Alfacinha – Simulation of Sequence Evolution with Neighbouring-site Dependencies

Alfacinha

:: DESCRIPTION

alfacinha is a source-package of object-oriented Python modules for sequence evolution allowing for neighbor-dependent substitutions under GPL license.This package is aimed at simulating the evolution of sequences along phylogenetic trees. It provides several modules to store and manipulate evolutionary models, to store and evolve a sequence, and store and manipulate evolutionary trees

::DEVELOPER

Leonor Palmeira.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Alfacinha Source Code

:: MORE INFORMATION

 

 

EvolSimulator 2.1.0 – Simulation Test Bed for Hypotheses of Genome Evolution

EvolSimulator 2.1.0

:: DESCRIPTION

EvolSimulator is a program that allows the simulation of evolution at the level of genes, gene families, and whole genomes. It was designed with the goal of investigating evolutionary phenomena like biased mutation regimes in different lineages, complicated patterns of selective pressure across sequences, and the confounding effects of paralogy and lateral genetic transfer.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 EvolSimulator

:: MORE INFORMATION

Citation

Beiko, R.G. and Charlebois, R.L. (2007).
A simulation test bed for hypotheses of genome evolution.
Bioinformatics 23:825-831.

PCAViz 1.2 – Visualizing Molecular Dynamics Simulations in the Web Browser

PCAViz 1.2

:: DESCRIPTION

PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Python

:: DOWNLOAD

PCAViz

:: MORE INFORMATION

Citation

J Chem Inf Model, 59 (10), 4087-4092 2019 Oct 28
PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser
Sayuri Pacheco, Jesse C Kaminsky, Iurii K Kochnev, Jacob D Durrant

GEvolutionS – Genome Evolution Simulation

GEvolutionS

:: DESCRIPTION

GEvolutionS simulates an evolutionary Genome rearrangement scenario with different genome rearrange operations. It operates on the most general model of genomes with a mixed collection on linear and circular genomes. The simulation process includes all classical rearrangement operations such as dcj, fissions, fusions, inversions, translocations, transpositions with choosable quantum.

::DEVELOPER

N/A

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

GEvolutionS

:: MORE INFORMATION

N/A

 

RuleBender 2.3 – Biological Rule-based Modeling, Simulation, and Visualization

RuleBender 2.3

:: DESCRIPTION

RuleBender is a novel visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry.

::DEVELOPER

RuleBender team

:: SCREENSHOTS

RuleBender

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 RuleBender

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012;13 Suppl 8:S3. doi: 10.1186/1471-2105-13-S8-S3. Epub 2012 May 18.
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry.
Smith AM1, Xu W, Sun Y, Faeder JR, Marai GE.

VCell 7.2 – Environment for Modeling & Simulation of Cell Biology

VCell 7.2

:: DESCRIPTION

VCell (Virtual Cell) 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. Such models can be based on both experimental data and purely theoretical assumptions.

::DEVELOPER

VCell Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

VCell

:: MORE INFORMATION

Citation

Moraru, II, J.C. Schaff, B.M. Slepchenko, and L.M. Loew. 2002.
The virtual cell: an integrated modeling environment for experimental and computational cell biology.
Ann N Y Acad Sci. 971:595-6. PMID 12438191

YASARA 19.12.14 – Molecular Graphics, Modeling & Simulation program

YASARA 19.12.14

:: DESCRIPTION

YASARA (Yet Another Scientific Artificial Reality Application)is a molecular-graphics, -modeling and -simulation program.With an intuitive user interface, photorealistic graphics and support for affordable shutter glasses, autostereoscopic displays and input devices, YASARA creates a new level of interaction with the ‘artificial reality’, that allows you to focus on your goal and forget about the details of the program.

YASARA View is available for free and contains the basic functions you need to explore a macromolecular structure interactively, comparable to other molecule viewers.

YASARA Model contains YASARA View and adds all the functions you need to explore, analyze and model small and macromolecules in a production environment. This includes many features you often miss: unlimited undo/redo, macro recorder, quad-buffered stereo with shutter glasses or the DTI virtual window .

YASARA Dynamics contains YASARA Model and adds support for molecular simulations.

YASARA Structure contains YASARA Dynamics and adds all the functions needed to predict and validate macromolecular structures, including ligand docking and highly accurate force fields with knowledge-based potentials, and an optional module for NMR structure determination.

::DEVELOPER

YASARA Biosciences

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

YASARA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 4. pii: btu426.
YASARA View – molecular graphics for all devices – from smartphones to workstations.
Krieger E1, Vriend G

Bioinformatics. 2002 Feb;18(2):315-8.
Models@Home: distributed computing in bioinformatics using a screensaver based approach.
Krieger E, Vriend G.

Circadian Modelling 2.0 – Simulations using Mathematical Models of Biological Clocks

Circadian Modelling 2.0

:: DESCRIPTION

Circadian Modelling is a flexible, user-friendly software interface for running simulations. It is aimed primarily at experimental biologists who wish to use modelling to rapidly simulate their own chosen phenotypes and experimental protocols.  Modules allow the simulation of experimental protocols with just a few mouse clicks. Users can fine-tune simulations to suit their particular interests.

::DEVELOPER

The Millar research group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Circadian Modelling

:: MORE INFORMATION

Citation

LockeJCW, MillarAJ, TurnerMS (2005)
Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana.
J Theor Biol234: 383–393

SmartCell v4.3 Beta3 – A Cell Network Simulation Program

SmartCell v4.3 Beta3

:: DESCRIPTION

SmartCell is a program developed to provide an idea of the evolution of a network in a whole, single cell. Based on stochastic algorithms, SmartCell needs multiple runs to have mean results.

::DEVELOPER

Serrano’s laboratory

:: SCREENSHOTS

SmartCell

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 SmartCell

:: MORE INFORMATION

Citation

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.
Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomás-Oliveira I, Serrano L.
Syst Biol (Stevenage). 2004 Jun;1(1):129-38.

TST 1.4.3 – Tissue Simulation Toolkit

TST 1.4.3

:: DESCRIPTION

TST is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.

::DEVELOPER

The Biomodeling and Biosystems Analysis Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux
  • C++ Compiler

:: DOWNLOAD

 TST

:: MORE INFORMATION

Citation

R M H Merks, & J A Glazier. (2005).
A cell-centered approach to developmental biology.
Physica A, 352(1), 113–130. doi:10.1016/j.physa.2004.12.028.