ArticleJournal of biological engineering2012
DeviceEditor visual biological CAD canvas.
Article in Journal of biological engineering, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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
33 citing papers in PubMed.
- Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction.ACS synthetic biology · 2026Article
- Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid.ACS synthetic biology · 2026Article
- RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling.Applied and environmental microbiology · 2025Article
- Binary vector copy number engineering improves Agrobacterium-mediated transformation.Nature biotechnology · 2025Article
- Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida.Communications biology · 2025Article
- Automated Platform for the Plasmid Construction Process.ACS synthetic biology · 2023Article
- The pGinger Family of Expression Plasmids.Microbiology spectrum · 2023Article
- Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.Applied and environmental microbiology · 2022Article
- Genetic circuit design automation with Cello 2.0.Nature protocols · 2022Review
- Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.Applied and environmental microbiology · 2020Article
- Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage.Nature communications · 2020Article
- An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism.Nature communications · 2020Article
- Leveraging host metabolism for bisdemethoxycurcumin production inMetabolic engineering communications · 2020Article
- The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.Frontiers in bioengineering and biotechnology · 2020Article
- Article
- Omics-driven identification and elimination of valerolactam catabolism inMetabolic engineering communications · 2019Article
- Article
- Plant Synthetic Biology: Quantifying the "Known Unknowns" and Discovering the "Unknown Unknowns".Plant physiology · 2019Review
- Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer.Nature communications · 2018Article
- Isolation and characterization of novel mutations in the pSC101 origin that increase copy number.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly.
resultsWe report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs.
conclusionsDeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.
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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.