Mechanistic modeling is an integral part of contemporary bioscience, used forhypothesis generation and testing, experiment design and interpretation and the design of therapeuticinterventions. The CompuCell3D modeling environment allow researchers with modest programingexperience to rapidly build and execute complex Virtual Tissue simulations of development,homeostasis, toxicity and disease in tissues, organs and organisms, covering sub-cellular, multi-celland continuum tissue scales. Virtual Tissue simulations developed using CompuCell3D run onWindows, Mac and Linux. CompuCell3D is open source, allowing users to extend, improve, validate,modify and share the core software. For more information please visit:

Goal: By the end of this one-week course, participants will have implemented a basic simulation oftheir particular biological problem of interest. Post-course support and collaboration will be available tocontinue simulation development.

Topics: Python scripting. Introduction to Reaction-Kinetics (RK) models. Introduction to SBML.Introduction to Virtual-Tissue simulations. Introduction to CompuCell3D. Basics of model building.Combining RK and Virtual-Tissue models. Extending CompuCell3D. Building a basic simulation of yoursystem.

Format: The workshop will include a limited number of lectures and numerous hands-on computertutorials. Each attendee will also present a mini-talk on their problem of interest. There will beconcurrent sessions for basic and advanced modelers.

Instructors: James A. Glazier (Indiana University), Julio Belmonte (North Carolina State University),Maciek Swat, Juliano Gianlupi (Indiana University), Andy Somogyi (Indiana University), James Sluka (Indiana University).

Target Audience: Experimental Biologists, Medical Scientists, Biophysicists, Mathematical Biologistsand Computational Biologists from advanced undergraduates to senior faculty, who have an interest indeveloping multi-scale Virtual-Tissue simulations, or learning how such simulations might help theirresearch. No specific programming or mathematical experience is required, though familiarity with amodeling environment (e.g. Mathematica®, Maple®, Python, or Matlab®) and how to represent basicconcepts like diffusion and chemical reactions mathematically, will be helpful. Note: An Introductory Python Tutorial will take place on August 11th. If you already know Python, youmay skip this part of the workshop.

Fees: There is no registration fee. We will provide coffee, tea, lunch, snacks and workshop materials.

Registration: Enrollment is limited and by application only. Kindly apply online with a c.v., a briefstatement describing your current research interests and the specific problem you would like to model.Students should also include a letter of support from their current advisor. Please submit all applicationmaterials electronically at by June 10, 2019.

Facilities: The workshop will be held at Indiana University, Bloomington, IN, USA. The nearest airportis Indianapolis, IN. Participants will be able to connect to the Internet using their own laptops.

For more information, please contact: CompuCell3D Team (

2019 IMAG Multiscale Modeling Consortium (MSM) Meeting

2019 IMAG’s NEXT TOP MODEL Video Competition

Links to the Winning Top Model videos are here!

Our multiscale modeling community does amazing, world-changing research, and in order to maximize its impact we are compelled to share it with the lay public and within our own community. In order to facilitate this sharing, IMAG’s Public Dissemination & Education (PDE) Task Force has launched this inaugural NEXT TOP MODEL Video Competition. We invite anyone who is doing research related to computational modeling to produce a short, promotional and educational video that describes your research and its impact for a lay audience (i.e. 5th grade education level).


Submitted videos will be eligible for posting on IMAG’s YouTube channel, and judged according to the rubric below by a panel of judges, including the co-leads of the PDE Task Force (Shayn Peirce-Cottler, Silivia Blemker, David Basanta, and Andrew McCulloch), high school science teachers, and high school students. Prizes (listed below) will be awarded to the top three videos.

Questions? Please contact Shayn Peirce-Cottler (

Click here for more details:



The mathematical sciences are part of everyday life. Modern communication, transportation, science, engineering, technology, medicine, manufacturing, security, finance, and many other disciplines depend on the mathematical sciences, even if we don’t always realize it. It is important for mathematical researchers to convey the importance of their work to diverse audiences. This often comes down to being able to quickly and simply describe what you are doing and why.

With that in mind, the National Academies’ Board on Mathematical Sciences and Analytics (BMSA) invites early career professionals and students who use mathematics in their work to submit short video “elevator speeches” describing how their work in mathematics is important and relevant to our everyday lives. This can be an unedited selfie video, an animation, or any other format. We just want to learn about why your work is important in 1-2 minutes.

The winning video will be announced and played during the 2019 SIAM Conference on Computational Science and Engineering in Spokane, Washington. The winning participant will receive $1000 and be featured on our website. You do not need to attend the conference or be a SIAM member to participate.

2019 MSM Consortium Meeting dates are set!


Wednesday March 6th, 2019- 8:30am to Thursday March 7th, 2019- 5:30pm

Co-chairs: Bruce Lee, MD, MBA and Jeff Holmes, MD, PhD

2018 IMAG Futures Meeting - archived information

Archived Videocast from March 21, 2018

Presentations and Discussions on the IMAG wiki agenda pages

 #MSM2018 Twitter feed


Goals and Objectives

Check-in on 2009 IMAG Futures challenges

Explore convergence of mechanistic, causal and predictive models

Produce 2018 IMAG Futures challenges

Interactive Agenda

Meeting Wikipage

View Attendees and Presentations


Tuesday, November 28, 2017 1:30pm to 2:30pm
Presenter: Patricia Brennen, RN, PhD

Webinar/Webcast Links: Webinar Link (WebEx)

Investigators are developing new and quite sophisticated models to interrogate large data sets. Characterizing model provenance and performance will enhance the reusability of models, and afford better model validation and determination of the conditions under which the models perform best. Thus, it is timely to consider how to formally characterize models, define relevant metadata and make models directly discoverable.  In this webinar, the Director of National Library of Medicine will lead a discussion to set the foundation of how to create a library of models that will enhance the integrity, discoverability and appropriate re-use of models.

IMAG and the MSM will conduct an online discussion with Dr. Brennen,, director of the National Library of Medicine, as a follow-up to the discussion we had with her during the IMAG 10th Anniversary MSM Consortium meeting (recorded audio here,  Please send any discussion topics, questions you have for her to in preparation for her webinar.

The purpose of the announcement is to invite applications from applicants who have an interest in performing high impact, cutting-edge scientific and computing activities necessary to establish an NIH Data Commons. The goal of the NIH Data Commons is to accelerate new biomedical discoveries by providing a cloud-based platform where investigators can store, share, access, and compute on digital objects (data, software, etc.) generated from biomedical research and perform novel scientific research including hypothesis generation, discovery, and validation. Applicants are encouraged to develop innovative approaches to one or more key computational, data, analytical and scientific capabilities of the Data Commons. These key capabilities are described in detail in the announcement.

Awards under Research Opportunity Announcement RM-17-026 will made using Other Transactions (OTs), which are not grants, cooperative agreements, or contracts. It is essential applicants carefully follow the instructions in the announcement as they likely will be different from what they are used to seeing.


Letters of Intent (LOIs) are required, and are due June 30, 2017 (5:00 PM United States Eastern Time).  LOIs will be used to select individuals or groups who will be invited to submit an application by July 12. Only those who are invited may apply. Applications submitted without an invitation from the NIH will be returned and not reviewed. NIH expects to make several OT awards under this announcement. The planned budget for this announcement is $21 million over a 4-year period.


Inquiries about RM-17-026 should be directed to:

FOA Link:

The National Institute of Biomedical Imaging and Bioengineering (NIBIB), in partnership with the National Institute on Aging (NIA), announces an opportunity for NIBIB-supported investigators to request administrative supplements to develop new tools, technologies and approaches for the prevention, diagnosis, treatment and understanding of Alzheimer's Disease and Alzheimer's-disease-related dementias (AD/ADRD). These supplements will be funded by NIA as part of the NIA strategic plan to support the development of innovative strategies to prevent, diagnose and treat AD/ADRD.

Administrative supplement requests should be submitted to PA-16-287, Administrative Supplements to Existing NIH Grants and Cooperative Agreements The requested supplemental budget cannot exceed $100,000 in direct costs for up to 12 months. The project and budget periods of the supplement request must be within the currently approved project period for the existing parent award.

Supplements will be considered for active NIBIB-funded projects that may have important application in AD/ADRD. Administrative supplements may be awarded to meet increased costs that are within the scope of the approved award, but were unforeseen when the application was submitted. For the purposes of this Notice, "within scope" may include the addition of an AD/ADRD-relevant component to a project employing or developing a broadly applicable technology. Applicants are strongly encouraged to discuss the aims of the proposed work with the NIBIB program officer assigned to the parent grant to assess suitability for this funding opportunity.

Requests must be received by July 3, 2017. 

The purpose of this funding opportunity is to develop new and/or enhance existing tools and technologies to facilitate high-resolution mapping of peripheral neural circuits.


The next quarterly deadline for pre-applications is approaching on August 1, 2017.


Only tool and technology categories listed on the SPARC FOA Priorities page for the current receipt date are responsive to this funding opportunity. Future receipt dates will have different priorities based on program needs. Current priorities include sample preparation, imaging and targeting, modeling and simulation, surgical access tools, neural interfaces, and serving as a consortium-wide service provider for specified activities.

Questions should be addressed to

Potential applicants may view the RM-17-009 Informational Webinar slides (PDF).

The SPARC team will be holding virtual office hours for potential applicants. We strongly encourage using these as an opportunity to ask questions and discuss your ideas with the SPARC team. Visit to sign up.

See the announcement here: RM-17-009 (PDF)

The Joint Program Committee-1 (JPC-1) Office has a job opening for a "Health Science Administrator", to "serve as a senior staff advisor to the Medical Simulation and Information Sciences Research Program Director"

The official announcement is available at:

Closing Date: June 6, 2017

Please refer comments or questions to Dr. Jan Harris, Director, JPC-1, at her Email address: