NDLI: Marked regulatory graphs: a formal framework to simulate biological regulatory networks with simple automata

Content Provider	IEEE Xplore Digital Library
Author	Bassano, V. Bernot, G.
Copyright Year	2003
Description	Author affiliation: Univ. d'Evry, France (Bassano, V.; Bernot, G.)
Abstract	In the field of biological regulation, models obtained from experimental biology are usually complex networks of induction and repression between genes. Due to the development of high throughput genomic, it is now necessary to treat large scale networks. The challenge is to automatically analyze their behavior. We propose a formal framework to define these biological regulatory networks. Our model is derived from R. Thomas representation, where a biological regulatory network can be seen as a discrete model. We propose a formal definition of such a representation. We separate the static part (description of the systems) from the dynamic part (we develop two semantics, synchronous or asynchronous, to illustrate our method). A software environment to support this framework is also described. This software, developed to be used by biologists, can be used to rapidly obtain a prototype describing the behavior of the system, for product simulations and to automize proofs of properties.
Sponsorship	IEEE Comput. Soc. Tech. Committee on Design Autom. IEEE Comput. Soc. Tech. Committee on Simulation
Starting Page	93
Ending Page	99
File Size	361756
Page Count	7
File Format	PDF
ISBN	0769519431
ISSN	10746005
DOI	10.1109/IWRSP.2003.1207035
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2003-06-09
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Biological system modeling Automata Computational biology Complex networks Throughput Genomics Bioinformatics Large-scale systems Software prototyping Virtual prototyping
Content Type	Text
Resource Type	Article
Subject	Computer Science

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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