Search for: All records

Programming in the large allows composition of processes executing code written using programming in the small. Traditionally, systems supporting programming in the large have included interpreters of OS command languages, but today, with the emergence of collaborative “big data” science, these systems also include cyberinfrastructures, which allow computations to be carried out on remote machines in the “cloud”. The rationale for these systems, even the traditional command interpreters, is human-centric computing, as they are designed to support quick, interactive development and execution of process workflows. Some cyberinfrastructures extend this human-centricity by also providing manipulation of visualizations of these workflows. To further increase the human-centricity of these systems, we have started a new project on cyber training - instruction in the use of command languages and visual components of cyberinfrastructures. Our objective is to provide scalable remote awareness of trainees' progress and difficulties, as well as collaborative and automatic resolution of their difficulties. Our current plan is to provide awareness based on a subway workflow metaphor, allow a trainer to collaborate with multiple trainees using a single instance of a command interpreter, and combine research in process and interaction workflows to support automatic help. These research directions can be considered an application of the general principle of integrating programming in the small and large. 

Green plants (Viridiplantae) include around 450,000–500,000 species of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.