IMAG/MSM Working Group on Multiscale Modeling and Viral Pandemics Mini Seminars

Nov 18, 2021

Welcome - The meeting will start at 3PM EDT

NOTE: THE MEETING WILL BE RECORDED, STREAMED AND PUBLICLY AVAILABLE�FOR THOSE MEMBERS UNABLE TO ATTEND

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Agenda

1. Welcome
2. Links, people, other info
3. Social media links
4. Quick Announcements
5. Upcoming Mini-Seminars and Request for Future Speakers
6. Elebeoba E. May, University of Houston. Title: Model-based Investigation of the Proinflammatory Microenvironment and Response to Gram-negative Bacteria.
7. Christian Forst, Icahn School of Medicine at Mount Sinai. Title: The interplay between the human microbiome and respiratory viruses: A multi scale story of influenza and COVID-19.
8. Request for Further Business

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People

Co-Lead: Reinhard Laubenbacher, PhD

Department of Medicine

Laboratory for Systems Medicine

University of Florida

reinhard.laubenbacher@medicine.ufl.edu

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Co-Lead: James A. Glazier, PhD

Dept. of Intelligent Systems Engineering and Biocomplexity Institute

Indiana University, Bloomington

jaglazier@gmail.com

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Web Administration, Slack: James P. Sluka, PhD

Dept. of Intelligent Systems Engineering and Biocomplexity Institute

Indiana University, Bloomington

jsluka@indiana.edu

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Activities Coordination: Bruce G. Shapiro, PhD, PMP

Laboratory for Systems Medicine

University of Florida

bruce.shapiro@medicine.ufl.edu

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Slack Channel

https://Msm-working-group.slack.com

Twitter

https://twitter.com/MsmViral

Our IMAG/MSM Wiki page

https://www.imagwiki.nibib.nih.gov/working-groups/multiscale-modeling-and-viral-pandemics Feel free to suggest additional content!

Or, use the Tiny URL: https://tinyurl.com/hkr97vfe

IMAG’s LinkedIn

https://www.linkedin.com/groups/12095434?lipi=urn%3Ali%3Apage%3Ad_flagship3_search_srp_all%3B1FVndkN2SD6P0xj2PYfqdQ%3D%3D

YouTube “MSM Working Group on Multiscale Modeling” https://www.youtube.com/channel/UCuDFvhgFziRRDcpRnT3vlrw

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Please follow the�group on Twitter!

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https://twitter.com/MsmViral

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If you could re-tweet the weekly announcements �(there are usually two, one for each speaker) �that would help boost attendance and community awareness.

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Announcements

�Any short (~1 minute) items such as;

• announcements
• meetings
• funding
• publications
• requests for help
• ???

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Schedule for Upcoming Meetings and mini-Seminars

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Nov 25: Thanksgiving Break

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Dec 2:

1. Clare Bryant, veterinary scientist at the University of Cambridge.
2. Reinhard Laubenbacher, New focus, New subgroup

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Dec 9:

1. Slim Fourati, Emory University School of Medicine.
2. Bingyang Wei, Texas Christian University. Title: Requirements engineering, i.e. how to develop software specifications that result in a product that the users want.

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Dec 16:

1. Russ Taylor, JHU. Title: Robotics for the ICU
2. TBD

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Dec 23: Christmas Break

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Dec 30: New Years Break

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Request for future speakers (Dec 9, …)

Rules of the Meeting

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Please mute your microphone and hold questions until after the presentations

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Mini-Seminar� Model-based Investigation of the Proinflammatory Microenvironment and Response to Gram-negative Bacteria.

Elebeoba E. May�University of Houston

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Intracellular pathogens like Francisella tularensis (Ft), a gram-negative Class A biothreat agent can trigger the release of cytokines, chemokines, and effector molecules into the microenvironment surrounding the infected cell, contributing to the formation of a proinflammatory microenvironment (PME). Immune cells recruited into the PME can be primed and activated by cytokine exposure promoting a more robust interaction between infiltrating immune cells and infected cells or, in the case of phagocytic cells, priming the cell to more effectively eliminate subsequent Ft infection. Macrophages and NK cells are central to the innate immune response to Ft and primary producers of TNF-α and IFN-γ, respective. Focusing on these key PME cytokines, which are found to modulate the in vivo response to Ft, we developed in silico and in vitro models to investigate the role of PME in macrophage activation and outcome of infection.

Mini-Seminar�The interplay between the human microbiome and respiratory viruses: A multi scale story of influenza and COVID-19

Christian Forst�Icahn School of Medicine at Mount Sinai

�The ongoing SARS-CoV-2 pandemic poses a threat to public health and economy, thus urges the scientific community to join efforts in the search of cures. Meanwhile, both influenza and COVID-19 are respiratory diseases caused by airborne RNA viruses. Microbes in the respiratory system have been proven to contribute to the outcome of the diseases. However, scientific advances from studying influenza infection have potentials to benefit the search of cure for SARS-CoV-2 infections. Here we present a comprehensive, multi-scale network analysis of the systems response to the virus. We have developed methods that integrate single-cell and bulk transcriptomic data. These integrated data were further related to the microbiome and clinical outcomes. By this approach we were able to identify cell-population specific key-regulators and host-processes that are hijacked by the virus for its advantage and that contribute to the severity of these infectious diseases.

Requests for Input/Suggestions

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We would like the subgroup leads to prepare brief presentations for the Thursday meetings, please let us know when you would like to present

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Ideas/help for publicising our Thursday mini-seminars more effectively and for speakers to invite

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Suggestions for agenda items and approaches to organizing the Steering Committee Meetings more effectively

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There have also been a number of requests for more explicit statements of goals and tasks from the WG leadership, we would appreciate your suggestions

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Please contact Reinhard Laubenbacher, James Glazier, James Sluka or Bruce Shapiro with your ideas on all of these issues

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fini

Have you made new research contacts or collaborations based on the Viral Pandemics working group?

• New collaborations that come out of this working group is an important metric of our success.

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• If you have new collaborations could you let the WG leads know?
• co-writing a paper?
• preparing a grant proposal?
• preparing a teaching or modeling resource?
• simply extensive discussions?

Additional Business

We ask that everyone sign up for subgroups using the Google Form at

https://forms.gle/Vf6RtapTeXfXLBaq6

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People are welcome to post tools and software to IMAG/MSM website, but be careful to be clear that a posting does not include endorsement by NIH

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Please register on IMAG/MSM web site https://www.imagwiki.nibib.nih.gov/index.php/�(Details are on the next slide)

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Charge to subgroups�(review):

Deliverable: White paper on the subgroup focus areas.�Due date: February 26, 2021

Steps to be taken:

1. Subgroup lead(s) write one or two paragraphs on the topic of the subgroup and the main problems to be focused on. Due to working group leads: January 17
2. Email to all subgroup members with this description and call for an initial meeting (if not happened yet) on or before January 26. Bruce can help with address lists and scheduling.
3. At the initial meeting, discussion of the main topics of a white paper that surveys the subgroup topic and lists major problems and potential solutions.
4. Subsequently, subgroup leads develop a document based on the meeting with sections for main topics and find leads for each of the sections. Completed by January 29.
5. Leads for main topics draw on other subgroup members to complete an initial draft by �February 12.
6. Entire subgroup edits, refines, expands document, including references etc. Final document delivered to working group leads by February 26.

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Should be added to the subgroup’s Wiki page

To register for the MSM�(Multiscale Modeling Consortium):

1. https://www.imagwiki.nibib.nih.gov/index.php/
2. In the upper right select “LOG IN”
3. Select “Create new account”
4. Select the “To edit the wiki as a MSM member”
5. Fill out the name, email etc. fields
6. In the “WG Involvement*” box scroll down and select

“Multiscale Modeling and Viral Pandemics”

1. In the “MSM funded project title” enter the title for any grants or other funding sources you would like to acknowledge.
2. “MSM Resources” you can leave blank
3. “MSM grant no.” enter the grant number for the project entered in #7. If there is no number enter 000000
4. Enter project start and end dates, these can be approximate.
5. The remaining fields are all optional.

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If you have any problems please contact JSluka@iu.edu

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Current Subgroup Updates

• The Drug Development subgroup was left off the initial subgroup joining form (Robert Stratford and Jim Sluka).
• If anyone is interested in joining this subgroup please email Bruce bruce.shapiro@medicine.ufl.edu

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• We may merge the slack channels for “drug development” and “therapeutics-and-medicine”

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• Merged sub groups:
• [Integration Within and Across Scales and challenges]
• [Integration Between Within-host and Population Scales]
• Now “Integration” LEADS: J Barhak, R Bowness, Y Liu, R Thompson

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• Merged sub groups:
• [Dissemination, training and outreach to the public, research community and Liaisons]
• [Health Equity]
• Leads: T Helikar, B Madamanchi, J Rice

Subgroup Roll Call and Feedback

Subgroup leads quick check in (subgroup list on next slides):

• Has your group met yet?
• Do you have a future meeting schedule set (date of next meeting, if scheduled)?
• Anything to report?

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Subgroups 1 of 2�(28 total subgroups)

Leads Names

Physiological Models

[Innate and Adaptive Immune Response] J Shoemaker, R Datta, V Zarnitsyna, E Schwartz

[Host-pathogen Interactions] Y Liu, J Thakar, W Garira

[Tissue Damage and Recovery] Y Jiang, K Ye

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Virus Models

[Viral Transport and Modes of Entry and Barrier Functions] MG Forest

[Viral Replication and Release] J Faeder, P Rangamani, EY Kim

[Viral Evolution] F Adler, A Zilman

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Therapeutics and Medicine

[Drug Development] R Stratford

[Vaccine Development] K Ye, E Schwartz

[Modeling individual responses to disease and treatment] G An, E Schwartz, T Mapder

[Modelling Decontamination of Surfaces/Materials] K Kiradjiev

[Machine Learning for Health Monitoring] G Lin, Y Jiang

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Individual Organ Systems

[Lungs] Y Jiang

[Heart],[Vasculature] C Lynch

[Kidney and Liver] M Rafailovich, C Mazza, C Mahapatra, C Yedjou

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[Comorbidities] J Barhak, G Gonzalez-Parra

Subgroups 2 of 2

Data

[Experimental and Clinical Data for Model Construction and Validation] S Schnell

[AI-based Data Processing, Heterogeneous Data Fusion] O Gevaert, Y Kevrekidis

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[Infection in experimental models including Relationship between in vivo � and in vitro responses and Infection in vivo model organisms] tbd

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[Infection in zoonotic reservoir animals and Interspecies Transmission] G An, J Rice, T Mapder

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[Coinfection and/or other pathogens] H. Dobrovolny

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[Emerging and Reemerging Diseases] A Gumel

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Modeling Technology

[Aerosol Transport in Lung, Lymph and Blood] M Tawhai, C Darquenne

[Integration] ** J Barhak, R Bowness, Y Liu, R Thompson

[Knowledge Acquisition and Modeling] SMR Naqvi, J Thakar

[Crowd-sourcing Models] R Laubenbacher, P Macklin

[Model Standards, Credibility, and Annotation] J Barhak, R Sheriff

�Social Issues

[Dissemination, training and outreach to the public, � research community and Liaisons] T Helikar, B Madamanchi, J Rice

[Health Equity] *** B Madamanchi

[Dissemination and Communication to funding agencies] J Glazier, R Laubenbacher

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** Merged two groups – � [Integration Within and Across Scales and challenges]

[Integration Between Within-host and Population Scales]

*** Merged

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Please Sign Up For Subgroups!

Subgroup Sign up

We ask that everyone sign up for subgroups using the Google Form at:

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https://forms.gle/Vf6RtapTeXfXLBaq6

�The form allows you to join a group and volunteer to lead. If you think subgroups overlap, feel free to sign up for multiple groups. We will likely combine some of the groups based on the number of participants and the number of people common across related groups.

Discussion of Recruitment of Subgroup Leads, Subgroup Members and WG Members

Procedure for the establishment of new subgroups:

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New subgroup proposals should include a brief description of the focus, at least one person who has agreed to lead the subgroup, and a rationale why the proposed subgroup focus is not covered by already existing subgroups.

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