Announcements

Integrating Machine Learning with Multiscale Modeling for Biomedical, Biological, and Behavioral Systems

Registration is now open

Integrating Machine Learning with Multiscale Modeling

for Biomedical, Biological, and Behavioral Systems

Goals: this meeting focuses on integrating machine learning methods with multiscale modeling methods guided by the fundamental principles of mathematics and physics.

Objectives: to identify the perspectives, challenges, and opportunities of integrating machine learning with multiscale modeling (ML-MSM) in biomedical, biological, and behavioral systems.

•Four approaches within ML-MSM modeling: ordinary differential equation (ODE) based, partial differential equation (PDE) based, theory-driven, and purely data-driven approaches

•Two application contexts: Digital Twins and Human Safety

2019 ML-MSM Meeting

October 24-25, 2019

Bethesda, Maryland (NIH Campus)

October 1, 2019  - Last day to register online

– Register early to participate in pre-meeting activities

 

 

User Training Workshop Developing Multi-Scale, Virtual Tissue Simulations with CompuCell3D

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: www.compucell3d.org

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 https://goo.gl/forms/lGMPVFrjhHZFyGdJ3 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 (compucell3d.iu@gmail.com).

Funding Opportunities

Application Due Date:
Monday, December 31, 2018, Thursday, January 31, 2019, Wednesday, July 31, 2019, Friday, January 31, 2020
Application Due Date:
Thursday, August 1, 2019

Webinars

Webinar Date
Sunday, May 31, 2015 - 12:00am to Monday, May 31, 2021 - 12:00am
Webinar Date
Friday, October 12, 2018 - 9:00am to Monday, November 2, 2020 - 4:00pm
Webinar Date
Friday, November 30, 2018 - 11:45am to Thursday, December 31, 2020 - 8:00am

MSM Meetings

The Society for Mathematical Biology promotes the development and dissemination of research at the interface between the mathematical and biological sciences through its annual meetings. The Annual Meeting of the Society for Mathematical Biology is the most important event organized and sponsored by the Society. It is the most visible yearly event organized by the Society and hence serves as a show case for the goals, ambitions and activities of the society.

Meeting Date:
Monday, July 22, 2019 to Friday, July 26, 2019
Meeting Location:
Montreal, Canada

User Training Workshop Developing Multi-Scale, Virtual Tissue Simulations with CompuCell3D

Mechanistic modeling is an integral part of contemporary bioscience, used forhypothesis generation and testing, experiment design and interpretation and the design of therapeuticinterventions.

Meeting Date:
Monday, August 5, 2019 to Sunday, August 11, 2019
Meeting Location:
Indiana University, Bloomington, IN

 

August 11th - 17th, 2019

Indiana University, Bloomington, IN, USA

 

Meeting Date:
Sunday, August 11, 2019 to Saturday, August 17, 2019
Meeting Location:
Indiana University, Bloomington, Indiana USA

This wiki contains information relevant to the IMAG (Interagency Modeling and Analysis Group) and the MSM (Multi-scale Modeling Consortium)Questions about IMAG and the MSM Consortium can be directed to NIBIBimag@mail.nih.gov.