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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 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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Paul Macklin

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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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Paul Macklin

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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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Paul Macklin

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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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Paul Macklin

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BioFVM -- our 3-D (and 2-D) diffusion solver for biology -- is open sourced and published in Bioinformatics. Here's a little more on the code .. 
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Paul Macklin

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This is really neat work, and it's very helpful to have the "big picture" of several papers in one place. Do you plan to submit this? 
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Thanks, but I meant for the in press destination ;-)

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Paul Macklin

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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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Paul Macklin

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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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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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Paul Macklin

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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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Paul Macklin

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I was about to write a post about how much I agree with this for any age. How gray on gray is a fail. How using the standard underline icon to denote all formatting options is a fail. (gmail) 

Then, I accidentally clicked the page, and my draft disappeared. Evidently, hovering your mouse over the "G+1" button makes the hidden editor UI reappear to resume the draft, but clicking it erases your post. I guess we're supposed to stumble across this user model. 

Thanks, Google, for proving the point of this article so nicely with your editor. 
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In his circles
186 people
Have him in circles
199 people
Raymond Roy's profile photo
Hoshim Rahmonov's profile photo
Michael Rininger's profile photo
Jacob Scott's profile photo
Phan Minh Thuật's profile photo
Bjørn Egil Møen-Knudseth's profile photo
Believers Loan's profile photo
Cali Nche's profile photo
Mariya Ptashnyk'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
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Married