Paper Info
Title
SyQUAL: a platform for qualitative modelling and simulation of biological systems
Abstract
Qualitative modelling in systems biology is increasingly adopted as it allows predicting important properties of biological systems even when quantitative information of such systems are unknown. Even though different tools for qualitative modelling have been recently proposed, their lack of automatism and their unstructured simulation core limit their applicability to non-complex biological networks. This paper presents SyQUAL, a platform for qualitative modelling and simulation of biological systems. It consists of two main layers: a Web-based framework that allows users to (i) import models described in the standard Systems Biology Markup Language (SBML), (ii) easily define properties to observe, and (iii) run simulations by hiding the underlying layer, that is, a SystemC-based core simulator that allows simulating the systems through a discrete event-based model of computation at different levels of details. The paper shows how SyQUAL has been applied to identify the attractors and to analyse the system robustness/sensitivity under perturbations of the Colitis-associated Colon Cancer (CAC) network.
Year
DOI
Venue
2016
10.1109/HLDVT.2016.7748270
2016 IEEE International High Level Design Validation and Test Workshop (HLDVT)
Keywords
Field
DocType
SyQUAL platform,qualitative modelling,biological system simulation,systems biology,quantitative information,noncomplex biological networks,Web-based framework,systems biology markup language,SBML,SystemC-based core simulator,discrete event-based model,CAC network,colitis-associated colon cancer network
Computer science,Biological network,Systems biology,SystemC,Theoretical computer science,Robustness (computer science),Model of computation,Modelling biological systems,SBML,Markup language
Conference
ISSN
ISBN
Citations 
1552-6674
978-1-5090-4271-5
0
PageRank 
References 
Authors
0.34
15
6
Name
Order
Citations
PageRank
Rosario Distefano1112.13
Nickolas Goncharenko200.34
Franco Fummi31001111.62
Rosalba Giugno481749.45
Gary D. Badery500.34
Nicola Bombieri631838.74