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Paul Macklin
Works at University of Southern California
Attended University of California, Irvine
Lives in Pasadena, CA USA
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Paul Macklin

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BioFVM 1.1.4 is released! Main focus is compatibility updates for PhysiCell.

BioFVM is a cross-platform, open source 3D diffusion solver written for biological and clinical problems. It has been optimized for desktop workstations and single compute nodes.

Project website: http://BioFVM.MathCancer.org
Download: http://BioFVM.SourceForge.net
Method Paper: http://dx.doi.org/10.1093/bioinformatics/btv730

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A nice article on mathematical modeling in biology, profiling +James Glazier , +Kristin Swanson and my lab.

Go go mighty modelers! :-)
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BioFVM Version 1.1.1 is out. (BioFVM is a 3-D open source diffusion solver for biology.)

This release updates compatibility with MultiCellDS (multicellular data standard) and upgrades pugixml (XML parser) from 1.5 to 1.7. This improves MultiCellDS save times by about 15%.

Here's the download link on SourceForge:

https://t.co/7sK7Afcagp



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Would love to see your talk!
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BioFVM Version 1.1.0 now supports saving MultiCellDS data.

BioFVM (finite volume method for biology) is an open source code to simulate diffusion of many substrates in 3D. See http://BioFVM.MathCancer.org

MultiCellDS (multicellular data standard) is a multi-institutional project to create a model-independent standard for simulation and experimental data. We're using it to advance open, reproducible science. See http://MultiCellDS.org

Learn more on how to work with BioFVM and MultiCellDS data at my most recent blog post here:

http://mathcancer.blogspot.com/2016/02/saving-multicellds-data-from-biofvm.html
Note: This is the fifth in a series of "how-to" blog posts to help new users and developers of BioFVM. Introduction. A major initiative for my lab has been MultiCellDS: a standard for multicellular data. The project aims to create model-neutral representations of simulation data (for both ...
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New release of BioFVM (Version 1.0.3): 

+ Introduces template project to help new users. 
+ Introduces new Matlab functions to read and plot data. 
+ Minor bug fixes. 
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A howto for setting up gcc for OpenMP projects in OSX, using MacPorts.

Since the version of "gcc" (an alias for clang) that ships with OSX / Xcode doesn't support OpenMP, gcc is necessary for many scientific projects that are parallelized with OpenMP. 
Note: This is the second in a series of "how-to" blog posts to help new users and developers of BioFVM and PhysiCell. This guide is for OSX users. Windows users should use this guide instead. A Linux guide is expected soon. These instructions should get you up and running with a minimal ...
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Paul Macklin

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BioFVM 1.1.3 is released! BioFVM is an open source, cross-platform C++ code to simulate 3D diffusion in biological problems.

Version 1.1.3 fixes bugs in Dirichlet nodes, which allow you to specify solution values in any voxel.

Download: http://BioFVM.MathCancer.org
Method paper: http://bioinformatics.oxfordjournals.org/content/32/8/1256.full 
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BioFVM Version 1.1.2 is out!

This version fixes bugs in the stopwatch functions (TIC, TOC, etc.) so they work consistently across platforms.

It also adds new uniform random number generator functions that provide easy access to the C++11 Mersenne Twister. This should make it easier to build models on top of BioFVM (e.g., cellular automata).

Download here: https://sourceforge.net/projects/biofvm/files/BioFVM/BioFVM%201.1.2/
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The State of Slashdot: Https, Poll Changes, Auto-Refresh, Videos, and More
As of yesterday, Slashdot now serves over https. In addition, the polls have been moved exclusively to the right rail, and will not show up with the other stories any longer. We've also disabled auto-refresh, and fixed various issues with search and other features. In the last few weeks, we've also ...
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Congrats, +Philip Gerlee! Definitely of interest to +babis hatzikirou!

Key Result: classic Fisher Equation tumor expansion velocity breaks under glioblastoma "go/grow" phenotype switch

Preprint link: http://arxiv.org/abs/1305.5036
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BioFVM warmup: 2D continuum simulation of necrotic 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 a C++ compiler in Windows or OSX.
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A howto for setting up gcc for OpenMP projects in OSX, using Homebrew.

Since the version of "gcc" (an alias for clang) that ships with OSX / Xcode doesn't support OpenMP, gcc is necessary for many scientific projects that are parallelized with OpenMP.

This version of the tutorial is much faster than using MacPorts.
Note: This is the third in a series of "how-to" blog posts to help new users and developers of BioFVM and PhysiCell. This guide is for OSX users. Windows users should use this guide instead. A Linux guide is expected soon. These instructions should get you up and running with a minimal ...
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Have him in circles
197 people
Hoshim Rahmonov's profile photo
Glenn Romero's profile photo
Jiří Halák's profile photo
Zeshan Masroor's profile photo
Chris Brulak's profile photo
somy naz's profile photo
Gibin Powathil's profile photo
Josh Isaac's profile photo
praveen kumar's profile photo
Work
Occupation
Biomathematician
Employment
  • University of Southern California
    Assistant Professor of Research Medicine, 2011 - present
  • University of Dundee
    Lecturer (permanent staff), 2010 - 2011
  • University of Texas Health Science Center, Houston
    Assistant Professor, 2007 - 2010
Places
Map of the places this user has livedMap of the places this user has livedMap of the places this user has lived
Currently
Pasadena, CA USA
Previously
Fremont, NE USA - Lincoln, NE USA - Minneapolis, MN USA - Irvine, CA USA - Houston, TX USA - Berlin, Germany - Hannover, Germany - Dundee, United Kingdom
Story
Tagline
Biomathematician - patient-specific cancer modeling
Education
  • University of California, Irvine
    Ph.D. Mathematics, 2003 - 2007
  • University of Minnesota, Twin Cities
    M.S. Mathematics, 2000 - 2003
  • University of Nebraska–Lincoln
    B.A. Mathematics and German, 1995 - 1999
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Gender
Male
Relationship
Married