Guidelines for visualizing and annotating rule-based models

Lily A. Chylek, Bin Hu, Michael L. Blinov, Thierry Emonet, James R. Faeder, Byron Goldstein, Ryan N. Gutenkunst, Jason M. Haugh, Tomasz Lipniacki, Richard G Posner, Jin Yang, William S. Hlavacek

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for illustrating and annotating rule-based models. An extended contact map represents the scope of a model by providing an illustration of each molecule, molecular component, direct physical interaction, post-translational modification, and enzyme-substrate relationship considered in a model. A map can also illustrate allosteric effects, structural relationships among molecular components, and compartmental locations of molecules. A model guide associates elements of a contact map with annotation and elements of an underlying model, which may be fully or partially specified. A guide can also serve to document the biological knowledge upon which a model is based. We provide examples of a map and guide for a published rule-based model that characterizes early events in IgE receptor (FcεRI) signaling. We also provide examples of how to visualize a variety of processes that are common in cell signaling systems but not considered in the example model, such as ubiquitination. An extended contact map and an associated guide can document knowledge of a cell signaling system in a form that is visual as well as executable. As a tool for model annotation, a map and guide can communicate the content of a model clearly and with precision, even for large models.

Original languageEnglish (US)
Pages (from-to)2779-2795
Number of pages17
JournalMolecular BioSystems
Volume7
Issue number10
DOIs
StatePublished - Oct 1 2011
Externally publishedYes

Fingerprint

Guidelines
IgE Receptors
Ubiquitination
Post Translational Protein Processing
Enzymes

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology

Cite this

Chylek, L. A., Hu, B., Blinov, M. L., Emonet, T., Faeder, J. R., Goldstein, B., ... Hlavacek, W. S. (2011). Guidelines for visualizing and annotating rule-based models. Molecular BioSystems, 7(10), 2779-2795. https://doi.org/10.1039/c1mb05077j

Guidelines for visualizing and annotating rule-based models. / Chylek, Lily A.; Hu, Bin; Blinov, Michael L.; Emonet, Thierry; Faeder, James R.; Goldstein, Byron; Gutenkunst, Ryan N.; Haugh, Jason M.; Lipniacki, Tomasz; Posner, Richard G; Yang, Jin; Hlavacek, William S.

In: Molecular BioSystems, Vol. 7, No. 10, 01.10.2011, p. 2779-2795.

Research output: Contribution to journalArticle

Chylek, LA, Hu, B, Blinov, ML, Emonet, T, Faeder, JR, Goldstein, B, Gutenkunst, RN, Haugh, JM, Lipniacki, T, Posner, RG, Yang, J & Hlavacek, WS 2011, 'Guidelines for visualizing and annotating rule-based models', Molecular BioSystems, vol. 7, no. 10, pp. 2779-2795. https://doi.org/10.1039/c1mb05077j
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B et al. Guidelines for visualizing and annotating rule-based models. Molecular BioSystems. 2011 Oct 1;7(10):2779-2795. https://doi.org/10.1039/c1mb05077j
Chylek, Lily A. ; Hu, Bin ; Blinov, Michael L. ; Emonet, Thierry ; Faeder, James R. ; Goldstein, Byron ; Gutenkunst, Ryan N. ; Haugh, Jason M. ; Lipniacki, Tomasz ; Posner, Richard G ; Yang, Jin ; Hlavacek, William S. / Guidelines for visualizing and annotating rule-based models. In: Molecular BioSystems. 2011 ; Vol. 7, No. 10. pp. 2779-2795.
@article{c43d8067887a4dcfaccb6d0a794831b3,
title = "Guidelines for visualizing and annotating rule-based models",
abstract = "Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for illustrating and annotating rule-based models. An extended contact map represents the scope of a model by providing an illustration of each molecule, molecular component, direct physical interaction, post-translational modification, and enzyme-substrate relationship considered in a model. A map can also illustrate allosteric effects, structural relationships among molecular components, and compartmental locations of molecules. A model guide associates elements of a contact map with annotation and elements of an underlying model, which may be fully or partially specified. A guide can also serve to document the biological knowledge upon which a model is based. We provide examples of a map and guide for a published rule-based model that characterizes early events in IgE receptor (FcεRI) signaling. We also provide examples of how to visualize a variety of processes that are common in cell signaling systems but not considered in the example model, such as ubiquitination. An extended contact map and an associated guide can document knowledge of a cell signaling system in a form that is visual as well as executable. As a tool for model annotation, a map and guide can communicate the content of a model clearly and with precision, even for large models.",
author = "Chylek, {Lily A.} and Bin Hu and Blinov, {Michael L.} and Thierry Emonet and Faeder, {James R.} and Byron Goldstein and Gutenkunst, {Ryan N.} and Haugh, {Jason M.} and Tomasz Lipniacki and Posner, {Richard G} and Jin Yang and Hlavacek, {William S.}",
year = "2011",
month = "10",
day = "1",
doi = "10.1039/c1mb05077j",
language = "English (US)",
volume = "7",
pages = "2779--2795",
journal = "Molecular BioSystems",
issn = "1742-206X",
publisher = "Royal Society of Chemistry",
number = "10",

}

TY - JOUR

T1 - Guidelines for visualizing and annotating rule-based models

AU - Chylek, Lily A.

AU - Hu, Bin

AU - Blinov, Michael L.

AU - Emonet, Thierry

AU - Faeder, James R.

AU - Goldstein, Byron

AU - Gutenkunst, Ryan N.

AU - Haugh, Jason M.

AU - Lipniacki, Tomasz

AU - Posner, Richard G

AU - Yang, Jin

AU - Hlavacek, William S.

PY - 2011/10/1

Y1 - 2011/10/1

N2 - Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for illustrating and annotating rule-based models. An extended contact map represents the scope of a model by providing an illustration of each molecule, molecular component, direct physical interaction, post-translational modification, and enzyme-substrate relationship considered in a model. A map can also illustrate allosteric effects, structural relationships among molecular components, and compartmental locations of molecules. A model guide associates elements of a contact map with annotation and elements of an underlying model, which may be fully or partially specified. A guide can also serve to document the biological knowledge upon which a model is based. We provide examples of a map and guide for a published rule-based model that characterizes early events in IgE receptor (FcεRI) signaling. We also provide examples of how to visualize a variety of processes that are common in cell signaling systems but not considered in the example model, such as ubiquitination. An extended contact map and an associated guide can document knowledge of a cell signaling system in a form that is visual as well as executable. As a tool for model annotation, a map and guide can communicate the content of a model clearly and with precision, even for large models.

AB - Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for illustrating and annotating rule-based models. An extended contact map represents the scope of a model by providing an illustration of each molecule, molecular component, direct physical interaction, post-translational modification, and enzyme-substrate relationship considered in a model. A map can also illustrate allosteric effects, structural relationships among molecular components, and compartmental locations of molecules. A model guide associates elements of a contact map with annotation and elements of an underlying model, which may be fully or partially specified. A guide can also serve to document the biological knowledge upon which a model is based. We provide examples of a map and guide for a published rule-based model that characterizes early events in IgE receptor (FcεRI) signaling. We also provide examples of how to visualize a variety of processes that are common in cell signaling systems but not considered in the example model, such as ubiquitination. An extended contact map and an associated guide can document knowledge of a cell signaling system in a form that is visual as well as executable. As a tool for model annotation, a map and guide can communicate the content of a model clearly and with precision, even for large models.

UR - http://www.scopus.com/inward/record.url?scp=80052771333&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80052771333&partnerID=8YFLogxK

U2 - 10.1039/c1mb05077j

DO - 10.1039/c1mb05077j

M3 - Article

VL - 7

SP - 2779

EP - 2795

JO - Molecular BioSystems

JF - Molecular BioSystems

SN - 1742-206X

IS - 10

ER -