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

The seminar series will transition into an interactive workshop for Summer 2019. We have invited modeling software developers willing to share and demo new tools of interest to the modeling community. 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 processes and tools to join us for the workshop.

Email seminar@reproduciblebiomodels.org to suggest new software you would like to present or demo during the workshop.

Details

Day/Time
First Wednesday of each month
12:00 pm EDT (4 pm UTC)

Location
Online using Zoom

Format
20 minute workshop #1
20 minute workshop #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.

October 2: Numerical Simulation

Paul Macklin

Associate Professor, Indiana University Bloomington

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems

Veronica Porubsky

PhD Fellow, University of Washington

Tellurium and Antimony: Model building, Simulation, and Analysis

Archive

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

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