Tag: Mode

regEfmtool 3.3 – Regulatory Elementary Flux Mode Tool

regEfmtool 3.3

:: DESCRIPTION

regEfmtool is a computational tool that combines the calculation of elementary flux modes in metabolic networks with transcriptional regulatory networks. regEfmtool is based on the open source software efmtool 

::DEVELOPER

regEfmtool team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 regEfmtool

:: MORE INFORMATION

Citation

regEfmtool: speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic.
Jungreuthmayer C, Ruckerbauer DE, Zanghellini J.
Biosystems. 2013 Jul;113(1):37-9. doi: 10.1016/j.biosystems.2013.04.002.

Autoosc 0.1 – Automated Analysis of Biological Oscillator Models using Mode Decomposition

Autoosc 0.1

:: DESCRIPTION

Autoosc is a Mathematica package for analyzing time-series of oscillatory signals, particularly those originating from biological/chemical systems.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Mathematica

:: DOWNLOAD

  Autoosc

:: MORE INFORMATION

Citation

Automated analysis of biological oscillator models using mode decomposition.
Konopka T.
Bioinformatics. 2011 Apr 1;27(7):961-7. doi: 10.1093/bioinformatics/btr069

NMFF – Normal Mode Flexible Fitting

NMFF

:: DESCRIPTION

NMFF (Normal Mode Flexible Fitting) is an evolving package of programs and methods that enable the flexible multi-resolution fitting of large atomically detailed structures into electron density maps from cryoEM, tomography and related lower resolution methods.The theory and methods behind NMFF are based on searching along a few lowest frequency normal mode vectors, constructed from a multi-resolution elastic network representation of the atomic structure of interest, to maximize the correlation between the computed electron density for the flexible model and the experimental density.

::DEVELOPER

NIH Research Resource Center for the Development of Multiscale Modeling Tools for Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

NMFF

:: MORE INFORMATION

Citation

F Tama, O Miyashita and CL Brooks, III. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.
Journal of Molecular Biology, 2004, 337 (4), 985-99.