Tag: Mathematica

MathDAMP 1.0.0 – Mathematica package for Differential Analysis of Metabolite Profiles

MathDAMP 1.0.0

:: DESCRIPTION

MathDAMP facilitates the visualization of differences between metabolite profiles acquired by hyphenated mass spectrometry techniques. Differences are highlighted by applying arithmetic operations to all corresponding signal intensities from whole raw (automatically preprocessed and normalized) datasets on a datapoint-by-datapoint basis. The results are visualized using density plots

::DEVELOPER

Martin Robert , Institute for Advanced Biosciences, Keio University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Mathematica
:: DOWNLOAD

 MathDAMP

:: MORE INFORMATION

Citation

MathDAMP: a package for differential analysis of metabolite profiles.
Baran, R., Kochi, H., Saito, N., Suematsu, M., Soga, T., Nishioka, T., Robert, M. and Tomita, M.
BMC Bioinformatics7: 530. (2006)

CplexA 20121212 – Mathematica Package to Study Macromolecular Assembly Control

CplexA 20121212

:: DESCRIPTION

CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions. The package is particularly suited to study gene expression at complex promoters controlled by multiple, local and distal, DNA binding sites for transcription factors.

::DEVELOPER

Biophysics Unit , University of the Basque Country

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

CplexA

:: MORE INFORMATION

Citaiton：

J. M. G. Vilar and L. Saiz, CplexA: a Mathematica package to study macromolecular-assembly control of gene expression, Bioinformatics 26, 2060-2061 (2010).

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.