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.

Summary: Following polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in some species. The process of characterizing whole genome fractionation requires identifying syntenic regions across genomes followed by post-processing of those syntenic datasets to identify and plot gene retention patterns. We have developed a tool, FractBias, to calculate and visualize gene retention and fractionation patterns across whole genomes. Through integration with SynMap and its parent platform CoGe, assembled genomes are pre-loaded and available for analysis, as well as letting researchers integrate their own data with security options to keep them private or make them publicly available. Availability and Implementation: FractBias is freely available as a web application at https://genomevolution.org/CoGe/SynMap.pl . The software is open source (MIT license) and executable with Python 2.7 or iPython notebook, and available on GitHub ( https://goo.gl/PaAtqy ). Documentation for FractBias is available on CoGepedia ( https://goo.gl/ou9dt6 ). Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.