IMAG/MSM Working Group on Multi-scale Modeling for Viral Pandemics
Mini Seminar and Discussion of Subgroups
November 19th, 2020
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
Mini-Seminar by Alan Perelson, Los Alamos National Laboratory, SARS-CoV-2 modeling
Mini-Seminar by Fred Adler, University of Utah, Rhinovirus, Undergraduate Education, and Multiscale Modeling of Viral Pandemics
Upcoming Mini-Seminars and Request for Future Speakers
Presentation of Current List of Subgroups and Proposed sub-Group Leads
Discussion of Recruitment of Subgroup Leads and Members
Discussion of Charge to Subgroups
Request for Further Business
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
Web Administration: James P. Sluka, PhD
Dept. of Intelligent Systems Engineering and Biocomplexity Institute
Indiana University, Bloomington
Activities Coordination: Bruce G. Shapiro, PhD, PMP
Laboratory for Systems Medicine
University of Florida
bruce.shapiro@medicine.ufl.edu
Slack Channel
https://app.slack.com/client/T01D79YF21Y/C01CSHLAPQF
To be functional we may need some people to volunteer to get the conversation started!
Mini-Seminar
Modeling within host viral infections and immunity.
Alan Perelson
Los Alamos National Laboratory
asp@lanl.gov
Mini-Seminar
Rhinovirus, Undergraduate Education, and Multiscale Modeling of Viral Pandemics
Fred Adler
University of Utah
asp@lanl.gov
I will briefly discuss our use of rhinovirus (the other common cold) to bridge scales from biochemistry to evolution, and then the structure of a course I am leading that uses the COVID pandemic to motivate mathematical modeling stretching from physics to economics. I will use these to present my vision of a unified structure linking the full suite of approaches of our group.
Schedule for Upcoming mini-Seminars
Nov 26th--NO MEETING, Thanksgiving
Dec 3rd, Jacob Barhak, The Reference Model Accumulates Knowledge With Human Interpretation.
Dec 3rd, Gary An, University of Vermont, Biological Heterogeneity and Parameter Space: Using agent-based models to unify knowledge regarding zoonotic transfer, vaccine development and in silico trials of multi-modal therapeutic strategies
Dec 10th, Amber Smith, University of Tennessee
Dec 10th, Grace Peng, NIBIB
Dec 17th, Reed Shabman and Liliana Brown, NIAID - NIH
Dec 17th, Filippo Castiglione, National Research Council of Italy, SARS-CoV-2 infection: a cohort study performed in-silico
Dec 24th--NO MEETING, Christmas Eve
Dec 31st--NO MEETING, New Year’s Eve
Jan 7th, Paul Macklin, Indiana University
Jan 7th, TBD
Jan 14th, TBDx2
Request for Suggestions for future speakers
Current Subgroup Topics and Provisional Lead Volunteers
Review Preliminary Assignments
Seeking volunteers/suggestions for additional leads
Subgroups 1 of 2�(30 total)
(Co)Leads Names (new)
Physiological Models
[Innate and Adaptive Immune Response] J Shoemaker, R Datta, V Zarnitsyna, E Schwartz
[Host-pathogen Interactions] Y Liu, J Shoemaker, R Thompson, J Thakar
[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, P Rangamani
[Viral Evolution] F Adler, A Zilman
Therapeutics and Medicine
[Drug Development] (missing from form) K Ye
[Vaccine Development] K Ye, E Schwartz
Modeling individual responses to disease and treatment G An, E Schwartz, T Mapder
(includes [Diagnosis],[In Silico Clinical Trials],[Personalization of Models],[Interpatient Variability])
[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, J Klaunig, C Yedjou
Comorbidities (including diabetes, age, obesity, immune suppression) J Barhak
Note: Names in blue were individuals that selected (Co)Lead on the group Google Form that were not previously identified as possible leads.
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, J Barhak, Y Kevrekidis, R Datta
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 (virus-virus, bacterial, eukaryotic) tbd
[Emerging and Reemerging Diseases] A Gumel
Modeling Technology
[Aerosol Transport in Lung, Lymph and Blood] M Tawhai, C Darquenne
[Integration Within and Across Scales and challenges] J Barhak, R Datta,Y Liu, C Liao,
[Integration Between Within-host and Population Scales] P Rangamani, R Thompson
[Knowledge Acquisition and Modeling] SMR Naqvi, J Thakar
[Crowdsourcing Software Development] R Laubenbacher, P Macklin
[Requirements for Model Credibility, Reproducibility], � includes standards for biological and computational models J Barhak, P Rangamani
Social Issues
Dissemination, training and outreach to the public, � research community and Liaisons J Rice
[To funding agencies] J Glazier, R Laubenbacher
[Health Equity] B Madamanchi
Please Sign Up For Subgroups
Subgroup Sign up
We ask that everyone sign up for subgroups using the Google Form at:
https://forms.gle/DQ38A4H8Aa2VcG3r5
�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:
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.
Objectives for subgroups (first 9 months)
Based on the proposal submitted to the MSM Steering Committee, the objectives for the working group as a whole and each of the subgroups are as follows:
(1 month) Each subgroup will develop a plan to achieve these objectives.
1. (3 months) Identify people working in this area to include a paragraph on their work.
- Recruit members (assemble the masses)
- Assemble into a directory of researchers. (bibliography for subgroup)
- Identify other subgroups that you should coordinate with
Objectives for subgroups (cont)
2. (6 months) Prepare a white paper, approx. 5pp in length, excluding references that does the following:
- describe the focus of the subgroup, the major problems within it, and the role modeling can play in it
- describe what models and data are available, and the extent of our biological knowledge, available experimental systems, etc.
- describe what is needed that does not exist yet: models, data, experimental approaches, etc.
- outline any action items that could get us there.
These white papers can form the basis of a collective publication on the topic of multi scale modeling and viral pandemics.
3. (9 months) Catalyze research projects through presentations, exchange of ideas, search for strategic opportunities.
Review of Web Site and Contents
https://www.imagwiki.nibib.nih.gov/working-groups/multiscale-modeling-and-viral-pandemics
We can add linked pages for each subgroup.
Action Items
Weekly discussion topics for Slack
Next Meeting (12/3/20)--Request for Agenda Items
Speakers for mini-Seminars needed in January. Please email Bruce bruce.shapiro@medicine.ufl.edu
1 page text personal introduction on research interests from members, with links to main research pages to post on Web Page and Slack
Please contact jsluka@indiana.edu if you have any issues with this document
Additional Business
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)
We ask that everyone sign up for subgroups using the Google Form at https://forms.gle/DQ38A4H8Aa2VcG3r5
To register for the MSM�(Multiscale Modeling Consortium):
“Multiscale Modeling and Viral Pandemics”
If you have any problems please contact JSluka@iu.edu
Subgroups 1 of 3�(55 total subgroups)
(Co)Lead Total (Co)Leads Names (new)
Physiological Models
[Innate Immune Response (non-cellular and cellular)] 1 24 J Shoemaker, R Datta
[Adaptive Immune Response] 2 21 V Zarnitsyna, R Datta, E Schwartz
[Host-pathogen Interactions] 1 27 Y Liu, J Shoemaker, R Thompson, J Thakar
[Tissue Damage and Recovery] 1 11 Y Jiang, K Ye
Virus Models
[Viral Transport] 0 9 tbd
[Viral Modes of Entry and Barrier Functions] 0 10 MG Forest
[Viral Replication] 2 11 J Faeder, P Rangamani, EY Kim, P Rangamani
[Viral Release] 0 6 tbd
[Viral Evolution] 1 10 F Adler, A Zilman
Therapeutics and Medicine
[Drug Development] (missing from form) ? ? K Ye
[Vaccine Development] 2 10 K Ye, E Schwartz
Modeling individual responses to disease and treatment
[Diagnosis] 0 4 tbd
[Prognosis] 0 5 tbd
[Modeling of Therapeutic Options] 1 28 G An, E Schwartz
[In Silico Clinical Trials] 0 15 G An, Y Jiang
[Personalization of Models] 0 21 tbd
[Interpatient Variability] 0 8 G An, T Mapder
[Modelling Decontamination of Surfaces/Materials] 1 4 K Kiradjiev
[Machine Learning for Health Monitoring] 1 15 G Lin, Y Jiang
new (Co)Leaders
total signed up
previously identified leads in black, new lead signups in blue
need a subgroup lead
Subgroups 2 of 3
Individual Organ Systems
[Lungs] 0 12 Y Jiang
[Heart] 0 1 tbd
[Vasculature] 0 8 C Lynch
[Nervous system] 0 3 tbd
[Kidney and Liver] 1 10 M Rafailovich, C Mazza, C Mahapatra, J Klaunig, C Yedjou
Comorbidities
[Diabetes] 1 10 J Barhak
[Age] 0 14 tbd
[Obesity] 0 11 tbd
[Immune suppression] 0 11 tbd
Data
[Experimental Data for Model Construction and Validation] 1 35 S Schnell
[Clinical Data] 1 19 S Schnell
[AI-based Data Processing, Heterogeneous Data Fusion] 4 19 O Gevaert, J Barhak, Y Kevrekidis, R Datta
Non-human Systems Infection in experimental models
[Relationship between in vivo and in vitro responses] 0 11 tbd
[Infection in vivo model organisms] 0 8 bd
[Infection in zoonotic reservoir animals] 1 7 G An, J Rice
[Interspecies Transmission] 1 8 T Mapder
Subgroups 3 of 3
Coinfection and/or other pathogens
[Virus - Virus] 0 14 tbd
[Bacteria] 0 11 tbd
[Eukaryotic infections] 0 6 tbd
[Emerging and Reemerging Diseases] 0 15 A Gumel
Modeling Technology
[Aerosol Transport in Lung, Lymph and Blood] 1 8 M Tawhai, C Darquenne
[Integration Within Scales] 2 22 J Barhak, R Datta
[Integration Across Scales] 1 27 Y Liu, C Liao, R Datta
[Model Integration Challenges] 0 21 tbd
[Integration Between Within-host and Population Scales] 1 24 P Rangamani, R Thompson
[Knowledge Acquisition and Modeling] 1 20 SMR Naqvi, J Thakar
[Crowdsourcing Software Development] 0 13 R Laubenbacher, P Macklin
Model Credibility, Reproducibility
[Requirements for Model Credibility, Reproducibility] 1 31 J Barhak, P Rangamani
[Standards for Biological Model Description] 0 21 tbd
[Standards for Computational and Mathematical Model Description] 0 29 tbd
Social Issues: Dissemination, Training and Communication
[Optim Model Design Deliv Target Users, Incl Policy Mkrs Clinicians] 0 15 tbd
[Training and Outreach for Both Scientific and General Communities] 3 20 J Rice, B Madamanchi, T Helikar
[Health Equity] 1 9 B Madamanchi
Dissemination, Training and Communication
[To the public] 2 22 J Rice
[To the research community] 0 23 tbd
[Liaison with other groups (MIDAS, ...)] 2 13 J Rice
[To funding agencies] 1 23 J Glazier, R. Laubenbacher
Subgroups Similarities
Most similar subgroups based on membership�(blue: subgroups in same main group, red subgroups in different main groups)
Modeling Technology : [Integration Across Scales]
Modeling Technology : [Integration Within Scales] Correlation 0.850 Signif. Prob <.0001
Physiological Models: [Innate Immune Response (non-cellular and cellular)]
Physiological Models: [Adaptive Immune Response] Correlation 0.793 Signif. Prob <.0001
Coinfection and/or other pathogens : [Virus - Virus]
Non-human Systems : [Relationship between in vivo and in vitro responses] Correlation 0.663 Signif. Prob <.0001
Comorbidities : [Obesity]
Comorbidities : [Age] Correlation 0.663 Signif. Prob <.0001
Non-human Systems : [Relationship between in vivo and in vitro responses]
Physiological Models : [Adaptive Immune Response] Correlation 0.655 Signif. Prob <.0001
Modeling Technology : [Crowdsourcing Software Development]
Modeling Technology : [Standards for Biological Model Description] Correlation 0.643 Signif. Prob <.0001
Modeling Technology : [Crowdsourcing Software Development]
Modeling Technology : [Model Integration Challenges] Correlation 0.643 Signif. Prob <.0001
Dissemination and Communication : [To the research community]
Dissemination and Communication : [To the public] Correlation 0.630 Signif. Prob <.0001
Modeling Technology : [Model Integration Challenges]
Modeling Technology : [Integration Across Scales] Correlation 0.623 Signif. Prob <.0001
Modeling Technology : [Model Integration Challenges]
Modeling Technology : [Integration Within Scales] Correlation 0.621 Signif. Prob <.0001
Comorbidities : [Obesity]
Comorbidities : [Diabetes] Correlation 0.605 Signif. Prob <.0001
Coinfection and/or other pathogens : [Virus - Virus]
Non-human Systems : [Infection in vivo model organisms] Correlation 0.602 Signif. Prob <.0001
Virus Models : [Viral Release]
Virus Models : [Viral Modes of Entry and Barrier Functions] Correlation 0.601 Signif. Prob <.0001
Other suggested subgroups and comments
Hierarchical Clustering, based on subgroup selections, to 20 groups
Subgroups Memeberships
There are 55 subgroups
OUTDATE Physiological Models: [Innate Immune Response �(non-cellular and cellular)]
OUTDATE Physiological Models: [Adaptive Immune Response]
OUTDATE Physiological Models: [Host-pathogen Interactions]
OUTDATE Subgroups
Repeat for remaining 52 subgroups