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 news.usc.edu.
Read the article: http://news.usc.edu/59091/usc-researcher-calls-for-common-standards-in-cancer-modeling/ (Feb. 21, 2014)
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:
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. :-)
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 MathCancer.org.
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!
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: http://physics.cancer.gov/report/2013report/PaulMacklin.aspx (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!)
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:
http://www.ams.org/notices/201303/
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!
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:
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).
Introducing CICO: The Consortium for Integrative Computational Oncology
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!