Software

Core software

The following API software is used to work with MultiCellDS files. Currently, C++ and Python are supported.

libMultiCellDS:: Code to read/write MultiCellDS files (version 1.0.0 or later), in C++ or Python.
Author/maintainer: Samuel Friedman
Project site: http://MultiCellDS.org
Download: https://gitlab.com/MultiCellDS/MultiCellDS

Third-party software

The following third-party software packages support MultiCellDS data. Software using the official MultiCellDS APIs (marked as API) are most likely to maintain standards compliance.

Simulation software

Chaste: Chaste is a general purpose agent-based modeling framework.
Project site: http://www.cs.ox.ac.uk/chaste/
Status: Beta testing a post-processing "converter" to transform Chaste simulation outputs to MultiCellXML, using the MultiCellDS C++ API.
BioFVM: BioFVM is an open source multi-substrate diffusion solver.
Author/maintainer: Paul Macklin
Project site: http://BioFVM.MathCancer.org
Status: BioFVM natively writes MultiCellXML output files. Read support is planned.
PhysiCell: PhysiCell is an open source 3-D agent-based simulator, suitable for simulating millions of cells on desktop workstations.
Author/maintainer: Paul Macklin
Project site: http://PhysiCell.MathCancer.org
Status: Native write support is in beta testing. Read support is planned. PhysiCell's internal data structures are very similar to phenotype datasets and digital cell lines.
CellSys: CellSys (not the one at Seville) is a 3-D simulation package for 2-D monolayers and 3-D spheroids.
Author/maintainer: Stefan Hoehme
Project site: http://www.hoehme.com/software/9-software/9-tisim
Status: Native write support is in beta testing, using the MultiCellDS API.
Tissue Simulation Toolkit (TST): Tissue Simulation Toolkit is a cellular Potts modeling framework for simulating tissues.
Author/maintainer: Roeland Merks
Project site: https://sourceforge.net/projects/tst/
Status: Full read and write support via the API have been implemented, with a release planned soon.

Image analysis

Software plugins for ImageJ are planned for release in 2017. This software will perform image segmentation and output MultiCellDS digital snapshots.

Data analysis

CellPD: CellPD (cell phenotype digitizer) is a user-friendly tool to convert cell count data into MultiCellDS digital cell lines, publication-quality plots, and fitted mathematical models.
Author/maintainer: Edwin Juarez
Project site: http://CellPD.MathCancer.org
Status: Native write support for digital cell lines.

Visualization and/or exploration

A talented team of undergraduate students at the University of Louisville, lead by Hermann Frieboes, developed a first 3-D data visualization and exploration tool. Further documentation is in the works, but Python code can be found at:

https://gitlab.com/MultiCellDS/visualization/tree/master

This work is in development, but the public release of MultiCellDS 1.0 will include an API and software tools to read/write digital cell lines and digital snapshots in MATLAB, C++, and python. All tools will be released with appropriate open source licenses. Commercial licenses may be available upon special request. We target an October 2015 release for MultiCellDS 1.0.

Parameter Identification

NCI Handbook Entry: Parameter Identification: This tutorial paper by Edwin Juarez uses Matlab to identify cell birth and death parameters, using synthetic flow cytometry data.
Reference: http://biorxiv.org/content/early/2015/12/31/035766
Download: http://mathcancer.org/NCI_handbook_parameters/

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