# Center for Reproducible Systems for Biomedical Modeling

> **NIH NIH P41** · UNIVERSITY OF WASHINGTON · 2022 · $1,289,405

## Abstract

OVERALL: PROJECT SUMMARY
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 achieving comprehensive models, we will make 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 will strive to build broadly-applicable domain-independent tools. However, to help us to test our tools, we
will initially focus on tools for systems biology models of cells. To ensure the center's tools advance modeling,
the tools will be developed in conjunction with several motivating collaborative and service projects that span a
wide range of modeling methods and biological and application domains.
To further advance the understandability, reproducibility, and reusability of biomedical modeling, we will (1)
promote the importance of reproducible modeling by organizing meetings and publishing perspectives; (2) train
researchers to conduct modeling reproducibly by organizing workshops and publishing tutorials; and (3) help
researchers and journals build, annotate, simulate, analyze, and verify models.
The center would be one of the first large-scale efforts to make biomedical modeling reproducible, and the
center would be timely given the increasing concern about the irreproducibility of biomedical research. We
anticipate that this unique center will accelerate the development of comprehensive predictive models by
enhancing the understandability, reusability, and reproducibility of biomedical modeling.

## Key facts

- **NIH application ID:** 10192514
- **Project number:** 5P41EB023912-04
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** Ion I. Moraru
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $1,289,405
- **Award type:** 5
- **Project period:** 2018-06-13 → 2024-02-29

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10192514

## Citation

> US National Institutes of Health, RePORTER application 10192514, Center for Reproducible Systems for Biomedical Modeling (5P41EB023912-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10192514. Licensed CC0.

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