Standard virtual biological parts: a repository of modular modeling components for synthetic biology

Cooling, Michael T.; Rouilly, Vincent; Mısırlı, Göksel; Lawson, James R.; Yu, Tingting; Hallinan, Jennifer; Wipat, Anil

doi:10.1093/bioinformatics/btq063

Cited by 89 publications

(88 citation statements)

References 23 publications

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“…Fig. 1 shows the various ways in which parts can be defined: directly as sequences (PromD, GeneD), or as named parts in popular databases, for example PromB from biofab [3], GeneP from the Parts Registry ( [13], and PromV and GeneV from the Virtual Parts Repository [7], which we use in our running example. These repositories contain promoters, genes, RBSs and terminators that have been used extensively by the synthetic biology community.…”

Section: User Input Languagementioning

confidence: 99%

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Constraint-Based Genetic Compilation

Ladroue

Kalvala

2015

Algorithms for Computational Biology

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Abstract. Synthetic biology aims at facilitating the design of new organisms via the standardization of biological parts and following engineering principles. We present atgc (Assistant To Genetic Compilation), a software tool that automatically builds a functional sequence of DNA from a minimal set of requirements. Through a simple language, the user provides in-house knowledge about their construct (e.g. relative placement of parts, number of restriction enzymes). atgc combines information from established biology, user knowledge and bioinformatics databases, and maps the problem to a constraint satisfaction setting. The solution is a functional DNA sequence ready to be assembled and transferred to a target organism.

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Section: User Input Languagementioning

confidence: 99%

“…The program does not simply search for codon alternatives to free up at least a minimal number of enzymes (lines 9-10). It also does it in such a way that the original sequence is minimally disrupted: each codon change is associated with a cost (lines [7][8]. If the original form is kept, the cost is 0.…”

Section: Biocompilationmentioning

confidence: 99%

Constraint-Based Genetic Compilation

Ladroue

Kalvala

2015

Algorithms for Computational Biology

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“…Previous efforts in synthetic biology largely focused on the creation of genetic devices and small modules that are constructed from these devices [228][229][230][231][232][233][234][235][236][237][238][239][240][241][242]. But to truly program cells, significant advances in strategies to assemble devices and modules into large scale systems are needed.…”

Section: J) Modified Modular Cloning(mod-moclo) Strategymentioning

confidence: 99%

Genetically Programmable Pathogen Sense and Destroy

Gupta¹,

Weiss²

2010

SciVee

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Twenty five percent of all the deaths worldwide are caused by infectious diseases. They are also the biggest cause of mortality among children under five years of age. Among them diarrheal diseases alone cause as many deaths as AIDS or TB and malaria combined. Also up to 80% of traveler's diarrhea is bacterial in nature. Vibrio cholerae (cholera), Salmonella spp (typhoid fever), Shigella spp (shigellosis) and a variety of enteropathogenic Escherichia coli strains are among the principle bacterial agents that cause this type of diarrhea.

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“…One reason is that this approach well matches the structure of biological systems on multiple levels: from cells [Hartwell et al, 1999] to organs and whole organisms [Cooling et al, 2010]. Snoep et al [Snoep et al, 2006] describe their vision of the construction of a comprehensive model describing a complete cellular system at the reaction level (i.e.…”

Section: Introductionmentioning

confidence: 99%

Modular Modeling of Biological Systems

Kiselev¹,

Kolpakov²

2013

Virtual Biology

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Motivation: Modeling of complex biological systems such as cells, organs or even whole organisms is not a trivial task because of their intricate structure. Although modern computers allow simulation for quite complex models, such models are difficult to support and work with. Modular approach facilitates the creation of complex models by representing them as combinations of submodels. On the other hand, there are a large number of models describing particular subsystems created by different authors using different formalisms and scales. These models may be reused as "bricks" in the creation of comprehensive overall models. Results:We have developed a modular approach to the modeling of complex biological systems. It includes a formal definition of graphical notation for modular models, an algorithm for the transformation of a modular model into a non-modular model which is appropriate for simulation using standard methods for solving ordinary differential equations (ODE), and an algorithm for simulating modular model based on the agent-model principles. The approach was implemented in software plug-in for BioUML platform. Availability:The developed software and the source code are freely available as a part of BioUML in both standalone and web versions at www.biouml.org.

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Standard virtual biological parts: a repository of modular modeling components for synthetic biology

Cited by 89 publications

References 23 publications

Constraint-Based Genetic Compilation

Constraint-Based Genetic Compilation

Genetically Programmable Pathogen Sense and Destroy

Modular Modeling of Biological Systems

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