PEDI – Scalable Parameter Estimation of Gene Circuit models

PEDI

:: DESCRIPTION

PEDI (Parameter Estimation by Decomposition and Integration) is a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits.

::DEVELOPER

Structural and Functional Bioinformatics Group, King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab

:: DOWNLOAD

  PEDI

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i98-107. doi: 10.1093/bioinformatics/btt232.
A framework for scalable parameter estimation of gene circuit models using structural information.
Kuwahara H1, Fan M, Wang S, Gao X.

PET 0.7.9 – Parameter Estimation Toolkit

PET 0.7.9

:: DESCRIPTION

PET (Parameter Estimation Toolkit)is a graphical user interface (GUI) for discovering rate constants, of molecular network models, that fit experimental data. It is designed for use by theoretical biologists to build regulatory network models and compare the models to experimental results.

::DEVELOPER

Jason Zwolak

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PET

:: MORE INFORMATION

Citation:

Methods Mol Biol. 2009;500:81-111.
Modeling molecular regulatory networks with JigCell and PET.
Shaffer CA, Zwolak JW, Randhawa R, Tyson JJ.

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

Botond Sipos

:: 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

ASIM 4.1 – Modelling, Simulation and Parameter Estimation in Biochemical Reacting Models

ASIM 4.1

:: DESCRIPTION

The ASIM is a set of computer programs which support the Bayesian model building of in silico biological pathways. It is organized as follows: (1) Pathway modeling with kinetic rate equations (differential equations) using the hybrid functional Petri net, (2) Parameter estimation of rate equations (3) Test on the ability of the constructed models in terms of predictability and biological robustness.

::DEVELOPER

Ryo Yoshida

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Fortran 77

:: DOWNLOAD

   ASIM

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 15;24(22):2592-601. doi: 10.1093/bioinformatics/btn483.
Bayesian learning of biological pathways on genomic data assimilation.
Yoshida R, Nagasaki M, Yamaguchi R, Imoto S, Miyano S, Higuchi T.

TROPICAL 1.0 – Simulation and Parameter Estimation of Reaction-diffusion Models

TROPICAL 1.0

:: DESCRIPTION

Tropical is a software for simulation and parameter estimation of reaction-diffusion models. Based on tiff images as input, Tropical estimates reaction and diffusion coefficients of user-defined differential equation models. Therefore Tropical allows the investigation of systems with inhomogeneous distribution of molecules, making it well suited for quantitative analyses of microscopy experiments such as Fluorescence recovery after photobleaching (FRAP).

::DEVELOPER

EILSLABS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • QT

:: DOWNLOAD

 please contact Jürgen Eils.

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Nov 1;22(21):2709-10. Epub 2006 Aug 29.
Tropical–parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images.
Ulrich M, Kappel C, Beaudouin J, Hezel S, Ulrich J, Eils R.

SBML-PET-MPI 1.2 – Parallel Parameter Estimation Tool for SBML based Models

SBML-PET-MPI 1.2

:: DESCRIPTION

SBML-PET-MPI is a parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models. The tool allows the user to perform parameter estimation, parameter uncertainty and identifiability analysis by collectively fitting multiple experimental data sets.

::DEVELOPER

Zhike Zi

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows with Cygwin/ Linux / Mac OsX

:: DOWNLOAD

 SBML-PET-MPI

:: MORE INFORMATION

Citation:

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.
Zi Z. (2011)
Bioinformatics. 2011 Apr 1;27(7):1028-9.

iParameterEstimation 0.3.1 – Maximum Likelihood Parameter Estimation Package

iParameterEstimation 0.3.1

:: DESCRIPTION

iParameterEstimation is a highly configurable maximum likelihood parameter estimation package for generalized Hidden Markov Models. Specific configuration files are included for training Twinscan, N-SCAN and their EST variants.

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 iParameterEstimation

:: MORE INFORMATION