Overview

The long-term goal of the Center for Reproducible Biomedical Modeling is to achieve comprehensive predictive models of biological systems, such as whole-cell models, that can guide precision medicine and synthetic biology. One promising way to build comprehensive models is to combine models of individual biological processes. This requires understandable, reproducible, reusable, and composable models of individual biological processes.

Unfortunately, few existing models are reproducible, reusable, or composable. For example, many reported models are not published, many reported simulation results are not reproducible, and few models are annotated.

Recently, researchers have developed several standard representations such as SBML and SED-ML to make models reusable and make simulation results reproducible. However, it is still difficult to understand, reproduce, and combine models because we lack tools for recording the data sources and assumptions used to build models, we lack tools for annotating the meanings of variables and equations, and we lack a universal simulator.

Toward our long-term goal of comprehensive models, the center is making models understandable, reproducible,  reusable,  and  composable  by  (1)  developing  these  missing  model  building, annotation, and simulation tools and (2) combining these and other existing tools into a user-friendly reproducible modeling workflow. Ultimately, we believe this workflow will help modelers create comprehensive models that can guide medicine and bioengineering.

We are striving to build broadly-applicable domain-independent tools. To ensure the center’s tools advance modeling, we will begin by testing on tools on systems biology modeling in conjunction with several motivating projects that span a wide range of modeling methods and applications.

To further advance the understandability, reproducibility, and reusability of biomedical modeling, the center is also (1) promoting the importance of reproducible modeling by organizing meetings and publishing perspectives; (2) training researchers to conduct modeling reproducibly by organizing workshops and publishing tutorials; and (3) helping researchers and journals build, annotate, simulate, analyze, and verify models.

We anticipate that this unique center will accelerate the development of comprehensive predictive models by enhancing the understandability, reusability, and reproducibility of biomedical modeling.

Team

Leadership

Herbert Sauro
Herbert SauroDirector
Professor, University of Washington
Ion Moraru
Ion MoraruDeputy Director
Professor, University of Connecticut School of Medicine

Model credibility

Herbert Sauro
Herbert SauroLead
Professor, University of Washington
Joe Hellerstein
Joe HellersteinInvestigator
Affiliate Professor, University of Washington
Chi-Chi May
Chi-Chi MayInvestigator
Associate Professor, University of Wisconsin
Lilly Tatka
Lilly TatkaConsultant
Ph.D. Student, University of Washington
Lucian Smith
Lucian SmithSoftware Engineer
University of Washington
Steve Ma
Steve MaConsultant
University of Washington
Anish Konanki
Anish KonankiSoftware Developer
University of Washington
Eva Liu
Eva LiuSoftware Developer
University of Washington
Longxuan Fan
Longxuan FanSoftware Developer
University of Washington

Model and simulation annotation

John Gennari
John GennariLead
Professor, University of Washington
David Nickerson
David NickersonCo-Lead
Senior Research Fellow, University of Auckland
Chi-Chi May
Chi-Chi MayInvestigator
Associate Professor, University of Wisconsin
Maxwell Neal
Maxwell NealConsultant
University of Washington
Anish Konanki
Anish KonankiSoftware Developer
University of Washington
Eva Liu
Eva LiuSoftware Developer
University of Washington
Longxuan Fan
Longxuan FanSoftware Developer
University of Washington

Online simulation and visualization

Ion Moraru
Ion MoraruLead
Professor, University of Connecticut School of Medicine
Eran Agmon
Eran AgmonCo-Lead
Assistant Professor, University of Connecticut Health Center
Michael Blinov
Michael BlinovInvestigator
Assistant Professor, University of Connecticut Health Center
Herbert Sauro
Herbert SauroConsultant
Professor, University of Washington
Lucian Smith
Lucian SmithConsultant
University of Washington
Alex Patrie
Alex PatrieSoftware Developer
University of Connecticut Health Center
Dan Vasilescu
Dan VasilescuSoftware Developer
University of Connecticut Health Center
Jim Shaff
Jim ShaffSoftware Developer
University of Connecticut Health Center

Technology integration, education & outreach

Herbert Sauro
Herbert SauroCo-Lead
Professor, University of Washington
Ion Moraru
Ion MoraruCo-lead
Professor, University of Connecticut School of Medicine
John Gennari
John GennariCo-Lead
Professor, University of Washington
Janis Shin
Janis ShinGraduate Student
University of Washington

Center Alumni

Anand Rampadarath
Anand RampadarathCurator
Assistant/ Model Curator, University of Auckland
Arthur Goldberg
Arthur Goldberg
Associate professor, Icahn School of Medicine at Mount Sinai
Balazs Szigeti
Balazs Szigeti
Postdoctoral scholar, Icahn School of Medicine at Mount Sinai
Bilal Shaikh
Bilal ShaikhSoftware Developer
Bioinformatician at Icahn School of Medicine at Mount Sinai
Ciaran Welsh
Ciaran Welsh
Software engineer, University of Washington
Dan Cook
Dan Cook
Research Professor, University of Washington
Gary Geng
Gary Geng
Graduate Student, University of Washington
Gnaneswara Marupilla
Gnaneswara Marupilla
Software developer, University of Connecticut School of Medicine
Jonathan Karr
Jonathan Karr
Formic Labs
Karin Lundengård
Karin LundengårdInvestigator
University of Auckland
Veronica Porubsky
Veronica PorubskyLead
Bioengineering Ph.D. Student, University of Washington
Woosub Shin
Woosub ShinInvestigator
University of Michigan
Yosef Roth
Yosef Roth
Research assistant, Icahn School of Medicine at Mount Sinai