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Recent news

Wednesday, Feb 24th, 2016
Saving MultiCellDS data from BioFVM: Note: This is the fifth in a series of "how-to" blog posts to help new users and developers of BioFVM. IntroductionA major initiative for my lab ... [read more]

Friday, Jan 22nd, 2016
BioFVM warmup: 2D continuum simulation of tumor growth: Note: This is the fourth in a series of "how-to" blog posts to help new users and developers of BioFVM. See below for guides to setting up ... [read more]

Open Source

I have been involved in open source software development since 2005. In the coming months, I plan to partly open source my agent model simulator. I am also developing an associated open data standard for multicellular simulation, experimental, and clinical data: the MultiCellDS Project.

Open source projects I have founded and maintain

PhysiCell Screenshot

PhysiCell: Physics-based cell model

This core technology, in development since 2007, models individual cells as agents. Each agent has a lattice-free position (center of mass), a velocity that is determined by the balance of biomechanical forces, and a phenotype that depends upon the cell's internal genomic/proteomic state and its sampling of the local microenvironment. Cell cycle progression and apoptotic and necrotic cell death are modeled as stochastic processes that vary with the microenvironment. Detailed, state-dependent "submodels" regulate the cell's fluid and biomass content. We are the first to model the critical process of nuclear cell calcification, and have the most detailed model of cell necrosis.

This agent model is the foundation of our cutting-edge patient calibration techniques, which can be uniquely constrained to patient immuno­his­to­chem­is­try and other his­to­path­o­log­ic (e.g., mor­pho­met­ric) mea­sure­ments. PhysiCell is capable of simulating 105 to 106 cells on desktop processors in complex 3-D tissue structures. Click here to read more.

Recent reference: Macklin et al. (2012)
Recent multimedia: DCIS simulations
Project website:

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BioFVM Screenshot

BioFVM: A biological transport solver

This code simulates the diffusive transport of multiple substrates (e.g., oxygen, glucose, growth factors, drugs) as they are secreted/released/absorbed by biological elements in 3-D tissues. We use this code to simulate the microenvironment and its interactions with cells. BioFVM is capable of simulating diffusive transport of 5-10 substrates on 1-10 million voxel meshes (generally 5-100 mm3) on desktop processors. Click here to read more. BioFVM has been peer reviewed in Bioinformatics. It is available as open source under the (3-clause) BSD license. BioFVM stats

Recent reference: Ghaffarizadeh et al. (2016)
Project website:
Alternate download site: click here

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MultiCellDS Screenshot


MultiCellDS (Multicellular data standard), an outgrowth of the earlier MultiCellXML project, aims to create a data standard for sharing multicellular experimental, simulation, and clinical data. Our ultimate goal is to foster a community that develops user-friendly tools that can read, write, and recombine data into better simulations and analyses for multicellular biology and predictive medicine. As part of this effort, we are developing MultiCellDB: a repository for a curated libary of digital cell lines and peer-reviewed simulation and experimental data.

A novel part of MultiCellDS is the digital cell line: a digital analogue of experimental cell lines that will help to collect biophysical cell line measurements coming from many research groups and make them readily accessible to an ecosystem of compatible computational models. Digital snapshots provide a unified, model-independent representation of simulation data, as well as segmented pathology, radiology, and experimental data.

In the past year, MultiCellDS has grown from a single-lab effort to an international community of mathematicians, biologists, data scientists, and clinicians, with contributors in the US, the United Kingdom, Germany, and elsewhere. We are currently preparing our first method paper on a repository of over 200 digital cell lines, many of which were created from brain and breast cancer patient data. Click here to read more!

Project website:

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MultiCellXML Screenshot


MultiCellXML is an XML-based data format for agent-based simulations of multicell systems. I designed this format to facilitate simulation data exchange, postprocessing, and visualization. Benchmark datasets and open-source postprocessing and visualisation code are provided.
Note: As of 2014, this project has been superceded by MultiCellDS.

Project website:

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EasyBMP Screenshot


EasyBMP is a simple, cross-platform, open source (revised BSD) C++ library designed for easily reading, writing, and modifying Windows bitmap (BMP) image files. I use it to write rasterized images in simulations, postprocessing, and visualization. EasyBMP stats

Project website:
Alternate download site: click here

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EasyBMPtoAVI Screenshot


EasyBMPtoAVI is a simple, cross-platform, open source C++ program for converting series of images into an uncompressed movie. I use this to efficiently generate animations of my simulations via SSH and download the zipped AVI file. EasyBMPtoAVI stats

Project website:
Alternate download site: click here

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