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Plenary Session 2.1 – Current IMAG Initiatives (IMAG Roundtable)

Organizers: Emrin Horgusluoglu, Bruce Lee

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Instructions to panelists

In advance of the meeting:

Please submit 1 slide per initiative using the template (Slide 3 in this deck) by June 21, 5pm ET.
Provide any other relevant accompanying materials that can be placed on the IMAG MSM wiki.

On day of the meeting (June 28):

Be prepared to make a brief (<2 minutes) introduction of yourself and your initiative (the slide that you submitted will be shown while you are introducing yourself).
Following the introductions, there will be a moderated Q&A that will comprise the majority of the session.

Be ready to discuss how multi-scale modeling is relevant to your initiative.
Be prepared to answer questions about your initiative from the audience.
Be prepared to discuss how peer review challenges are addressed through your initiative processes. This session shouldn't focus too much on why specific proposals were scored in particular ways or issues that would be more applicable to a Center for Scientific Review (CSR) discussion.

Examples of Topics for Discussion:

How is your initiative currently relevant to MSM?
What types of MSM activities are already occurring?
What are potential MSM activities for the future?
How do others get involved in your initiatives?
How are proposals for your initiative being reviewed?

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Name of Initiative [TEMPLATE SLIDE]

1. Funding agencies

2. Goals of the initiative

3. Current MSM activities

4. Relevant Links

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AI driven initiatives

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Wendy Nilsen, NSF

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NIH Bridge2AI Grace Peng, NIH

3 Pillars:

People - Diversity
Ethics - Culture of Inquiry
Data - datasheet & model cards

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Mauricio Rangel-Gomez

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Contact: Ilana Goldberg ilana.goldberg@nih.gov

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Emily Greenspan, NCI

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Emily Greenspan, NCI

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The National Institutes of Health’s (NIH) Nutrition for Precision’s Health’s (NPH) AIMINGS Center has a new funding opportunity

RFA seeks research projects that develop and utilize AI and other computer-aided approaches to facilitate precision nutrition
Great opportunity for investigators to receive funding for a project that can eventually enhance into a larger project or an R01 application
Awardees will be connected with a community of researchers working on AI for precision nutrition
Deadline is October 12, 2023
For more information and to apply: PHICOR.ORG/RFA

Bruce Y. Lee

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Mechanism driven initiatives

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Grace Peng - MSM

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(PO Frederick Leve) AFOSR Synthetic Biology Multi-Disciplinary University Research Initiatives (MURIs)

1. Two relevant AFOSR MURIs with two different teams with PIs, Prof. Domitilla Del Vecchio and Ron Weiss (MIT)

2. Understand context dependence and mitigate it in design of composed synthetic biological circuits. This will provide a path to intelligent cells as computers themselves.

3. Both projects address the multi-scale modeling of synthetic biological circuits in cell and within multi-cellular configurations, by time and spatial scale separation and uncertainty quantification at different scales.

4. https://scripts.mit.edu/~ddv/research.php#box1

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Software driven initiatives

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The ASKEM Workbench (Joshua Elliott)

Support the scientist’s modeling process from discovery through to publishing

Distribution Statement A: Approved for public release. Distribution is unlimited.

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Live paper (transparent workflow for efficient knowledge sharing and reuse)

latest progress (prototypes)

in design/research stage

Discovering and gathering modeling resources (literature, parameter values, datasets, models)

Dedicated space for simulation parameterization to support calibration, optimization and rapid creation of scenarios and interventions

Simulation output comparison with support for explanation

Modeling by building on existing models

Model structure comparison, model extraction from code and papers, and iterative model augmentation

non-linear and iterative workflow

Distribution Statement A: Approved for public release. Distribution is unlimited.

Graphics Source: Uncharted Software Inc.

The Terarium workbench is envisioned to support the scientist’s modeling process from discovery through publishing. Within the workbench, scientists will be able to discover and gather all the resources required for modeling. This includes relevant literature, parameter values, data sets and models. Scientists will be able to reuse and edit existing models. To support this, the workbench will allow scientists to compare model structure, extract the model from code and papers and iteratively augment and edit the model. Scientists will be able to run simulations and compare iterations with machine assistance for explaining results. There will be a dedicated space for parameterization to support calibration, optimization, and rapid creation of scenarios and interventions. Finally, the workbench will support the scientist in making their workflow transparent to better enable efficient knowledge sharing and reuse within the scientific community. To date, Uncharted has developed prototypes for a search and discovery space and a workspace to reuse existing models.

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Emily Greenspan, NCI

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Evaluation of Medical AI Using In Silico Tools

Presenter: Elena Sizikova

Goal: generate tools to support medical AI development and evaluation using in silico, physics-based simulations

Current Activities:

Medical AI Evaluation

Data and tools for evaluating medical AI using in silico methods

Virtual Patients

Digital Mammography (DM)

Digital Breast Tomosynthesis (DBT)

Computational Tools for In Silico Trials

Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) modeling pipeline

Digital Phantoms

Highly detailed, anatomically correct multi-scale breast models

Mass Present?

1. Breast Model Generation and Compression

2. Mass Generation

3. Mass Insertion

4. X-Ray Projection

5. AI Analysis

OSEL Accelerating patient access to innovative, safe, and effective medical devices through best-in-the-world regulatory science

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NCI Informatics Tools for Cancer Research

itcr.cancer.gov

Program Lead: Juli Klemm, PhD ( juli.klemm@nih.gov )

Dave Miller

ITCR is a trans-NCI program supporting investigator-initiated, research-driven informatics technology development spanning all aspects of cancer research. All four NCI extramural divisions are participating in the program: Division of Cancer Biology (DCB), Division of Cancer Control and Population Science (DCCPS), Division of Cancer Prevention (DCP), Division of Cancer Treatment and Diagnosis (DCTD). The NCI Center for Biomedical Informatics and Information Technology (CBIIT) is coordinating program activities across the divisions.

The scope of the ITCR program is to serve informatics needs that span the cancer research continuum. Moreover, ITCR provides support for informatics resources across the development lifecycle, including the development of innovative methods and algorithms, early stage software development advanced stage software development, and sustainment of high-value resources on which the community has come to depend.

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Experiment driven initiatives

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NIAID: Systems Biology for Infectious Diseases

A community integrating experimental biology, computational tools and modeling across temporal and spatial scales to develop strategies that predict and alleviate disease severity across multiple human pathogens

https://www.niaid.nih.gov/research/systems-biology-consortium

Reed Shabman

reed.shabman@nih.gov

Ask me about the SysBio codeathon in Chicago, Sep 25th-28th!

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Mechanistic Modeling of Cancer Biology

cancer.gov/csbc

@NCIsysbio

physics.cancer.gov

@NCIPhySci

Eric Johnson-Chavarria, PhD

eric.johnsonchavarria@nih.gov

Physical Sciences - Oncology Network

Hannah Dueck, PhD

hannah.dueck@nih.gov

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Extra Slides for IMAG Initiatives

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RFI from NIH ACD WG on NAMs in Biomedical Research

https://grants.nih.gov/grants/guide/notice-files/NOT-OD-23-140.html

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Wendy Nilsen, NSF

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(PO Frederick Leve) AFOSR Traditional Grants

1. Two relevant AFOSR with PIs, Prof. Indika Rajapakse (University of Michigan) and Prof. Melvin Leok

2. First project: Control systems theory developed around hypergraphs and tensors and validated on wound healing and tissue generation data-driven dynamics. Second Project: Mathematical theory in computational mechanics to handle multi-scale, multi-physics systems symplectic discretizations that preserve multi-symplecticities over interconnections using Dirac Connections.

3. Current MSM activities

4. https://rajapakse.lab.medicine.umich.edu/research and https://mathweb.ucsd.edu/~mleok/#research

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The National Institutes of Health’s (NIH) Nutrition for Precision’s Health’s (NPH) AIMINGS Center has a new funding opportunity

RFA seeks research projects that develop and utilize AI and other computer-aided approaches to facilitate precision nutrition
Great opportunity for investigators to receive funding for a project that can eventually enhance into a larger project or an R01 application
Awardees will be connected with a community of researchers working on AI for precision nutrition
Deadline is October 12, 2023
For more information and to apply: PHICOR.ORG/RFA