ENISI multiscale modeling of mucosal immune responses driven by high performance computing

Vida Abedi; Raquel Hontecillas; Stefan Hoops; Nathan Liles; Adria Carbo; Pinyi Lu; Casandra Philipson; Josep Abassaganya-Riera

doi:10.1109/BIBM.2015.7359768

ENISI multiscale modeling of mucosal immune responses driven by high performance computing

Vida Abedi, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Adria Carbo, Pinyi Lu, Casandra Philipson, Josep Abassaganya-Riera

Department of Public Health Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

7 Scopus citations

Abstract

Computational modeling tools have increasingly important roles in our understanding of biological processes. Computer simulations guide experimental and clinical efforts in an unprecedented rate. This study presents ENteric Immunity Simulator - multiscale modeling (MSM) platform developed for high performance computing (HPC). ENISI MSMv2 is designed for modeling mucosal immune responses. The system scales to 109 agents in HPC simulations. This is an important step towards building large scale information processing representations of immune responses that integrate multiple modeling technologies and spatiotemporal scales ranging from nanoseconds to years and from molecules to systems. Our HPC-driven ENISI MSM platform combines the study of molecular pathways controlling T cell differentiation and tissue level interactions between cells to characterize novel mechanisms of immunoregulation at the gut mucosa.

Original language	English (US)
Title of host publication	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editors	lng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	680-684
Number of pages	5
ISBN (Electronic)	9781467367981
DOIs	https://doi.org/10.1109/BIBM.2015.7359768
State	Published - Dec 16 2015
Event	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States Duration: Nov 9 2015 → Nov 12 2015

Publication series

Name	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Conference

Conference	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Country/Territory	United States
City	Washington
Period	11/9/15 → 11/12/15

All Science Journal Classification (ASJC) codes

Software
Artificial Intelligence
Health Informatics
Biomedical Engineering

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10.1109/BIBM.2015.7359768

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Abedi, V., Hontecillas, R., Hoops, S., Liles, N., Carbo, A., Lu, P., Philipson, C., & Abassaganya-Riera, J. (2015). ENISI multiscale modeling of mucosal immune responses driven by high performance computing. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, & J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 680-684). Article 7359768 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359768

Abedi, Vida ; Hontecillas, Raquel ; Hoops, Stefan et al. / ENISI multiscale modeling of mucosal immune responses driven by high performance computing. Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. editor / lng. Matthieu Schapranow ; Jiayu Zhou ; Xiaohua Tony Hu ; Bin Ma ; Sanguthevar Rajasekaran ; Satoru Miyano ; Illhoi Yoo ; Brian Pierce ; Amarda Shehu ; Vijay K. Gombar ; Brian Chen ; Vinay Pai ; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 680-684 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

@inproceedings{38fb974a2bc94e33a12903bc44e2e4b0,

title = "ENISI multiscale modeling of mucosal immune responses driven by high performance computing",

abstract = "Computational modeling tools have increasingly important roles in our understanding of biological processes. Computer simulations guide experimental and clinical efforts in an unprecedented rate. This study presents ENteric Immunity Simulator - multiscale modeling (MSM) platform developed for high performance computing (HPC). ENISI MSMv2 is designed for modeling mucosal immune responses. The system scales to 109 agents in HPC simulations. This is an important step towards building large scale information processing representations of immune responses that integrate multiple modeling technologies and spatiotemporal scales ranging from nanoseconds to years and from molecules to systems. Our HPC-driven ENISI MSM platform combines the study of molecular pathways controlling T cell differentiation and tissue level interactions between cells to characterize novel mechanisms of immunoregulation at the gut mucosa.",

author = "Vida Abedi and Raquel Hontecillas and Stefan Hoops and Nathan Liles and Adria Carbo and Pinyi Lu and Casandra Philipson and Josep Abassaganya-Riera",

note = "Funding Information: This work was supported in part by NIAID Contract No. HHSN272201000056C to JBR, and funds from the Nutritional Immunology and Molecular Medicine Laboratory (URL: www.nimml.org). Publisher Copyright: {\textcopyright} 2015 IEEE.; IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 ; Conference date: 09-11-2015 Through 12-11-2015",

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doi = "10.1109/BIBM.2015.7359768",

language = "English (US)",

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publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "680--684",

editor = "Schapranow, {lng. Matthieu} and Jiayu Zhou and Hu, {Xiaohua Tony} and Bin Ma and Sanguthevar Rajasekaran and Satoru Miyano and Illhoi Yoo and Brian Pierce and Amarda Shehu and Gombar, {Vijay K.} and Brian Chen and Vinay Pai and Jun Huan",

booktitle = "Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015",

address = "United States",

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Abedi, V, Hontecillas, R, Hoops, S, Liles, N, Carbo, A, Lu, P, Philipson, C & Abassaganya-Riera, J 2015, ENISI multiscale modeling of mucosal immune responses driven by high performance computing. in LM Schapranow, J Zhou, XT Hu, B Ma, S Rajasekaran, S Miyano, I Yoo, B Pierce, A Shehu, VK Gombar, B Chen, V Pai & J Huan (eds), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359768, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Institute of Electrical and Electronics Engineers Inc., pp. 680-684, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 11/9/15. https://doi.org/10.1109/BIBM.2015.7359768

ENISI multiscale modeling of mucosal immune responses driven by high performance computing. / Abedi, Vida; Hontecillas, Raquel; Hoops, Stefan et al.
Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. ed. / lng. Matthieu Schapranow; Jiayu Zhou; Xiaohua Tony Hu; Bin Ma; Sanguthevar Rajasekaran; Satoru Miyano; Illhoi Yoo; Brian Pierce; Amarda Shehu; Vijay K. Gombar; Brian Chen; Vinay Pai; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. p. 680-684 7359768 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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AU - Abedi, Vida

AU - Hontecillas, Raquel

AU - Hoops, Stefan

AU - Liles, Nathan

AU - Carbo, Adria

AU - Lu, Pinyi

AU - Philipson, Casandra

AU - Abassaganya-Riera, Josep

N1 - Funding Information: This work was supported in part by NIAID Contract No. HHSN272201000056C to JBR, and funds from the Nutritional Immunology and Molecular Medicine Laboratory (URL: www.nimml.org). Publisher Copyright: © 2015 IEEE.

PY - 2015/12/16

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N2 - Computational modeling tools have increasingly important roles in our understanding of biological processes. Computer simulations guide experimental and clinical efforts in an unprecedented rate. This study presents ENteric Immunity Simulator - multiscale modeling (MSM) platform developed for high performance computing (HPC). ENISI MSMv2 is designed for modeling mucosal immune responses. The system scales to 109 agents in HPC simulations. This is an important step towards building large scale information processing representations of immune responses that integrate multiple modeling technologies and spatiotemporal scales ranging from nanoseconds to years and from molecules to systems. Our HPC-driven ENISI MSM platform combines the study of molecular pathways controlling T cell differentiation and tissue level interactions between cells to characterize novel mechanisms of immunoregulation at the gut mucosa.

AB - Computational modeling tools have increasingly important roles in our understanding of biological processes. Computer simulations guide experimental and clinical efforts in an unprecedented rate. This study presents ENteric Immunity Simulator - multiscale modeling (MSM) platform developed for high performance computing (HPC). ENISI MSMv2 is designed for modeling mucosal immune responses. The system scales to 109 agents in HPC simulations. This is an important step towards building large scale information processing representations of immune responses that integrate multiple modeling technologies and spatiotemporal scales ranging from nanoseconds to years and from molecules to systems. Our HPC-driven ENISI MSM platform combines the study of molecular pathways controlling T cell differentiation and tissue level interactions between cells to characterize novel mechanisms of immunoregulation at the gut mucosa.

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M3 - Conference contribution

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T3 - Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

SP - 680

EP - 684

BT - Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

A2 - Schapranow, lng. Matthieu

A2 - Zhou, Jiayu

A2 - Hu, Xiaohua Tony

A2 - Ma, Bin

A2 - Rajasekaran, Sanguthevar

A2 - Miyano, Satoru

A2 - Yoo, Illhoi

A2 - Pierce, Brian

A2 - Shehu, Amarda

A2 - Gombar, Vijay K.

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A2 - Pai, Vinay

A2 - Huan, Jun

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Y2 - 9 November 2015 through 12 November 2015

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Abedi V, Hontecillas R, Hoops S, Liles N, Carbo A, Lu P et al. ENISI multiscale modeling of mucosal immune responses driven by high performance computing. In Schapranow LM, Zhou J, Hu XT, Ma B, Rajasekaran S, Miyano S, Yoo I, Pierce B, Shehu A, Gombar VK, Chen B, Pai V, Huan J, editors, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 680-684. 7359768. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). doi: 10.1109/BIBM.2015.7359768

ENISI multiscale modeling of mucosal immune responses driven by high performance computing

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