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Author Gostner, Roswitha ♦ Baldacci, Bianca ♦ Morine, Melissa J ♦ Priami, Corrado
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2014
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Graphical modeling of biological systems ♦ Systems biology
Abstract Modeling biological systems to understand their mechanistic behavior is an important activity in molecular systems biology. Mathematical modeling typically requires deep mathematical or computing knowledge, and this limits the spread of modeling tools among biologists. Graphical modeling languages have been introduced to minimize this limit. Here, we survey the main graphical formalisms (supported by software tools) available to model biological systems with a primary focus on their usability, within the framework of modeling reaction pathways with two-dimensional (2D) (possibly nested) compartments. Considering the main characteristics of the surveyed formalisms, we synthesise a new proposal (Style) and report the results of an online survey conducted among biologists to assess usability of available graphical formalisms. We consider this proposal a guideline developed from what we learned in the survey, which can inform development of graphical formalisms to model reaction pathways in 2D space.
ISSN 03600300
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2014-07-01
Publisher Place New York
e-ISSN 15577341
Journal ACM Computing Surveys (CSUR)
Volume Number 47
Issue Number 2
Page Count 21
Starting Page 1
Ending Page 21


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Source: ACM Digital Library