EPISIM 1.5.2 – Multi-Scale Modeling and Simulation Platform

EPISIM 1.5.2

:: DESCRIPTION

The EPISIM Platform provides the two ready-to-use and easy-to-install software systems EPISIM Modeller and EPISIM Simulator. EPISIM Modeller enables graphical multi-scale modeling of cellular behaviour in a multicellular context using process diagrams. The graphical cell behavioral models are automatically translated into executable code. This code can be loaded with EPISIM Simulator to conduct either a 2D or a 3D tissue simulation.

::DEVELOPER

The TIGA Center (TISSUE IMAGING AND ANALYSIS CENTER)

:: SCREENSHOTS

EPISIM

:: REQUIREMENTS

  •  Linux /Windows/MacOsX

:: DOWNLOAD

 EPISIM

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 15;29(2):223-9. doi: 10.1093/bioinformatics/bts659. Epub 2012 Nov 18.
Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI.
Sütterlin T1, Kolb C, Dickhaus H, Jäger D, Grabe N.

MS4 0.2 – Multi Scale Selector of Sequence Signatures

MS4 0.2

:: DESCRIPTION

MS4 is a method that selects among all the segments of similarity detected by the N-local decoding algorithm (Didier et al., 2007) those on which a classification of unaligned set of sequences is based.

::DEVELOPER

Claudine Devauchelle (devauchelle@genopole.cnrs.fr) @ Laboratoire de Mathématiques et Modélisation d’Évry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Python

:: DOWNLOAD

MS4

:: MORE INFORMATION

Citation

Eduardo Corel et al.
MS4 – Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences
BMC Bioinformatics 2010, 11:406 doi:10.1186/1471-2105-11-406

BSubtilis 1.0 – Multi-Scale, Agent Based Model of B. Subtilis Phenotype Switching

BSubtilis 1.0

:: DESCRIPTION

BSubtilis is the ABM ( Agent Based Model) designed to mimic the B. subtilis competence phenotype. The model was tuned to simulate a colony of B. subtilis cells where competence emerged in 10–20% of the population. BSubtilis make the following observations and predictions about genetic “noise”: a) random spatial-temporal interactions lead to competence, b) daughter cells which inherit portions of the competence machinery are more likely to exhibit the competence phenotype, and c) dilution events like cell division inhibit competence emergence until stationary phase.

::DEVELOPER

The Giddings Lab at Boise State

:: SCREENSHOTS

BSubtilis

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 BSubtilis

:: MORE INFORMATION

Citation

Theor Biol Med Model. 2013 Apr 3;10:23. doi: 10.1186/1742-4682-10-23.
Agent-based modeling of competence phenotype switching in Bacillus subtilis.
Stiegelmeyer SM, Giddings MC.