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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 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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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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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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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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This is part of the NCI handbook of math methods. 

The open source code is at http://BioFVM.MathCancer.org

Thanks!
Simulating multi-substrate diffusive transport in 3-D tissues with BioFVM Samuel H Friedman, Ahmadreza Ghaffarizadeh, Paul Macklin doi: http://dx.doi.org/10.1101/035709 Abstract Info/History Metrics Preview PDF ...
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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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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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Thanks for posting this! Please let us know if you have any questions. 

Best -- Paul 
Simulating multi-substrate diffusive transport in 3-D tissues with BioFVM Samuel H Friedman, Ahmadreza Ghaffarizadeh, Paul Macklin doi: http://dx.doi.org/10.1101/035709 Abstract Info/History Metrics Preview PDF ...
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Here's a tutorial I wrote on setting up a 64-bit gcc environment on Windows, using MinGW-w64, MSYS, and Notepad++. It includes instructions on modifying your system path, as well as a quick test of the compiler, make, and OpenMP.

Once done, you should be ready to build BioFVM and PhysiCell projects on Windows. Similar tutorials are on the way for Linux and OSX.
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In his circles
188 people
Have him in circles
200 people
Steven Moldin's profile photo
Roeland Merks's profile photo
Carl Kesselman's profile photo
Zeshan Masroor's profile photo
Jason Statham's profile photo
DoubleTake Auto Spa's profile photo
luis alfredo aaron leonis's profile photo
Jack Rory Staunton's profile photo
Karyn Traphagen'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