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Moving the blog to

Hi, everyone!

Blogspot has been a great platform for me, but in the end, editing posts with source code and mathematics has been too much of a headache in the neglected blogspot and google UIs.

Elsewhere in the universe, WordPress has developed and encouraged a great ecosystem of plugins that let you do LaTeX and code syntax highlighting directly in your posts with ease. I can’t spend hours and hours on fixing mangled posts. It’s time to move on.

So as of today, I am moving to a self-hosted blog at

I will leave old posts at and gradually migrate them here to Thanks for following me over the last few years.

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Banner and Logo Contest : MultiCellDS Project

As the MultiCellDS (multicellular data standards) project continues to ramp up, we could use some artistic skill.

Right now, we don’t have a banner (aside from a fairly barebones placeholder using a lovely LCARS font) or a logo. While I could whip up a fancier banner and logo, I have a feeling that there is much better talent out there. So, let’s have a contest!

Here are the guidelines and suggestions:

  1. The banner should use the text MultiCellDS Project. It’s up to artist (and the use) whether the “multicellular data standards” part gets written out more fully (e.g., below the main part of the banner). 
  2. The logo should be shorter and easy to use on other websites. I’d suggest MCDS, stylized similarly to the main banner. 
  3. Think of MultiCell as a prefix: MultiCellDS, MultiCellXML, MultiCellHDF, MultiCellDB. So, the “banner” version should be extensible to new directions on the project. 
  4. The banner and logo should be submitted in a vector graphics format, with all source.
  5. It goes without saying that you can’t use clip art that you don’t have rights to. (i.e., use your own artwork or photos, or properly-attributed creative commons-licensed art.) 
  6. The banner and logo need to belong to the MultiCellDS project once done.
  7. We may do some final tweaks and finalization on the winning design for space or other constraints. But this will be done in full consultation with the winner.  

So, what are the perks for winning?

  1. Permanent link to your personal research / profession page crediting you as the winner. 
  2. A blog/post detailing how awesome you and your banner and logo are.  
  3. Beer / coffee is on me next time I see you. SMB 2015 in Atlanta might be a good time to do it!
  4. If we ever make t-shirts, I’ll buy yours for you. 🙂 
  5. You get to feel good for being awesome and helping out the project!

So, please post here, on the @MultiCellDS twitter feed, or contact me if you’re interested.  Once I get a sense of interest, I’ll set a deadline for submissions and “voting” procedures.


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2015 Speaking Schedule

Here is my current speaking schedule for 2015. Please join me if you can!

Feb. 13, 2015: Seminar at the Institute for Scientific Computing Research, Lawrence Livermore National Laboratory (LLNL)
Title: Scalable 3-D Agent-Based Simulations of Cells and Tissues in Biology and Cancer [abstract]

See Also:

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2014 Speaking Schedule

Here is my current speaking schedule for 2014. Please join me if you can!

Feb. 16, 2014: American Association for the Advancement of Science (AAAS) Annual Meeting, Chicago
Title: Integrating Next-Generation Computational Models of Cancer Progression and Outcome [abstract]
invited by the National Cancer Institute 

May 9, 2014: European Society for Medical Oncology (ESMO) 2014 IMPAKT Breast Cancer Conference, Brussels, Belgium
Title: Calibrating breast cancer simulations with patient pathology: Progress and future steps [programme]
Plenary talk

May 13, 2014: Wolfson Centre for Mathematical Biology at the University of Oxford, Oxford, UK
Title: Advances in parallelized 3-D agent-based cancer modeling and digital cell lines [abstract]

June 19, 2014: Biostatistics Seminar, University of Southern California, Los Angeles
Title: Simulating 3-D systems of 500k cells with an agent-based model, and digital cell lines [link]

Aug. 18, 2014: COMBINE (Computational Modeling in Biology Network) 2014 Symposium, University of Southern California, Los Angeles
Title: Digital cell lines and MultiCellDS: Standardizing cell phenotype data for data-driven cancer simulations[Program]

See Also:

2013 public speaking schedule

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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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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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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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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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USC PSOC to host interdisciplinary cancer symposium

*** UPDATE: Registration has been extended to September 19, 2012, 5:00 pm Pacific Time. ***

The NCI-funded, Physical Sciences in Oncology Center (PSOC) at USC is hosting its second annual symposium on interdisciplinary cancer research on September 27, 2012 from 7 am to 6 pm.  The event is free but registration is required.

The symposium will include a great diversity of expertise, spanning cell analysis, cancer evolution, modeling, drug delivery, and therapeutic response.  We also have two fascinating keynote speakers: David A. Kirby, author of Lab Coats in Hollywood, and Corby Kummer, senior editor and acclaimed food critic for the Atlantic Monthly. Here’s the confirmed lineup:

Cell Analysis: 
Eun Sok Kim (University of Southern California)
Cagri Savran (Purdue University)

Mathematical Modeling:
Paul Newton (University of Southern California, and Co-Director of CICO)
Paul M. Kulesa  (Stowers Institute)

Cancer Evolution/Tumor Structures:
Dwayne Stupack (University of California San Diego)
Lin Chen (University of Southern California)

Drug Delivery/Therapeutic Response:
Yannis G. Kevrekidis (Princeton University)
David Agus (University of Southern California)
Debra Auguste, Harvard University

It should be a wonderful event, and I hope you can attend!

You can find the full flyer and description here.

You can find the agenda here.

Click here to register (due by September 19, 2012).

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Introducing CICO: The Consortium for Integrative Computational Oncology

We’ve had some exciting times in the Macklin Math Cancer Lab!

On May 18th, Paul Newton and I received received significant startup funding from the USC James H. Zumberge Research and Innovation Fund to establish the Consortium for Integrative Computational Oncology (CICO).  We’re grateful for this opportunity to build a new resource for USC and the broader cancer community!

CICO seeks to develop and promote cross-disciplinary, integrative collaborations across the USC (particularly the Viterbi School of Engineering and the Keck School of Medicine) in clinically-oriented cancer modeling.  Among our guiding principles:

  • Computational modeling of cancer must be driven by clinical needs. Modelers need to work hand-in-hand with clinicians at all steps of the modeling process.
  • Computational oncology works at its fullest potential when working with clinical data. This focus:  
    • drives advances in mathematical model design, 
    • allows us to evaluate and choose between competing models, 
    • helps biologists to test, validate, and refine current cancer biology orthodoxy, 
    • helps clinicians to better interpret their data, and 
    • is most likely to lead to computational tools that will make an impact in the clinic.
  • Integrative computational oncology holds the potential to integrate advances from mathematical modeling, experiments, and clinical data into comprehensive tools that give a better understanding of cancer than any of these individual pieces alone.  
  • Integrative computational oncology must include student education at its core, to create a true “ecosystem” of clinically-focused modeling students from the undergraduate to postdoctoral level. 

You’ll be hearing a lot more about CICO as we ramp up in the coming year!

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