Tag: Simulation

ChemChains 1.22 – Simulation & Analysis of Logical Models

ChemChains 1.22

:: DESCRIPTION

ChemChains is a logical network simulation and analysis suite. The driving force behind the development of this tool was to be able to study and visualize the complex dynamics of biological signal transduction networks. While many research groups tend to focus on continuous models, our group took a different approach by using Boolean modeling technique as an alternative. Utilizing this approach allows us to focus on the dynamics of the network without having to deal with a sheer number parameters that are necessary when working with continuous models. The most prominent feature of ChemChains is that it allows users to interact with the model in a continuous manner, as they do in the laboratory experiments (e.g., users have the ability to set inputs to a percentage ON, as opposed to only 0 or 1). This allows laboratory biologists to utilize ChemChains as a complementary tool to for their laboratory experiments.

::DEVELOPER

MathBio research group, University of Nebraska at Omaha

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows with Cygwin / Linux

:: DOWNLOAD

 ChemChains

:: MORE INFORMATION

Citation

Helikar T. and Rogers J. A. (2009)
ChemChains: A platform for simulation and analysis of biochemical networks aimed to laboratory scientists.
BMC Syst. Biol. 3, 58.

CSim 20000614 – Simulation program for Somatic Cancer Evolution

CSim 20000614

:: DESCRIPTION

 CSim simulates the evolution of a cancer starting with one cancer cell which divides and acquires mutations through the process of unequal sister chromatid exchange. The simulation starts with one cell with one chromosome pair containing 16 genes each, four essential genes (E1 to E4), four neutral genes (N1 to N4), four oncogenes (O1 to O4) and four tumor suppressor genes (T1 to T4). The order of these genes on the chromosomes can be varied as well as the frequency of mutations, the maximum length of genes involved in USCE and the number of cell divisions.  The simulation only considers the end result of reciprocal USCE where one chromatid loses and the sister chromatid gains a contiguous stretch of genetic material.

::DEVELOPER

The Independent Institute of Systems Sciences ,Aachen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CSim

:: MORE INFORMATION

CES 1.0 – Codon Evolution Simulation

CES 1.0

:: DESCRIPTION

CES simulates the evolution of a locus where the resident allele is allowed to evolve across its synonymous genotype space following the allele substitution model described in SELLA and HIRSH (2005).

::DEVELOPER

Michael A. Gilchrist, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CES

:: MORE INFORMATION

Citation

Michael A. Gilchrist, Premal Shah and Russell Zaretzki
Measuring and Detecting Molecular Adaptation in Codon Usage Against Nonsense Errors During Protein Translation
Genetics December 2009 vol. 183 no. 4 1493-1505

GeneExplorer 2.1.0 – Simulation of Gene Expression

GeneExplorer 2.1.0

:: DESCRIPTION

GeneExplorer is an interactive simulation of gene expression that allows the user to:

Explore a sample gene:
Explore the correspondence between DNA, pre-mRNA, mature mRNA, and protein
Map the functional elements of a gene.
Create mutations in a gene and explore their effects.
Design a gene of their own and see how it is expressed.

::DEVELOPER

Brian White

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

GeneExplorer

:: MORE INFORMATION

Aipotu 1.3.2 – Simulation Linking Genetics, Biochemistry, Molecular Biology & Evolution

Aipotu 1.3.2

:: DESCRIPTION

Aipotu creates a utopia that simulates the genetics, biochemistry, molecular biology, and evolution of organisms in a biologically reasonable and pedagogically relevant way.

::DEVELOPER

Brian White

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Aipotu

:: MORE INFORMATION

MDLab – Molecular Dynamics Simulation Prototyping Environment

MDLab

:: DESCRIPTION

MDLab (MDL) is a user-friendly environment for prototyping molecular dynamics simulation protocols and numerical methods, built with the scripting language Python. Our goal is to provide developers of propagator scheme and force computation algorithms with (1) mathematical syntax which enables them to develop these methods using array and matrix operations, and (2) a set of domain-specific libraries which enable testing and debugging of these methods using real biological systems.

::DEVELOPER

Izaguirre Lab at Notre Dame

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MDLab

:: MORE INFORMATION

Citation

T. Cickovski, S. Chatterjee, A. Wenger, C. Sweet and J. A. Izaguirre.
MDLab: A Molecular Dynamics Simulation Prototyping Environment.
J Comput Chem. 2010 May;31(7):1345-56.

MCRobot 2.1 – Illustrates the basic principles of Markov chain Monte Carlo Simulation

MCRobot 2.1

:: DESCRIPTION

MCRobot (Markov Chain Robot) is a simulation program that illustrates principles involved with the Markov Chain Monte Carlo (or MCMC) methods currently used in Bayesian statistical analyses.

::DEVELOPER

Paul O. Lewis

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MCRobot

:: MORE INFORMATION

FEST 0.0.6 – Simulations and Likelihood Calculations of Pair-wise Family Relationships

FEST 0.0.6

:: DESCRIPTION

The software FEST is an R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data.

::DEVELOPER

Thore Egeland

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FEST

:: MORE INFORMATION

Citation

Skare, Sheehan, Egeland (2009),
“Identification of distant family relationships“,
Bioinformatics, 25(18):2376-2382.

MGA-SIMULATE – Simulation of Genotypes and Quantiative Phenotyps

MGA-SIMULATE

:: DESCRIPTION

MGA-SIMULATE is a package of programs for simulation of genotypes and quantiative phenotyps given a pedigree structure, genetic map, alleleic frequencies and mode of inheritance for a quantitative trait.

::DEVELOPER

Laboratory of the Methods of Genetic Analysis , Institute of Cytology and Genetics, Novosibirsk, Russia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MGA-SIMULATE

:: MORE INFORMATION

neuroants – Simulation of Ant Colony

neuroants

:: DESCRIPTION

neuroants was used in “The computationally complete ant colony”. Both a discrete and a continuous version is available. The discrete version has a terminal interface (curses) or a graphics inteface (through GL -mesa).

::DEVELOPER

Michael Lachmann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 neuroants

:: MORE INFORMATION