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From Boolean Network Model to Continuous Model Helps in Design of Functional Circuits.

ABSTRACT: Computational circuit design with desired functions in a living cell is a challenging task in synthetic biology. To achieve this task, numerous methods that either focus on small scale networks or use evolutionary algorithms have been developed. Here, we propose a two-step approach to facilitate the design of functional circuits. In the first step, the search space of possible topologies for target functions is reduced by reverse engineering using a Boolean network model. In the second step, continuous simulation is applied to evaluate the performance of these topologies. We demonstrate the usefulness of this method by designing an example biological function: the SOS response of E. coli. Our numerical results show that the desired function can be faithfully reproduced by candidate networks with different parameters and initial conditions. Possible circuits are ranked according to their robustness against perturbations in parameter and gene expressions. The biological network is among the candidate networks, yet novel designs can be generated. Our method provides a scalable way to design robust circuits that can achieve complex functions, and makes it possible to uncover design principles of biological networks.

SUBMITTER: Shao B

PROVIDER: S-EPMC4464762 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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From Boolean Network Model to Continuous Model Helps in Design of Functional Circuits.

Shao Bin B Liu Xiang X Zhang Dongliang D Wu Jiayi J Ouyang Qi Q

PloS one 20150610 6

Computational circuit design with desired functions in a living cell is a challenging task in synthetic biology. To achieve this task, numerous methods that either focus on small scale networks or use evolutionary algorithms have been developed. Here, we propose a two-step approach to facilitate the design of functional circuits. In the first step, the search space of possible topologies for target functions is reduced by reverse engineering using a Boolean network model. In the second step, con ...[more]

PMID: 26061094

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Project description:BackgroundLicensure and registration are the traditional approaches to ensure minimally acceptable standards of care for practice. However, due to advances in medical technology and changes in clinical practice, the knowledge and skills obtained from basic education and training may rapidly become out of date. There is no mandated, structured and ongoing mechanism to assess all doctors' competence in Hong Kong. This paper assessed doctors' perceived needs for continuous professional development, and to identify facilitators and barriers that are likely to influence the implementation of compulsory continuous professional development for maintaining professional competence and ensuring patient safety.MethodsAn explanatory sequential mixed method design with two distinct interactive phases was adopted comprising a postal self-administered questionnaire survey among a random sample of 2,459 of doctors (Phase 1), followed by individual interviews of a stratified sample of 30 questionnaire respondents for the subsequent qualitative analysis (Phase 2).ResultsThe majority of doctors (over 90%) agreed the importance of continuous professional development to update knowledge and skills. However, just 30.7% of non-specialists compared with 65.4% of specialists agreed it would be desirable for continuous professional development to be a requirement for renewal of licenses. A relatively higher percentage of non-specialists compared with specialists reported barriers to participation such as accessibility, availability and relevance of the content of the programmes. Facilitators for uptake included more convenient schedule and location, relevant content, and incentives for participation such as making this a pre-condition for enrolling in government-funded services.ConclusionsTo address the needs of individual doctors, the spheres of practice, personal preferences and learning styles should be considered in deciding the content and processes of continuous professional development. Flexibility is also an important principle. A learning model, incentives for participation and a compliance strategy (instead of deterrence) could be effective strategy for continuous professional development.

Dataset Information

From Boolean Network Model to Continuous Model Helps in Design of Functional Circuits.

Publications

From Boolean Network Model to Continuous Model Helps in Design of Functional Circuits.

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