ArticleSystems and synthetic biology2010
Evolving cell models for systems and synthetic biology.
Article in Systems and synthetic biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Evolving modular genetic regulatory networks with a recursive, top-down approach.Systems and synthetic biology · 2015Article
- Integrating ethical analysis "into the DNA" of synthetic biology.Medicine, health care, and philosophy · 2015Article
- Evolving robust gene regulatory networks.PloS one · 2015Article
- How to make a synthetic multicellular computer.PloS one · 2014Article
- Modeling formalisms in Systems Biology.AMB Express · 2011Article
- The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology.Bioinformatics (Oxford, England) · 2011Article
- Functional Information: Towards Synthesis of Biosemiotics and Cybernetics.Entropy (Basel, Switzerland) · 2010Article
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Authors and funding
5 authors.
Funding
Abstract
This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm's results as well as of the resulting evolved cell models.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.