Tag: Biological Modeling

BayesMD – Biological Modeling for Motif Discovery

BayesMD

:: DESCRIPTION

BayesMD is a flexible, fully Bayesian model for motif discovery consisting of motif, background and alignment modules. BayesMD can be customized to different kind of biological applications, e.g. microarray, ChIP-chip, ditag, CAGE data analysis by integrating appropriately chosen features and functionalities.

::DEVELOPER

BayesMD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Matlab

:: DOWNLOAD

  BayesMD

:: MORE INFORMATION

Citation:

J Comput Biol. 2008 Dec;15(10):1347-63. doi: 10.1089/cmb.2007.0176.
BayesMD: flexible biological modeling for motif discovery.
Tang MH, Krogh A, Winther O.

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.

xCellerator 0.91 – Mathematica Package for Biological Modeling

xCellerator 0.91

:: DESCRIPTION

xCellerator (also called xlr8r) is the second-generation of cellerator. It is separately funded and lgpl licensed. xCellerator is a Mathematica® package designed to aide biological modeling via the automated conversion of chemical reactions into ODEs and their subsequent solution via numerical integration.

xCellerator is similar to Cellerator but the implementation is fundamentaly different; it consequently runs 100 – 1000 times faster then Cellerator.

::DEVELOPER

Biological Network Modeling Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

xCellerator

:: MORE INFORMATION

Citation

Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations.
Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED.
Bioinformatics. 2003 Mar 22;19(5):677-8.

Pointillist 2.1.2 – MATLAB Codes of Iterative Framework for Biological Modeling

Pointillist 2.1.2

:: DESCRIPTION

Pointillist is a set of MATLAB codes for inferring the set of elements affected by a perturbation of a biological system, based on multiple types of evidence. The integration methods in Pointillist are general-purpose and may be applied to integrate data from any existing and future technologies without requiring training datasets.

::DEVELOPER

Computational Biology, Institute for Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Pointillist ; maunal ;  Java version

:: MORE INFORMATION

Citation:

Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, Bolouri H. “A data integration methodology for systems biology.” Proc Natl Acad Sci U S A 2005; 102(48) 17296-17301.