ArticleBriefings in bioinformatics2010
SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs.
Article in Briefings in bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed.
- Biocircuits in plants and eukaryotic algae.Frontiers in plant science · 2022Review
- Synthetic Biology in Plants, a Boon for Coming Decades.Molecular biotechnology · 2021Review
- Chemical master equation closure for computer-aided synthetic biology.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator.Journal of chemical and engineering data · 2014Article
- Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks.Current opinion in chemical engineering · 2014Article
- PromoterCAD: Data-driven design of plant regulatory DNA.Nucleic acids research · 2013Article
- Stochastic model reduction using a modified Hill-type kinetic rate law.The Journal of chemical physics · 2012Article
- Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities.Briefings in bioinformatics · 2012Article
- Computational tools for the synthetic design of biochemical pathways.Nature reviews. Microbiology · 2012Review
- proTeOn and proTeOff, new protein devices that inducibly activate bacterial gene expression.ACS chemical biology · 2011Article
- Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.PloS one · 2011Article
- Standard biological parts knowledgebase.PloS one · 2011Article
- Stochastic simulations of the tetracycline operon.BMC systems biology · 2011Article
- SynBioSS-aided design of synthetic biological constructs.Methods in enzymology · 2011Article
- A biobrick library for cloning custom eukaryotic plasmids.PloS one · 2011Article
- Mathematical models in biology: from molecules to life.Wiley interdisciplinary reviews. Systems biology and medicineReview
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications.
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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.