Figure: An early test of our new 3-D agent-based cell model, growing from 10 to 80,000 agents in about 25 days (24-threaded simulation required about 5 hours). Rendered in 3D using POVRAY (with a cutaway view). [Read more ...]

Saturday, October 26, 2013

Website updates ...

I'm in the process of rolling out some updates to my website. The first thing you'll see is a new talk / tutorial on computational modeling of biological processes, based upon my recent talk at the USC PS-OC Short Course in October 2013. I'll make another post here when it's ready. It will include MATLAB source code to run through the models.

In the medium term, I hope to update my list of projects to better reflect current efforts by my lab, particularly in (1) integrative modeling of cancer metastases using high-throughput in vitro experiments and sophisticated bioengineered tissues for calibration and validation, and (2) development of standardizations for cell- and tissue-scale models and experiments.

In the longer term, I hope to switch my website layout a bit to be more like the USC PSOC website. I wrote that site about a year ago, and I like the CSS and structure a lot better. :-)

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Saturday, July 20, 2013

Interview at the 2013 NCI PS-OC Annual Meeting

I recently had the opportunity to be interviewed by Pauline Davies at the 2013 Physical Sciences-Oncology Annual Meeting. (I gave one of the addresses–"Exploring Possibilities for Next-Generation Computational Cancer Models that Work Together"–at the meeting; agenda available here.) The interview (largely in layman's terms) discusses mathematical and computational modeling of cancer, the potential role for computational modeling in understanding cancer and making predictions that could help patients and their doctors make treatment choices, and the need for model and data standardizations to enable better predictions in the future. The interview draws parallels to hurricane predictions, where multiple models can read/write standardized data and be combined to improve their accuracy.

My interview can be found here, as can the entire set of selected 2013 interviews. You can find more information on my lab and work at

I really want to thank Pauline Davies, Jonathan Franca-Koh and the NCI Office of Physical Sciences in Oncology for the opportunity for this discussion!

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Tuesday, March 26, 2013

USC URAP to fund 3-person undergrad multidisciplinary cancer modeling team

We just got word from the USC Undergraduate Research Associates Program (URAP) that I will have funding for a 3-person, multidisciplinary team of undergraduates starting summer 2013. This project will aim to assemble a team consisting of a computer programmer, a mathematician, and a biologist to jointly develop and refine user interfaces to make computational modeling of cancer faster and more accessible to a wider group of students. This work goes hand-in-hand with our educational goals in the Consortium for Integrative Comptuational Oncology. More details to come (including a job poster and selection details), but this should be a very fun and worthwhile project.

I'm really grateful to the URAP for this opportunity to fund some bright USC undergraduates in a neat project. Last year, two of our interns (Margy Gunnar and Alice Hyun) were funded under this program, and it was a fantastic experience (at least for me!)

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Tuesday, February 12, 2013

Macklin Lab featured on March 2013 cover of Notices of the American Mathematical Society

I'm very excited to be featured on this month's cover of the Notices of the American Mathematical Society. The cover shows a series of images from a multiscale simulation of a tumor growing in the brain, made with John Lowengrub while I was a Ph.D. student at UC Irvine. (See Frieboes et al. 2007, Macklin et al. 2009, and Macklin and Lowengrub 2008.) The "about the cover" write-up (Page 325) gives more detail.

The inside has a short interview on our more current work, particularly 3-D agent-based modeling. You should also read Rick Durrett's perspective piece on cancer modeling (Page 304)—it's a great read! (And yup, Figure 3 is from our patient-calibrated breast cancer modeling in Macklin et al. 2012. ;-) )

The entire March 2013 issue can be accessed for free at the AMS Notices website:

I want to thank Bill Casselman and Rick Durrett for making this possible. I had a lot of fun in the process, and I'm grateful for the opportunity to trade ideas!

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Tuesday, January 1, 2013

2013 Speaking Schedule

Here is my current speaking schedule for 2013. Please join me if you can!
March 22, 2013: Mathematical Biology Seminar, Department of Mathematics, Duke University, Durham, North Carolina
Title: From integration of multiscale data to emergent phenomena: the prognosis for patient-calibrated computational oncology [abstract]
April 19, 2013: Fourth Annual National Cancer Institute Physical Sciences in Oncology Center (NCI PS-OCs) Network Investigators' Meeting, Phoenix, Arizona 
Title: Exploring possibilities for next-generation computational cancer models that work
together (a conversation starter) [abstract]
Plenary talk
May 30, 2013: Mathways into Cancer II International Workshop, Carmona, Spain
Title: From multiscale data integration to predictions of emergent phenomena: the
prognosis for patient-calibrated computational oncology [abstract]
Plenary talk
June 12, 2013: Annual Meeting for the Society of Mathematical Biology (SMB), Mini-Symposium 11: Agent-based simulations in oncology: applications to therapeutics, Tempe, Arizona. 
Title: Progress towards user-friendly, 3-D multiscale agent-based simulators for large (500k+ cells) cancer systems: application to in situ growth and tumor-stroma interactions [abstract]
June 12, 2013: Annual Meeting for the Society of Mathematical Biology (SMB), Mini-Symposium 26: Patient-Specific Modeling of Cancer, Tempe, Arizona. 
Title: Patient-calibrated 3-D simulations of ductal carcinoma in situ (DCIS) with comedonecrosis and calcification [abstract]

See Also:
2014 public speaking schedule

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