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]

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Paul Macklin calls for common standards in cancer modeling

At a recent NCI-organized mini-symposium on big data in cancer, Paul Macklin called for new data standards in Multicellular data in simulations, experiments, and clinical science. USC featured the talk (abstract here) and the work at

Read the article: (Feb. 21, 2014)

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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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Paul Macklin interviewed at 2013 PSOC Annual Meeting

Paul Macklin gave a plenary talk at the 2013 NIH Physical Sciences in Oncology Annual Meeting. After the talk, he gave an interview to the Pauline Davies at the NIH on the need for data standards and model compatibility in computational and mathematical modeling of cancer. Of particular interest:

Pauline Davies: How would you ever get this standardization? Who would be responsible for saying we want it all reported in this particular way?

Paul Macklin: That’s a good question. It’s a bit of the chicken and the egg problem. Who’s going to come and give you data in your standard if you don’t have a standard? How do you plan a standard without any data? And so it’s a bit interesting. I just think someone needs to step forward and show leadership and try to get a small working group together, and at the end of the day, perfect is the enemy of the good. I think you start small and give it a go, and you add more to your standard as you need it. So maybe version one is, let’s say, how quickly the cells divide, how often they do it, how quickly they die, and what their oxygen level is, and maybe their positions. And that can be version one of this standard and a few of us try it out and see what we can do. I think it really comes down to a starting group of people and a simple starting point, and you grow it as you need it.

Shortly after, the MultiCellDS project was born (using just this strategy above!), with the generous assistance of the Breast Cancer Research Foundation.

Read / Listen to the interview: (2013)

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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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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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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]

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2014 public speaking schedule

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