1 of 21

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

Dec 9, 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

Agenda

Welcome
Links, people, other info
Social media links
Quick Announcements
Upcoming Mini-Seminars and Request for Future Speakers
Slim Fourati, Emory University School of Medicine. Title: Ab initio molecular signatures predictive of susceptibility to viral infection
Bingyang Wei, Texas Christian University. Title: Just Enough Requirements Engineering for Non-Computer Science Majors
Request for Further Business

2 of 21

People

Co-Lead: Reinhard Laubenbacher, PhD

Department of Medicine

Laboratory for Systems Medicine

University of Florida

reinhard.laubenbacher@medicine.ufl.edu

Co-Lead: James A. Glazier, PhD

Dept. of Intelligent Systems Engineering and Biocomplexity Institute

Indiana University, Bloomington

jaglazier@gmail.com

Web Administration, Slack: James P. Sluka, PhD

Dept. of Intelligent Systems Engineering and Biocomplexity Institute

Indiana University, Bloomington

jsluka@indiana.edu

Activities Coordination: Bruce G. Shapiro, PhD, PMP

Laboratory for Systems Medicine

University of Florida

bruce.shapiro@medicine.ufl.edu

3 of 21

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

4 of 21

Please follow the�group on Twitter!

https://twitter.com/MsmViral

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

5 of 21

Announcements

�Any short (~1 minute) items such as;

announcements
meetings
funding
publications
requests for help
???

6 of 21

Schedule for Upcoming Meetings and mini-Seminars

Dec 16:

Russ Taylor, JHU. Title: Autonomy and Semi-Autonomous Behavior in Surgical Robot Systems.
Jane Parker, University of Reading, Department of Food and Nutrition Services. Title: Post covid olfactory dysfunction.

Dec 23: Christmas Break

Dec 30: New Years Break

Jan 6:

Jeremie Guedj, INSERM, France. Title: Quantifying the relationship between SARS-CoV-2 viral load and infectiousness.
TBD

Request for future speakers (Jan 6, …)

7 of 21

Rules of the Meeting

Please mute your microphone and hold questions until after the presentations

8 of 21

Mini-Seminar�Ab initio molecular signatures predictive of�susceptibility to viral infection

Slim Fourati�Emory University School of Medicine

The response to respiratory viruses varies substantially between individuals, and little is known on molecular predictors from the early stages of infection. Here we conduct a community-based analysis to determine whether pre- or early post-exposure molecular factors could predict physiologic responses to viral exposure. Using peripheral blood gene expression profiles collected from healthy subjects prior to exposure to one of four respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV), as well as up to 24 h following exposure, we find that it is possible to construct models predictive of symptomatic response using profiles even prior to viral exposure. Analysis of predictive gene features reveals little overlap among models; however, in aggregate, these genes are enriched for common pathways. Heme metabolism, the most significantly enriched pathway, is associated with a higher risk of developing symptoms following viral exposure. This study demonstrates that pre-exposure molecular predictors can be identified and improves our understanding of the mechanisms of response to respiratory viruses.

9 of 21

Mini-Seminar�Just Enough Requirements Engineering�for Non-Computer Science Majors

Bingyang Wei�Texas Christian University

�

10 of 21

Requests for Input/Suggestions

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

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

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

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

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

11 of 21

fini

12 of 21

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.

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?

13 of 21

Additional Business

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

https://forms.gle/Vf6RtapTeXfXLBaq6

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

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

14 of 21

Charge to subgroups�(review):

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

Steps to be taken:

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
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.
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.
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.
Leads for main topics draw on other subgroup members to complete an initial draft by �February 12.
Entire subgroup edits, refines, expands document, including references etc. Final document delivered to working group leads by February 26.

Should be added to the subgroup’s Wiki page

15 of 21

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

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

“Multiscale Modeling and Viral Pandemics”

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

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

16 of 21

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

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

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

Merged sub groups:

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

17 of 21

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?

18 of 21

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

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

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

Individual Organ Systems

[Lungs] Y Jiang

[Heart],[Vasculature] C Lynch

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

[Comorbidities] J Barhak, G Gonzalez-Parra

19 of 21

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

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

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

[Coinfection and/or other pathogens] H. Dobrovolny

[Emerging and Reemerging Diseases] A Gumel

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

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

[Integration Between Within-host and Population Scales]

*** Merged

20 of 21

Please Sign Up For Subgroups!

Subgroup Sign up

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

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.

21 of 21

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

Procedure for the establishment of new subgroups:

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.