SyQUAL: a platform for qualitative modelling and simulation of biological systems

2016 IEEE International High Level Design Validation and Test Workshop (HLDVT) Pub Date : 2016-10-01 DOI:10.1109/HLDVT.2016.7748270

Rosario Distefano, N. Goncharenko, F. Fummi, R. Giugno, Gary D Bader, N. Bombieri

{"title":"SyQUAL: a platform for qualitative modelling and simulation of biological systems","authors":"Rosario Distefano, N. Goncharenko, F. Fummi, R. Giugno, Gary D Bader, N. Bombieri","doi":"10.1109/HLDVT.2016.7748270","DOIUrl":null,"url":null,"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.","PeriodicalId":166427,"journal":{"name":"2016 IEEE International High Level Design Validation and Test Workshop (HLDVT)","volume":"29 2 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"2","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"2016 IEEE International High Level Design Validation and Test Workshop (HLDVT)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/HLDVT.2016.7748270","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}

引用次数: 2

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.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

SyQUAL:一个生物系统定性建模和模拟的平台

系统生物学中越来越多地采用定性建模，因为它可以预测生物系统的重要特性，即使这些系统的定量信息是未知的。尽管最近提出了不同的定性建模工具，但它们缺乏自动性和非结构化的模拟核心限制了它们对非复杂生物网络的适用性。本文介绍了SyQUAL，一个生物系统的定性建模和仿真平台。它由两个主要层组成:一个基于web的框架，允许用户(i)导入用标准系统生物学标记语言(SBML)描述的模型，(ii)轻松定义要观察的属性，以及(iii)通过隐藏底层来运行模拟，即基于systemc的核心模拟器，允许在不同细节级别上通过离散的基于事件的计算模型来模拟系统。本文展示了SyQUAL如何应用于识别吸引子并分析结肠炎相关结肠癌(CAC)网络扰动下的系统鲁棒性/敏感性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

2016 IEEE International High Level Design Validation and Test Workshop (HLDVT)

自引率

0.00%

发文量