Predictive models of cells are needed to understand biology, rationally design microorganisms, and precisely treat disease. Numerous challenges must be overcome to develop predictive models of entire cells. This seminar aims to stimulate discussion about how to overcome these challenges and foster an interdisciplinary cell modeling community.

Tools for Modeling Biological Systems Seminar Series

Motivation

Each month we feature a researcher who has developed a tool or method to support complex modeling, or an expert in theoretical approaches which can be used to address modeling challenges. We will discuss experimental, computational, and mathematical challenges to modeling, current state-of-the-art techniques, and future directions for the field. We are looking for students, postdoctoral researchers, and faculty who value collaborative problem-solving and are interested in learning about the most recent developments in modeling biological systems.

Join the Cell-Modeling-Seminar Google Group to receive mailing list updates or email Eran Agmon to suggest new software or modeling results that you would like to present during upcoming seminars or workshops.

Details

Day/Time
Friday, December 1, 2023
4 PM EST | 3 PM CST |1 PM PST

Location
Online using Zoom
(registration required)

Format
20-minute presentation #1
20-minute presentation #2
20-minute group discussion

Organizers

Eran Agmon 
University of Connecticut, US

Herbert Sauro
University of Washington, US

Archive

Videos of past seminars will be available at YouTube .

Suggestions

Please reach out to us by email with questions or suggestions for the seminar.

Multiscale Multicellular Modeling: Challenges and Opportunities

December 1, 2023
Multiscale Multicellular Modeling:
Current Challenges and Future Directions

T.J. Sego
Assistant Professor
University of Florida

Dr. Sego’s overarching research seeks to build and enable informative and predictive mathematical and computational models of complex biological systems. Dr. Sego’s basic research interests focus on the coordination and action of the human immune response to viral infections, especially in the context of spatially resolved, dynamic multicellular systems and lung epithelial and endothelial tissues. Dr. Sego uses computational models to elucidate the mechanisms of tissue-, organ- and organism-level host-pathogen interactions in terms of individual cells, and likewise to describe the properties, processes and interactions of those cells in terms of subcellular states. Dr. Sego leverages his multidisciplinary background and experience leading model-based biological and biomedical research to develop technologies targeting multicellular, agent-based and multiscale simulation tools, interactive and high-performance simulation, and collaborative and community-driven research projects.

December 1, 2023
Multi-Scale Multicellular Agent-Based Virtual-Tissue Simulations

James Glazier
Professor
Indiana University

Dr. Glazier is a biophysicist known for his contributions to the field of multiscale modeling, pattern formation, and morphogenesis in biological systems. He is a co-inventor of the Cellular Potts Model (CPM, also known as the Glazier-Graner-Hogeweg model) formalism for simulating the dynamics of cells in biological tissues. Dr. Glazier has been influential in promoting the use of computational modeling and simulation in the study of complex biological phenomena. He moved to the Department of Physics at Indiana University in 2002, where he established the Biocomplexity Institute to advance interdisciplinary study of biological systems.

Multiscale Multicellular Modeling: Challenges and Opportunities Archive

December 1, 2023: Multiscale Multicellular Modeling: Challenges and Opportunities: Dr. T.J. Sego and Dr. James Glazier

Tools for Modeling Biological Systems Archive

April 14, 2021: An electrical engineer’s thoughts on bioengineering: Dr. Jay Bardhan

May 12, 2021: PETab and SBstoat: Dr. Joe Hellerstein and Dr. Daniel Weindl

June 9, 2021:
libOmexMeta: Dr. David Nickerson

July 14, 2021: SBML network viewer & sbmlutils: Dr. Jin Xu and Dr. Mattias König

Modeling Biology by Domain Archive

January 14, 2020: Protein Signaling: Uri Alon and Herbert Sauro

February 11, 2020: Gene Expression: Melissa Kinney and David Arnosti

March 9, 2020: Cardiac Tissue: Miguel A. Aon and Patrick Boyle

April 14, 2020: Population Dynamics: Ines Thiele and Eberhard Voit

May 12, 2020: Whole-Cell Modeling: Jonathan Karr

June 9, 2020: Neurological Systems: Bill Lytton

July 14, 2020:
Cancer: Paola Vera-Licona

August 11, 2020: Metabolism: Matthaias König and Vissily Hatzimanikatis

September 8, 2020: Whole-cell Modeling: Luis Serrano and Markus Covert

Modeling Software Workshop Archive

October 2, 2019: Model Simulation

Paul Macklin

Associate Professor, Indiana University Bloomington

PhysiCell

Veronica Porubsky

Ph.D. Fellow, University of Washington

Tellurium/ libRoadRunner

September 4, 2019: Data Aggregation

Yasset Perez-Riverol

Proteomics Team Coordinator, European Bioinformatics Institute
OmicsDI

Yosef Roth

PhD Fellow, Icahn School of Medicine at Mount Sinai

Datanator

August 7, 2019: Model Validation

Rick Gerkin

Associate Research Professor, Arizona State University

SciDash/SciUnit/NeuronUnit

Christian Lieven

Postdoctoral Fellow, Technical University of Denmark

memote

July 3, 2019: Modeling Languages

Carlos Lopez

Assistant Professor, Vanderbilt University

PySB

Morgan Madec 

Associate Professor, University of Strasbourg

SPICE for Biochemical and Biological Systems

June 5, 2019: Parameter Estimation

Victor Zavala 

Associate Professor, University of Wisconsin-Madison

Scalable Nonlinear Programming Framework for Parameter Estimation

Joel Paulson 

Assistant Professor, Ohio State University

Parameter Estimation and Model Reduction

Cell Modeling Seminar Archive

April 2, 2019: Jacky Snoep 

Professor, University of Stellenbosch

Data and model management using the FAIRDOMHub

March 5, 2019: Andrew Hessel 

CEO, Humane Genomics

GP-write and the future of engineering living organisms: a personal perspective

February 5, 2019: Barbara Bakker 

Professor, University Medical Center Groningen

Computational models and network-based drug design for metabolic disease

January 8, 2019: Stephen Larson 

Co-founder, OpenWorm Foundation and CEO, MetaCell

OpenWorm: Building a whole animal simulation

December 4, 2018: Bill Hlavacek

Scientist, Los Alamos National Laboratory

Leveraging qualitative observations of system behavior in model development

November 6, 2018: Sheriff Rahuman

Project Leader, European Bioinformatics Institute

Leveraging public data repositories for cell modeling