:: DESCRIPTION
Moose is the core of a modern software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Front Neuroinform. 2008;2:6. doi: 10.3389/neuro.11.006.2008. Epub 2008 Dec 19.
PyMOOSE: Interoperable Scripting in Python for MOOSE.
Ray S, Bhalla US.
:: DESCRIPTION
CompuCell3D (CC3D) runs 3D multiscale multi-cell simulations, integrating the GGH model , PDE solvers (reaction-diffusion), and cell type automata (differentiation). CompuCell3D runs in parallel with the CompuCellPlayer visualization engine.
CompuCell3D was originally written to model morphogenesis, the process in embryonic development where cells cluster into patterns which eventually differentiate into organs, muscle or bone. Through integration of multiple mathematical models into a software implementation with easy to use XML based syntax scientists were able to build models within few hours as opposed to weeks when writing source code from scratch. compuCell3D is based on Glazier-graner-Hogeweg model (GGH) also known as the Cellular Potts Model (CPM).The model is capable of capturing key cellular behaviors: cell clustering as well as growth, division, death, intracellular adhesion, and volume and surface area constraints;
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier
A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation
PLoS Comput Biol 7(10): e1002155. doi:10.1371/journal.pcbi.1002155
:: DESCRIPTION
scaleboot is an add-on package of R. This is for calculating approximately unbiased (AU) p-values from a set of multiscale bootstrap probabilities for a hypothesis.
::DEVELOPER
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N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genome Biol. 2014;15(10):474.
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.
Harmanci A1, Rozowsky J, Gerstein M.
