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.

Biomodeling Workshop

Motivation

Multi-scale models require the representation and integration of a diverse list of biological processes (e.g. RNA expression, protein signalling, metabolism, cell growth, etc.) and modeling each process contains its own unique challenges. Each month we will focus on a particular process and discuss its A) experimental, computational, and mathematical challenges to modeling B) current state of the art, and C) future directions.  We are looking for students, postdoctoral researchers, and faculty who value collaborative problem solving and are interested in learning about the most recent developments modeling

Email seminar@reproduciblebiomodels.org to join our mailing list or to suggest new software or modeling results you would like to demo or present during upcoming seminar or workshop series. 

Details

Day/Time
Second Tuesday of each month
12:00 pm EDT (4 pm UTC)

Location
Online using Zoom

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

Organizers

Samuel Miravet Verde
Center for Genomic Regulation, ES

Veronica Porubsky
University of Washington, US

Yosef Roth
Icahn School of Medicine at Mount Sinai, US

Jonathan Karr
Icahn School of Medicine at Mount Sinai, 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.

Upcoming Seminars

December 10: Modeling Metabolism

January 14 : Modeling Protein Signalling

February 18: Gene Expression

March 10: Tissue Modeling

April 14 : Population/Microbiome Modeling

May 12 : Whole-Cell Modeling

June 9: Neural Models

July 14: Cancer Modeling

Modeling Software Workshop Archive

October 2, 2019: Model Simulation

Paul Macklin

Associate Professor, Indiana University Bloomington

PhysiCell

Veronica Porubsky

PhD 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