BACKGROUND: Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. RESULTS: This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. CONCLUSIONS: The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators--experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community.

Abstract wonglediff is a program that tests the sensitivity of arbitrary program executables or processes to changes that are introduced by a process that runs in parallel. On Unix and Linux kernels, wonglediff creates a supervisor process that runs applications and, on the fly, introduces desired changes to their process state. When execution terminates, it then summarizes the resulting changes in the output files. The technique employed has a variety of uses. This paper describes an implementation of wonglediff that checks the sensitivity of programs to random changes in the floating‐point rounding modes. It runs a program several times, ‘wongling’ it each time: randomly toggling the IEEE‐754 rounding mode of the program as it executes. By comparing the resulting output, one gets a poor man's numerical stability analysis for the program. Although the analysis does not give any kind of guarantee about a program's stability, it can reveal genuine instability, and it does serve as a particularly useful and revealing idiot light. In our implementation, differences among the output files from the program's multiple runs are summarized in a report. This report is in fact an HTML version of the output file, with inline mark‐up summarizing individual differences among the multiple instances. When viewed with a browser, the differences can be highlighted or rendered in many different ways. Copyright © 2004 John Wiley & Sons, Ltd.

Changes to Pascal, embodied in the proposed ISO Pascal standard, affected Fischer and LeBlanc's runtime error checking implementation designed for Wirthian Pascal. Three kinds of runtime errors became obsolete; two were introduced, and one was apparently neglected. A criticism is made of Fischer and LeBlanc's conclusion that runtime errors will always be with us.