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Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean(More)
We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set(More)
D-gluconate which is primarily catabolized via the Entner-Doudoroff (ED) pathway, has been implicated as being important for colonization of the streptomycin-treated mouse large intestine by Escherichia coli MG1655, a human commensal strain. In the present study, we report that an MG1655 Deltaedd mutant defective in the ED pathway grows poorly not only on(More)
Molecular biologists routinely clone genetic constructs from DNA segments and formulate plans to assemble them. However, manual assembly planning is complex, error prone and not scalable. We address this problem with an algorithm-driven DNA assembly planning software tool suite called Raven (http://www.ravencad.org/) that produces optimized assembly plans(More)
Multipart and modular DNA part libraries and assembly standards have become common tools in synthetic biology since the publication of the Gibson and Golden Gate assembly methods, yet no multipart modular library exists for use in bacterial systems. Building upon the existing MoClo assembly framework, we have developed a publicly available collection of(More)
We present a framework that allows us to construct and formally analyze the behavior of synthetic gene circuits from specifications in a high level language used in describing electronic circuits. Our back-end synthesis tool automatically generates genetic-regulatory network (GRN) topology realizing the specifications with assigned biological "parts" from a(More)
Reality-based interfaces (RBIs) such as tabletop and tangible user interfaces draw upon ideas from embodied cognition to offer a more natural, intuitive, and accessible form of interaction that reduces the mental effort required to learn and operate computational systems. However, to date, little research has been devoted to investigating the strengths and(More)
There is a pressing need for design automation tools for synthetic biology systems. Compared to electronic circuits, cellular information processing has more complex elementary components and a greater complexity of interactions among components. Moreover, chemical computation within a cell is strongly a↵ected both by other computations simultaneously(More)
MoClo Planner is an interactive visualization system for collaborative bio-design, utilizing a multi-touch interactive surface. The system integrates the information gathering, design, and specification of complex synthetic biological constructs using the Modular Cloning (MoClo) assembly method. Modular Cloning is a hierarchical DNA construction method that(More)