ArticlePloS one2011
Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed.
- From prompts to genomes: A constraint-first framework for AI-driven sequence design across life and viruses.PLoS computational biology · 2026Article
- Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.BMC bioinformatics · 2024Article
- Verifiable biology.Journal of the Royal Society, Interface · 2023Review
- Genetic circuit design automation with Cello 2.0.Nature protocols · 2022Review
- Genetic circuit design automation for yeast.Nature microbiology · 2020Article
- The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.Frontiers in bioengineering and biotechnology · 2020Article
- Repository-based plasmid design.PloS one · 2020Article
- Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology.Processes (Basel, Switzerland) · 2018Article
- Deep learning to predict the lab-of-origin of engineered DNA.Nature communications · 2018Article
- A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering.Yeast (Chichester, England) · 2018Article
- Design Automation in Synthetic Biology.Cold Spring Harbor perspectives in biology · 2017Review
- Article
- Process-based design of dynamical biological systems.Scientific reports · 2016Article
- Synthetic biology to access and expand nature's chemical diversity.Nature reviews. Microbiology · 2016Review
- The LASER database: Formalizing design rules for metabolic engineering.Metabolic engineering communications · 2015Article
- Towards a behavioral-matching based compilation of synthetic biology functions.Acta biotheoretica · 2015Article
- Signal-to-Noise Ratio Measures Efficacy of Biological Computing Devices and Circuits.Frontiers in bioengineering and biotechnology · 2015Article
- Functional optimization of gene clusters by combinatorial design and assembly.Nature biotechnology · 2014Article
- Biological 2-input decoder circuit in human cells.ACS synthetic biology · 2014Article
- Interactive assembly algorithms for molecular cloning.Nature methods · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSynthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts.
resultsWe illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively.
conclusionsEugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly.
Indexed as
Identifiers
What OpenQuestion holds
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.