Tag: Simulating

DCell 1.4 – Deep Neural Network simulating Cell Structure and Function

DCell 1.4

:: DESCRIPTION

DCell is a neural network model of budding yeast, a basic eukaryotic cell. The model structure corresponds exactly to a hierarchy of 2,526 cellular subsystems.

::DEVELOPER

Ma Laboratory / Ideker Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DCell

:: MORE INFORMATION

Citation:

Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T.
Using deep learning to model the hierarchical structure and function of a cell.
Nat Methods. 2018 Apr;15(4):290-298. doi: 10.1038/nmeth.4627. Epub 2018 Mar 5. PMID: 29505029; PMCID: PMC5882547.

LibSBMLSim 1.4.0 – The library for Simulating SBML models

LibSBMLSim 1.4.0

:: DESCRIPTION

LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs). LibSBMLSim provides simple command-line tool and several APIs to load an SBML model, perform numerical integration (simulate) and export its results. Both explicit and implicit methods are supported on libSBMLSim.

::DEVELOPER

Funahashi Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LibSBMLSim

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1474-6. doi: 10.1093/bioinformatics/btt157.
LibSBMLSim: A reference implementation of fully functional SBML simulator.
Takizawa H, Nakamura K, Tabira A, Chikahara Y, Matsui T, Hiroi N, Funahashi A.

Dawg 1.2 – Simulating Sequence Evolution

Dawg 1.2

:: DESCRIPTION

Dawg (DNA Assembly with Gaps) is an application designed to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation.

::DEVELOPER

Reed A. Cartwright

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 Dawg

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8.
DNA assembly with gaps (Dawg): simulating sequence evolution.
Cartwright RA

DNemulator 20 – Simulating DNA Sequencing Errors, Polymorphisms, Cytosine Methylation and Bisulfite Conversion

DNemulator 20

:: DESCRIPTION

DNemulator is a package for simulating DNA sequencing errors, polymorphisms, cytosine methylation and bisulfite conversion

::DEVELOPER

Martin Frith

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DNemulator

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(13):e100. doi: 10.1093/nar/gks275
A mostly traditional approach improves alignment of bisulfite-converted DNA.
Frith MC, Mori R, Asai K.

Microscope Simulator 2.3.0 – Simulating a Fluorescent Torus

Microscope Simulator 2.3.0

:: DESCRIPTION

Microscope Simulator enables a scientist to simulate what a given 3D scene should look like under a fluorescence microscope. 3D scenes can be constructed from primitives or imported files in VTK, OBJ, or PLY format.

::DEVELOPER

CISMM (Computer Integrated Systems for Microscopy and Manipulation)

:: SCREENSHOTS

micro_sim

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Microscope Simulator

:: MORE INFORMATION

TreeSim 2.4 / TreeSimGM 2.3 – Simulating Trees under the Birth-Death Model / under a General Model

TreeSim 2.4 / TreeSimGM 2.3

:: DESCRIPTION

TreeSim is an R package for simulating phylogenetic trees.

TreeSimGM: Simulating Phylogenetic Trees under a General Model

::DEVELOPER

Computational Evolution group at ETH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • R package

:: DOWNLOAD

  TreeSim , TreeSimGM

:: MORE INFORMATION

Citation

Syst Biol. 2011 Oct;60(5):676-84. doi: 10.1093/sysbio/syr029. Epub 2011 Apr 11.
Simulating trees with a fixed number of extant species.
Stadler T.

EvoFBA – Simulating Evolution of Constraint Based Models of Cellular Metabolism

EvoFBA

:: DESCRIPTION

EvoFBA is a MATLAB implementation of the evolutionary and ecological dynamics simulations of growing E.coli populations

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • MatLab

:: DOWNLOAD

EvoFBA

:: MORE INFORMATION

Citation

BMC Evol Biol, 16 (1), 163
Metabolic Modelling in a Dynamic Evolutionary Framework Predicts Adaptive Diversification of Bacteria in a Long-Term Evolution Experiment
Tobias Großkopf, Jessika Consuegra , Joël Gaffé, John C Willison, Richard E Lenski, Orkun S Soyer, Dominique Schneider

rlsim 1.4 – Simulating RNA-seq library Preparation with Parameter Estimation

rlsim 1.4

:: DESCRIPTION

The rlsim package is a collection of tools for simulating RNA-seq library construction, aiming to reproduce the most important factors which are known to introduce significant biases in the currently used protocols: hexamer priming, PCR amplification and size selection.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Biopython

:: DOWNLOAD

  rlsim

:: MORE INFORMATION

Citation:

Botond Sipos, Tim Massingham and Nick Goldman (2013):
rlsim – a package for simulating RNA-seq library preparation with parameter estimation.
http://bit.ly/rlsim-doc

SimulaTE 1.13 – Simulating Complex Landscapes of Transposable Elements of Populations

SimulaTE 1.13

:: DESCRIPTION

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

SimulaTE

:: MORE INFORMATION

Citation:

SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler R.
Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772.

MimicrEE – Simulating Genotypes and Phenotypes in experimentally evolving populations

MimicrEE

:: DESCRIPTION

MimicrEE (Mimicing Experimental Evolution) is a tool for forward simulations of entire genomes. It basically allowes to simulate adaptation from standing genetic variation, thus no ‘de novo’ mutations are supported. It has been tested with 8,000 individulas having 2,000,000 million SNPs.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

MimicrEE

:: MORE INFORMATION

Exit mobile version