offers the first freely available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) the concentration-based thermodynamic feasibility constraint. It allows heterogenous computation series suited for network pruning, leak analysis, FVA, and systematic probing of metabolic objectives for network curation controlled by an intuitive description file. The metabolic network can be supplied in SBML, CellNetAnalyzer, and plain text format. FASIMU uses the optimization capabilities of free (lp solve and GLPK) and commercial solvers (CPLEX, LINDO). The results can be visualized in Cytoscape or BiNA using newly developed plugins.

::DEVELOPER

Andreas Hoppe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CPLEX and BiNA
  • Java

:: DOWNLOAD

FASIMU

:: MORE INFORMATION

Citation

FASIMU: flexible software for flux-balance computation series in large metabolic networks
Andreas Hoppe , Sabrina Hoffmann , Andreas Gerasch , Christoph Gille and Hermann-Georg Holzhütter
BMC Bioinformatics 2011, 12:28

POPSIM 2.13 – Population Simulation program

POPSIM 2.13

:: DESCRIPTION

POPSIM creates a virtual representation of every individual,makes no prior assumptions but the Medelian rules and allows for populations of several million individuals size to be generated and to be followed over hundreds of generations.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows

:: DOWNLOAD

 POPSIM

:: MORE INFORMATION

Citation

Hampe J, Wienker T, Schreiber S, Nürnberg T (1998).
POPSIM: A general population simulation program.
Bioinformatics 14: 458-464

SimRNA 3.20 – Simulations of RNA Conformational Dynamics

SimRNA 3.20

:: DESCRIPTION

SimRNA is a tool for simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and its applications include RNA 3D structure prediction.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SimRNA

:: MORE INFORMATION

Citation

Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM.
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Nucleic Acids Res. 2016 Apr 20;44(7):e63. doi: 10.1093/nar/gkv1479. Epub 2015 Dec 19. PMID: 26687716; PMCID: PMC4838351.

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